Contacts of the strand formed by residues 109 - 127 (chain A) in PDB entry 3M4D
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 THR 109 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
107A ILE* 3.9 9.4 - - + +
108A ASP* 1.3 85.1 - - - +
110A LYS* 1.3 66.5 + - - +
148A TYR* 4.9 9.0 - - - +
149A VAL 5.3 1.7 + - - -
149B VAL* 3.9 21.6 - - + +
150B GLN 3.7 7.6 - - - -
151B PRO* 4.0 15.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 110 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
109A THR* 1.3 75.9 - - - +
111A GLU* 1.3 59.5 + - - +
146A LEU* 4.1 13.7 - - + -
147A LYS 3.6 10.8 - - - +
148A TYR* 4.7 4.7 - - + +
149B VAL* 3.5 5.3 - - - +
150B GLN* 2.8 59.1 + - + +
151B PRO 3.6 3.8 - - - -
152B ASP* 2.8 29.5 + - - -
173B ASN* 2.7 35.2 + - - +
174B MET* 4.0 4.3 - - - +
175B VAL* 3.7 29.2 - - + +
181B PRO* 3.8 15.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 111 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
110A LYS* 1.3 74.1 - - - +
112A TYR* 1.3 64.2 + - - +
113A ASN* 3.1 29.3 + - - +
145A THR 3.7 0.7 - - - +
146A LEU* 3.5 10.8 - - - +
147A LYS* 2.8 64.8 + - + +
147B LYS* 4.3 10.9 - - - +
148B TYR 3.8 13.5 - - - +
149B VAL* 4.4 11.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 112 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
110A LYS 4.0 0.2 + - - -
111A GLU* 1.3 73.0 - - - +
113A ASN* 1.3 76.5 + - - +
114A SER* 3.8 21.5 - - - -
144A HIS* 2.8 38.9 + + + -
145A THR 3.6 4.9 - - - -
146A LEU* 5.2 3.6 - - + -
146B LEU 3.8 0.9 - - - +
147B LYS* 3.5 1.2 - - - -
148B TYR* 2.9 54.1 + + + +
150B GLN* 3.2 31.9 - - - +
180B GLY 4.9 4.3 - - - -
181B PRO* 4.1 21.8 - - + -
178C ASN* 2.9 34.4 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 113 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
111A GLU* 3.1 30.6 + - - +
112A TYR* 1.3 93.5 + - - +
114A SER* 1.3 61.8 + - - +
115A THR* 5.6 1.6 - - - +
144A HIS* 3.2 4.7 - - - -
145A THR* 2.8 52.4 + - - +
147A LYS* 3.7 19.1 + - - -
145B THR* 5.0 4.9 - - + +
146B LEU 3.3 4.3 - - - +
147B LYS* 3.4 32.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 114 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
112A TYR* 3.8 12.8 - - - -
113A ASN* 1.3 74.9 - - - +
115A THR* 1.3 63.9 + - - +
116A LEU* 6.0 0.5 - - - +
142A ILE* 5.4 1.6 - - - +
143A GLY 3.4 5.6 + - - -
144A HIS* 3.5 23.9 - - - -
144B HIS 3.7 0.9 - - - +
145B THR* 3.2 3.8 - - - +
146B LEU* 2.8 45.7 + - - +
178C ASN 4.2 13.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 115 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
113A ASN* 5.3 1.9 - - - +
114A SER* 1.3 77.7 + - - +
116A LEU* 1.3 62.5 + - - +
117A THR* 3.5 25.4 - - + -
141A SER 3.7 0.9 - - - +
142A ILE* 3.4 6.9 - - - +
143A GLY* 2.8 44.2 + - - +
143B GLY* 5.4 0.2 - - - -
144B HIS 3.3 5.8 - - - +
145B THR* 2.8 30.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 116 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114A SER* 4.3 0.9 - - - +
115A THR* 1.3 72.5 - - - +
117A THR* 1.3 66.8 + - - +
118A TYR* 4.8 16.4 - - + -
140A VAL* 4.1 17.0 - - + -
141A SER 3.6 3.4 - - - +
142A ILE* 3.6 32.1 - - + -
142B ILE 3.9 1.2 - - - +
143B GLY* 3.3 1.4 - - - -
144B HIS* 2.9 44.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 117 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
115A THR* 3.5 23.8 - - + -
116A LEU* 1.3 81.2 - - - +
118A TYR* 1.3 62.7 + - - +
139A ASN* 5.2 1.0 + - - +
140A VAL* 3.3 5.2 - - - +
141A SER* 2.6 55.2 + - - +
141B SER* 6.0 3.4 - - - -
142B ILE 3.3 9.2 - - - -
143B GLY* 3.7 12.3 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 118 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116A LEU* 4.8 17.3 - - + -
117A THR* 1.3 79.1 - - - +
119A GLY* 1.3 59.7 + - - +
120A PHE* 4.5 24.0 - + + -
139A ASN* 3.1 15.5 - - - +
140A VAL* 3.9 15.5 - - + -
141B SER* 4.5 2.7 - - - -
142B ILE* 2.9 73.5 + - + +
144B HIS* 4.7 14.8 + + - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 119 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118A TYR* 1.3 77.3 - - - +
120A PHE* 1.3 73.8 + - - -
138A ALA* 3.3 4.0 - - - +
139A ASN* 3.0 45.3 + - - +
140B VAL 3.1 14.6 - - - -
141B SER* 4.0 4.5 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 120 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118A TYR* 4.5 25.4 - + + -
119A GLY* 1.3 85.9 - - - -
121A ASN* 1.3 64.0 + - - +
136A ILE* 6.5 0.4 - - + -
137A GLY 3.4 8.7 - - - +
138A ALA* 4.1 15.9 - - + -
139A ASN* 5.6 0.4 - - - -
139B ASN* 3.5 1.8 - - - +
140B VAL* 3.0 41.4 + - + +
142B ILE* 6.3 2.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 121 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
120A PHE* 1.3 79.8 - - - +
122A GLY* 1.3 64.8 + - - +
123A ASN* 5.4 1.8 - - - +
135A LEU* 3.8 13.2 - - - +
136A ILE* 3.6 7.9 - - - +
137A GLY* 2.7 55.3 + - - +
139A ASN* 4.5 10.5 + - - +
138B ALA 3.3 15.5 - - - +
139B ASN* 3.7 11.4 - - + +
123G ASN* 5.5 0.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 122 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121A ASN* 1.3 77.9 + - - +
123A ASN* 1.3 64.5 + - - +
135A LEU 3.5 5.8 - - - -
136A ILE* 4.9 5.6 - - - -
137B GLY* 3.2 2.5 - - - -
138B ALA* 2.9 33.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 123 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121A ASN* 5.4 3.1 - - - +
122A GLY* 1.3 75.9 - - - +
124A VAL* 1.3 66.8 + - - +
125A THR* 3.7 11.5 - - - +
134A GLY* 2.9 5.4 - - - -
135A LEU* 2.7 62.9 + - + +
121B ASN* 5.3 2.9 + - - -
135B LEU* 2.8 37.4 - - - +
136B ILE 3.5 5.2 - - - -
137B GLY* 3.5 14.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 124 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
123A ASN* 1.3 82.4 - - - +
125A THR* 1.3 69.7 + - - +
132A ILE* 4.3 13.2 - - + -
133A GLY 3.3 18.4 - - - +
134A GLY* 4.1 1.1 - - - -
135B LEU* 3.4 2.3 + - - -
136B ILE* 2.8 47.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 125 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
123A ASN* 3.7 9.0 - - - +
124A VAL* 1.3 80.2 - - - +
126A GLY* 1.3 60.4 + - - +
132A ILE* 3.6 7.1 - - - +
133A GLY* 3.1 37.0 + - - +
134A GLY* 4.3 1.9 + - - +
134B GLY 3.3 10.8 - - - +
135B LEU* 3.3 33.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 126 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
125A THR* 1.3 81.1 - - - +
127A ASP* 1.3 63.2 + - - +
131A LYS* 3.1 16.2 - - - -
132A ILE* 4.7 3.8 - - - -
133B GLY* 3.4 4.2 - - - -
134B GLY* 2.8 31.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 127 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
126A GLY* 1.3 73.8 - - - +
128A ASP* 1.3 55.6 + - - +
129A THR* 2.4 44.1 + - - -
130A GLY* 3.1 9.9 + - - -
131A LYS* 2.9 51.9 + - - +
131B LYS* 4.1 23.4 + - + +
132B ILE 3.4 9.2 - - - +
133B GLY* 4.4 0.7 - - - -
----------------------------------------------------------
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