Contacts of the helix formed by residues 115 - 137 (chain B) in PDB entry 5DFV
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with ASN 115 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
126A PHE* 5.2 0.2 - - - -
113B PHE 3.5 3.5 - - - -
114B VAL* 1.3 78.6 - - - +
116B LYS* 1.3 80.8 + - - +
117B ASP* 3.3 35.8 + - - +
118B GLN* 4.2 12.5 - - + +
119B ILE* 3.1 21.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 116 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
126A PHE* 4.1 16.1 - - + -
142A ASN* 5.5 4.3 - - - +
114B VAL 3.8 2.2 + - - -
115B ASN* 1.3 81.6 + - - +
117B ASP* 1.3 76.0 + - - +
119B ILE* 3.1 18.6 - - - +
120B ALA* 3.1 17.2 + - - +
195B ASP* 5.1 1.8 + - - +
198B PHE* 3.5 36.3 - - + +
199B SER* 3.7 25.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 117 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
115B ASN* 3.3 22.9 + - - +
116B LYS* 1.3 90.7 - - - +
118B GLN* 1.3 67.9 + - - +
120B ALA* 2.9 8.4 + - - +
121B LYS* 2.9 23.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 118 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
115B ASN* 4.0 16.4 + - + +
117B ASP* 1.3 79.4 - - - +
119B ILE* 1.3 57.0 + - - +
121B LYS* 3.4 32.8 + - - +
122B ASP* 2.9 62.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 119 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
119A ILE* 4.0 7.4 - - + +
122A ASP* 3.4 39.9 - - + +
123A VAL* 3.6 27.6 - - + -
126A PHE* 4.5 5.6 - - + -
114B VAL* 4.4 13.0 - - + +
115B ASN 3.1 17.5 + - - +
116B LYS* 3.1 22.4 - - - +
118B GLN* 1.3 74.4 - - - +
120B ALA* 1.3 59.6 + - - +
122B ASP* 3.4 8.2 + - + -
123B VAL* 3.1 31.9 + - + +
198B PHE* 4.1 20.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 120 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116B LYS* 3.2 18.8 - - + +
117B ASP* 2.9 7.2 + - - +
119B ILE* 1.3 78.6 - - - +
121B LYS* 1.3 64.1 + - - +
123B VAL 3.8 0.2 + - - -
124B LYS* 3.3 31.1 + - - +
194B ILE* 4.1 4.1 - - + +
195B ASP* 4.4 16.4 - - - +
198B PHE* 4.2 30.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 121 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117B ASP 2.9 12.1 + - - +
118B GLN* 3.6 36.3 + - - +
120B ALA* 1.3 74.2 - - - +
122B ASP* 1.3 60.5 + - - +
124B LYS* 3.3 14.0 + - + +
125B GLN* 2.9 45.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 122 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114A VAL* 4.5 4.5 - - - +
119A ILE* 3.3 31.8 - - + +
122A ASP* 4.6 8.7 - - - +
118B GLN* 2.9 53.0 + - - +
119B ILE* 3.6 16.0 - - + +
121B LYS* 1.3 78.2 - - - +
123B VAL* 1.3 57.0 + - - +
125B GLN* 3.3 9.2 + - - +
126B PHE 2.8 24.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 123 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
119A ILE* 3.8 21.8 - - + -
123A VAL* 3.8 20.0 - - + -
197A LEU* 6.3 0.9 - - + -
198A PHE* 3.9 8.7 - - + -
119B ILE* 3.1 19.0 + - + +
120B ALA 4.3 3.6 - - - +
121B LYS 3.2 0.2 - - - -
122B ASP* 1.3 71.5 - - - +
124B LYS* 1.3 61.6 + - - +
126B PHE* 3.2 7.5 + - - +
127B TYR* 2.9 27.4 + - - +
150B PHE* 4.0 21.5 - - + -
194B ILE* 4.2 20.2 - - + -
198B PHE* 4.0 12.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 124 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
120B ALA* 3.3 18.7 + - - +
121B LYS* 3.3 12.7 + - + +
123B VAL* 1.3 78.7 - - - +
125B GLN* 1.3 53.5 + - - +
127B TYR* 3.0 3.0 + - - +
128B ASP* 2.7 41.5 + - - +
191B HIS* 3.6 47.8 + - + +
194B ILE* 3.9 25.8 - - + -
195B ASP* 2.7 39.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 125 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114A VAL* 3.6 22.5 - - + +
121B LYS* 2.9 33.8 + - + +
122B ASP* 3.6 8.5 - - - +
124B LYS* 1.3 75.9 - - - +
126B PHE* 1.3 63.8 + - - +
128B ASP* 3.4 8.4 + - + +
129B GLN* 3.1 37.4 + - - +
582F SER* 3.3 30.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 126 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114A VAL* 4.2 23.5 - - + +
116A LYS* 3.6 28.5 - - + -
119A ILE* 3.7 13.2 - - + -
198A PHE* 3.4 55.0 - + + -
122B ASP 2.8 20.7 + - - +
123B VAL* 3.5 5.8 - - - +
125B GLN* 1.3 72.5 - - - +
127B TYR* 1.3 65.2 + - - +
129B GLN* 3.5 6.4 + - - +
130B ALA* 3.2 18.0 + - + +
146B VAL* 3.6 30.7 - - + -
150B PHE* 3.9 12.8 - + - -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 127 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
123B VAL 2.9 13.6 + - - +
124B LYS* 3.4 8.3 - - - +
126B PHE* 1.3 79.8 - - - +
128B ASP* 1.3 67.5 + - - +
130B ALA* 2.8 10.7 + - + +
131B LEU* 2.8 49.2 + - + +
147B VAL* 4.5 14.6 - - + -
150B PHE* 3.8 44.2 - + + -
151B HIS* 2.6 34.8 + + - -
158B GLY* 3.0 34.0 + - - -
159B SER* 4.3 2.7 - - - -
190B CYS* 3.9 12.6 - - + -
191B HIS* 4.5 7.6 - + - -
194B ILE* 4.5 8.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 128 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
124B LYS* 2.7 22.3 + - - +
125B GLN* 3.6 9.8 - - + +
127B TYR* 1.3 81.0 - - - +
129B GLN* 1.3 57.9 + - + +
131B LEU* 3.4 3.4 + - - +
132B GLN* 2.9 43.3 + - - +
159B SER* 4.1 3.6 + - - -
161B THR* 3.7 7.2 + - - -
162B LEU* 3.6 15.3 - - + +
191B HIS* 2.6 38.7 + - - -
582F SER* 5.9 0.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 129 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
113A PHE* 3.6 17.6 - - + +
114A VAL* 3.1 40.3 + - - +
125B GLN* 3.1 29.3 + - - +
126B PHE* 3.8 7.2 + - - +
127B TYR 3.1 0.6 - - - -
128B ASP* 1.3 76.1 - - + +
130B ALA* 1.3 59.8 + - - +
132B GLN* 4.5 0.7 - - - +
133B GLN* 3.1 38.3 + - - +
582F SER* 3.0 30.5 + - - +
594F ILE* 3.8 29.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 130 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
126B PHE* 3.2 14.0 + - + +
127B TYR* 2.8 11.8 + - + +
129B GLN* 1.3 75.0 - - - +
131B LEU* 1.3 65.9 + - - +
133B GLN* 3.3 11.7 + - - +
134B ALA* 3.0 21.5 + - - +
143B ALA* 3.8 7.8 - - - +
146B VAL* 3.8 24.7 - - + -
147B VAL* 3.4 23.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 131 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
127B TYR* 2.8 33.9 + - + +
128B ASP* 3.6 9.2 - - - +
130B ALA* 1.3 73.8 - - - +
132B GLN* 1.3 63.4 + - - +
134B ALA* 3.7 4.7 + - - +
135B VAL* 3.6 16.3 - - - +
147B VAL* 3.5 15.8 - - + +
158B GLY* 3.9 16.4 - - - -
159B SER* 4.1 1.8 - - - +
162B LEU* 3.7 27.4 - - + -
165B LEU* 5.0 5.7 - - + +
166B THR* 3.8 21.1 - - - +
169B VAL* 3.3 44.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 132 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
128B ASP* 2.9 33.1 + - - +
129B GLN* 3.9 2.2 - - - +
131B LEU* 1.3 73.9 - - - +
133B GLN* 1.3 65.5 + - - +
135B VAL* 3.0 4.7 + - - +
136B VAL* 2.9 30.3 + - - +
162B LEU* 3.8 19.8 - - + +
165B LEU* 3.9 9.6 - - + -
581F THR* 2.5 38.8 + - - +
582F SER* 4.7 2.2 + - - -
594F ILE* 3.7 24.7 - - + +
595F TYR* 3.7 7.9 - - + -
597F TYR* 2.9 29.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 133 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
113A PHE* 4.0 25.5 - - + -
129B GLN* 3.1 29.2 + - - +
130B ALA* 4.1 3.2 - - - +
132B GLN* 1.3 76.0 - - - +
134B ALA* 1.3 62.3 + - - +
137B ASP* 3.1 42.1 + - + +
140B ALA* 3.3 8.9 - - + +
143B ALA* 3.5 23.1 - - + +
594F ILE* 4.7 6.7 - - + -
595F TYR* 4.3 15.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 134 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
130B ALA 3.0 17.2 + - - +
131B LEU 3.8 6.3 - - - +
132B GLN 3.1 0.4 + - - -
133B GLN* 1.3 76.4 - - - +
135B VAL* 1.3 61.3 + - + +
137B ASP 3.8 6.9 - - - +
140B ALA* 4.3 1.8 - - - -
143B ALA* 3.7 7.8 - - - +
144B LYS* 3.8 45.6 - - + +
147B VAL* 4.3 6.1 - - + -
169B VAL* 5.1 1.8 - - + -
172B ASN* 5.5 0.9 - - - +
174B LEU* 4.3 12.7 - - + +
354E THR* 3.9 11.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 135 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
131B LEU 3.6 7.6 - - - +
132B GLN 3.0 6.2 + - - +
134B ALA* 1.3 79.4 - - - +
136B VAL* 1.3 65.1 + - + +
137B ASP 3.5 2.4 - - - +
138B ASP* 5.6 0.2 - - - -
165B LEU* 3.5 31.2 - - + +
168B SER* 4.4 5.6 - - - -
169B VAL* 3.2 35.7 - - + +
172B ASN* 5.1 4.3 - - - +
174B LEU* 6.0 0.2 - - + -
354E THR* 2.8 31.0 + - - +
355E GLY 3.5 35.4 - - - +
394E ASP* 4.2 6.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 136 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
132B GLN* 2.9 26.8 + - - +
135B VAL* 1.3 77.7 - - + +
137B ASP* 1.3 62.4 + - - +
138B ASP* 3.9 1.6 + - - +
165B LEU* 5.0 3.4 - - + -
394E ASP* 4.3 7.2 - - - +
595F TYR* 3.4 37.2 - - + +
597F TYR* 3.9 24.7 - - + +
651F TYR* 3.6 40.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 137 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
133B GLN* 3.1 34.1 + - + +
134B ALA 3.8 9.2 - - - +
135B VAL 4.1 2.2 - - - +
136B VAL* 1.3 79.8 - - - +
138B ASP* 1.3 75.9 + - - +
139B ASP* 3.7 5.8 + - - +
140B ALA* 3.8 17.5 + - + +
354E THR* 5.1 1.2 - - - +
595F TYR* 4.4 11.9 + - - +
----------------------------------------------------------
Back to top of page
A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
------------------------------------------------------------
Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il