Contacts of the helix formed by residues 117 - 138 (chain B) in PDB entry 5TQW
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 LYS 117 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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112B ASN* 5.1 1.6 + - - -
116B LEU* 1.3 74.9 - - - +
118B GLU* 1.3 67.4 + - + +
119B SER* 3.8 20.6 - - - +
120B GLN* 3.3 42.2 + - + +
121B ILE* 3.3 23.3 + - - +
263B SER* 3.9 7.0 - - - +
439B GLU* 4.7 13.6 + - - -
443B ARG* 4.4 16.1 - - - +
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Residues in contact with GLU 118 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117B LYS* 1.3 74.6 - - + +
119B SER* 1.3 58.4 + - - +
121B ILE* 3.0 16.9 + - - +
122B LEU* 2.9 38.4 + - + +
263B SER* 2.9 32.8 + - - +
264B LEU* 3.3 31.9 - - + +
265B CYS* 3.2 20.1 + - - +
268B ILE* 3.5 32.5 - - - +
269B VAL* 5.2 0.2 - - - +
314B HIS* 5.4 6.1 + - - -
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Residues in contact with SER 119 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117B LYS* 3.8 17.5 - - - +
118B GLU* 1.3 79.0 - - - +
120B GLN* 1.3 60.8 + - - +
122B LEU* 3.2 20.4 + - - +
123B SER* 2.9 26.7 + - - -
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Residues in contact with GLN 120 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
106B LEU* 5.8 2.9 - - - +
116B LEU* 4.8 7.9 - - + +
117B LYS* 3.3 54.4 + - + +
118B GLU 3.2 0.4 - - - -
119B SER* 1.3 80.1 - - - +
121B ILE* 1.3 58.9 + - + +
123B SER* 2.4 24.2 + - - -
124B LEU* 2.9 13.3 + - - +
161B HIS* 4.4 4.0 + - - -
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Residues in contact with ILE 121 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116B LEU* 3.7 31.2 - - + +
117B LYS 3.3 17.0 - - - +
118B GLU* 3.0 10.4 + - - +
120B GLN* 1.3 74.8 - - - +
122B LEU* 1.3 60.7 + - + +
124B LEU* 3.2 14.1 + - + +
125B LEU* 2.9 27.3 + - + +
211B VAL* 4.4 13.2 - - + -
214B CYS* 3.4 39.7 - - + +
215B ILE* 3.9 28.0 - - + -
264B LEU* 5.6 3.1 - - + -
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Residues in contact with LEU 122 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118B GLU* 2.9 28.2 + - + +
119B SER* 3.3 25.6 - - - +
120B GLN 3.2 0.4 - - - -
121B ILE* 1.3 77.4 - - + +
123B SER* 1.3 59.8 + - - +
125B LEU* 3.3 10.3 + - + +
126B SER* 2.9 28.1 + - - -
268B ILE* 4.6 24.2 - - + -
272B MET* 5.6 9.6 - - + -
307B ILE* 3.7 30.5 - - + +
308B LEU* 4.9 6.7 - - + +
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Residues in contact with SER 123 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
119B SER 2.9 11.3 + - - -
120B GLN* 2.4 30.0 + - - +
122B LEU* 1.3 72.0 - - - +
124B LEU* 1.3 58.5 + - - +
126B SER* 3.4 6.9 + - - -
127B ASP* 2.9 41.1 + - - +
159B ILE 5.2 3.4 + - - -
161B HIS* 4.2 7.7 + - - -
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Residues in contact with LEU 124 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103B LEU* 4.0 19.3 - - + -
116B LEU* 5.5 2.5 - - + -
120B GLN 2.9 14.0 + - - +
121B ILE* 3.2 19.3 + - + +
123B SER* 1.3 77.6 + - - +
125B LEU* 1.3 57.8 + - - +
127B ASP 3.3 0.2 + - - -
128B ILE* 2.8 47.6 + - + +
150B ILE* 4.7 0.9 - - + -
161B HIS* 3.4 40.4 - - + +
207B PHE* 6.4 0.2 - - + -
210B MET* 5.5 7.4 - - + -
211B VAL* 5.3 11.0 - - + -
214B CYS* 3.7 34.3 - - + -
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Residues in contact with LEU 125 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121B ILE* 2.9 16.5 + - + +
122B LEU* 3.3 10.3 + - + +
124B LEU* 1.3 75.2 - - - +
126B SER* 1.3 62.2 + - - +
129B GLY* 2.9 26.9 + - - -
207B PHE* 4.1 11.4 - - + -
211B VAL* 4.2 15.5 - - + -
272B MET* 3.8 18.8 - - + -
275B TRP* 3.6 34.5 - - + -
304B MET* 3.7 42.3 - - + +
307B ILE* 5.2 11.9 - - + -
308B LEU* 5.8 4.0 - - + -
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Residues in contact with SER 126 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
122B LEU 2.9 17.0 + - - -
123B SER* 3.6 8.7 - - - -
124B LEU 3.2 0.2 - - - -
125B LEU* 1.3 79.3 - - - +
127B ASP* 1.3 60.2 + - - +
130B SER* 2.9 31.4 + - - -
133B ARG* 5.9 0.3 + - - -
308B LEU* 3.7 39.0 - - - +
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Residues in contact with ASP 127 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
123B SER* 2.9 19.1 + - - +
124B LEU 3.8 2.5 - - - +
126B SER* 1.3 78.6 + - - +
128B ILE* 1.3 59.6 + - - +
130B SER* 2.6 23.6 + - - -
131B GLY* 2.9 11.1 + - - -
159B ILE 3.7 8.1 - - - +
160B ILE* 3.9 16.0 - - - +
161B HIS* 3.2 51.3 + - + +
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Residues in contact with ILE 128 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
124B LEU* 2.8 37.1 + - + +
127B ASP* 1.3 69.6 - - - +
129B GLY* 1.3 59.9 + - - +
131B GLY* 3.3 2.5 + - - +
132B ILE* 2.9 32.1 + - + +
145B LEU* 4.7 2.7 - - + -
150B ILE* 3.7 21.1 - - + -
161B HIS* 3.3 34.3 - - + +
162B LYS* 4.3 0.2 - - - -
163B ILE* 3.8 24.9 - - + -
207B PHE* 3.5 23.1 - - + -
210B MET* 3.9 17.0 - - + -
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Residues in contact with GLY 129 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
125B LEU 2.9 22.8 + - - -
128B ILE* 1.3 79.4 - - - +
130B SER* 1.3 56.2 + - - +
132B ILE* 3.2 8.8 - - - +
133B ARG* 2.9 37.9 + - - +
207B PHE* 3.8 4.5 - - - -
301B PHE* 4.3 0.5 - - - -
304B MET* 3.7 18.6 - - - -
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Residues in contact with SER 130 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
126B SER 2.9 17.2 + - - -
127B ASP* 2.6 23.2 + - - -
129B GLY* 1.3 72.9 - - - +
131B GLY* 1.3 59.4 + - - +
133B ARG* 3.5 18.0 - - - +
134B TYR* 2.9 28.1 + - - +
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Residues in contact with GLY 131 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
127B ASP 2.9 14.2 + - - -
128B ILE* 3.3 5.6 + - - -
129B GLY 3.2 0.2 - - - -
130B SER* 1.3 78.3 + - - +
132B ILE* 1.3 57.7 + - - +
134B TYR* 3.1 9.8 + - - +
135B LEU* 2.9 35.3 + - - +
163B ILE* 4.8 7.9 - - - -
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Residues in contact with ILE 132 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
128B ILE* 2.9 19.8 + - + +
129B GLY* 3.2 14.1 - - - +
131B GLY* 1.3 74.2 - - - +
133B ARG* 1.3 61.1 + - - +
135B LEU* 4.2 9.6 - - + +
136B HIS* 3.0 44.4 + - + +
142B HIS* 5.9 0.9 - - + -
145B LEU* 3.8 31.9 - - + -
163B ILE* 4.4 7.6 - - + -
203B ASP* 4.8 6.7 - - + +
204B TYR* 5.2 8.1 - - + -
207B PHE* 3.6 40.4 - - + -
279B MET* 6.0 0.7 - - + -
301B PHE* 4.1 21.5 - - + -
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Residues in contact with ARG 133 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
126B SER 5.9 0.2 + - - -
129B GLY 2.9 21.3 + - - +
130B SER* 3.5 18.0 - - - +
132B ILE* 1.3 76.4 - - - +
134B TYR* 1.3 57.0 + - - +
136B HIS* 3.5 1.3 + - - +
137B GLU* 3.0 39.2 + - - +
297B GLN* 4.1 9.6 - - + +
301B PHE* 2.5 77.8 + - + +
304B MET* 3.4 21.1 - - - +
305B ASP* 2.7 23.1 + - - -
308B LEU* 4.8 11.7 - - - +
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Residues in contact with TYR 134 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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67B LYS 4.9 10.7 + - - -
130B SER 2.9 16.3 + - - +
131B GLY* 3.1 11.9 + - - +
133B ARG* 1.3 76.5 - - - +
135B LEU* 1.3 70.7 + - + +
137B GLU* 3.2 28.8 - - - +
138B ASN* 2.5 58.7 + - - -
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Residues in contact with LEU 135 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
131B GLY 2.9 20.3 + - - +
132B ILE* 3.5 8.5 + - + +
134B TYR* 1.3 92.1 - - + +
136B HIS* 1.3 61.2 + - + +
137B GLU 3.2 1.6 - - - -
138B ASN* 2.8 14.0 + - - +
140B ILE* 2.7 70.8 + - + +
142B HIS* 4.5 19.5 - - + +
163B ILE* 4.5 21.5 - - + -
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Residues in contact with HIS 136 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
132B ILE* 3.0 28.3 + - + +
133B ARG* 4.2 3.1 - - - +
135B LEU* 1.3 73.4 - - + +
137B GLU* 1.3 65.0 + - - +
139B LYS* 3.9 6.8 + - - +
140B ILE 3.1 23.1 - - - +
141B ILE* 4.3 5.7 - - + -
200B ALA* 3.5 27.6 - - + +
203B ASP* 3.6 25.8 + - + +
204B TYR* 3.3 41.4 + + - +
301B PHE* 4.5 6.8 - - + -
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Residues in contact with GLU 137 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
133B ARG* 3.0 27.0 + - - +
134B TYR* 3.2 34.6 - - - +
136B HIS* 1.3 79.2 - - - +
138B ASN* 1.3 62.2 + - - +
139B LYS* 3.2 9.9 + - - +
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Residues in contact with ASN 138 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67B LYS* 4.8 15.2 + - - -
134B TYR* 2.5 60.2 + - - -
135B LEU* 2.8 11.7 + - - +
137B GLU* 1.3 80.6 - - - +
139B LYS* 1.3 68.9 + - - +
140B ILE* 3.2 23.7 - - + +
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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) + - + + + + + -
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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