Contacts of the helix formed by residues 131 - 143 (chain s) in PDB entry 5GJQ
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 GLY 131 (chain s).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1s THR 3.3 6.9 + - - -
2s THR* 3.2 24.7 - - - +
129s GLY 3.0 1.2 - - - -
130s SER* 1.3 77.5 + - - +
132s SER* 1.3 65.8 + - - +
133s VAL 3.2 2.2 - - - -
134s TYR* 2.9 21.8 + - - +
135s ALA 3.3 8.5 + - - -
163s ALA* 4.0 1.0 - - - +
167s ASP* 3.5 15.9 - - - -
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Residues in contact with SER 132 (chain s).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24r ASN* 5.1 5.5 + - - -
26r VAL* 6.1 0.2 - - - +
2s THR* 4.3 3.1 - - - +
127s SER* 3.2 46.4 + - - -
128s VAL* 3.8 5.4 - - - -
129s GLY 2.6 22.6 + - - -
130s SER 3.4 1.2 - - - -
131s GLY* 1.3 78.8 - - - +
133s VAL* 1.3 69.0 + - - +
135s ALA 3.2 1.4 + - - -
136s TYR* 3.0 29.6 + - - -
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Residues in contact with VAL 133 (chain s).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
137d PHE* 3.3 37.4 - - + +
138d LEU* 3.6 32.9 - - + +
24r ASN* 4.0 10.3 - - - +
25r ILE* 3.8 24.9 - - + -
26r VAL* 3.9 12.3 - - + -
130s SER 4.6 4.7 - - - +
131s GLY 4.3 3.6 - - - -
132s SER* 1.3 83.1 + - - +
134s TYR* 1.3 83.4 + - + +
136s TYR* 3.6 8.7 + - + +
137s GLY 3.7 6.1 + - - -
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Residues in contact with TYR 134 (chain s).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32c ALA* 5.2 3.2 - - + +
33c GLN* 1.8 46.9 + - - +
137d PHE* 3.3 37.9 - + - -
140d LEU* 4.5 4.9 - - + -
141d SER* 3.2 35.2 + - - -
130s SER 4.5 4.9 - - - -
131s GLY* 2.9 13.5 + - - +
133s VAL* 1.3 85.3 - - + +
135s ALA* 1.3 66.2 + - - +
137s GLY 3.2 4.5 + - - -
138s VAL* 3.7 5.8 - - - +
162s GLN* 4.8 0.4 - - - +
163s ALA* 3.8 18.8 - - - +
166s ARG* 3.5 33.7 - - + -
167s ASP* 4.0 30.3 - - + -
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Residues in contact with ALA 135 (chain s).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2s THR* 3.9 20.9 - - + -
4s LEU* 4.2 20.2 - - + -
127s SER* 3.7 19.7 - - - +
131s GLY 3.3 1.4 + - - -
132s SER 3.2 2.1 + - - +
134s TYR* 1.3 79.7 - - - +
136s TYR* 1.3 62.8 + - - +
137s GLY 3.2 0.2 + - - -
138s VAL* 3.4 4.8 + - - +
139s MET* 3.0 27.0 + - - +
159s ALA* 4.0 18.2 - - - +
163s ALA* 4.2 0.9 - - + +
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Residues in contact with TYR 136 (chain s).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
138d LEU* 4.7 4.9 - - + -
166d GLU* 3.8 4.3 - - - +
170d ARG* 2.6 46.4 + - - -
26r VAL* 4.0 25.1 - - + -
28r MET* 3.7 19.6 - - + +
125s THR* 4.2 3.8 - - - -
126s PHE* 3.6 9.3 - - - -
127s SER* 3.2 36.9 + - - -
132s SER* 3.0 26.0 + - - +
133s VAL* 3.7 10.1 - - - +
134s TYR 3.2 0.2 - - - -
135s ALA* 1.3 76.9 - - - +
137s GLY* 1.3 64.0 + - - +
139s MET* 3.8 26.5 - - + -
140s ASP* 2.9 39.6 + - - +
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Residues in contact with GLY 137 (chain s).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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138d LEU 4.0 9.9 - - - -
141d SER* 3.8 15.0 - - - -
142d ILE* 3.6 11.4 - - - +
166d GLU* 3.6 16.0 + - - +
133s VAL 3.7 3.4 + - - -
134s TYR 3.2 4.2 + - - -
135s ALA 3.1 1.6 - - - -
136s TYR* 1.3 82.3 - - - +
138s VAL* 1.3 60.3 + - - +
141s ARG* 3.3 26.9 + - - +
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Residues in contact with VAL 138 (chain s).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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141d SER* 4.4 6.0 + - - +
142d ILE* 4.6 2.4 - - - +
145d ARG* 5.1 17.9 - - + +
146d TYR* 5.4 1.6 + - - -
134s TYR 3.7 11.9 - - - +
135s ALA 3.7 11.2 - - - +
137s GLY* 1.3 73.2 - - - +
139s MET* 1.3 67.1 + - - +
141s ARG* 3.2 6.2 + - - +
142s GLY* 2.9 21.8 + - - -
155s LEU* 3.8 14.2 - - + +
158s ARG* 4.4 11.7 - - + -
159s ALA* 3.8 36.1 - - + +
162s GLN* 4.1 21.1 - - + -
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Residues in contact with MET 139 (chain s).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4s LEU* 3.7 24.5 - - + -
5s ALA 4.3 0.7 - - - +
6s PHE* 3.6 41.1 - - + -
125s THR* 3.8 23.6 - - + -
126s PHE 3.9 13.5 - - - +
127s SER* 4.7 1.6 - - - -
135s ALA 3.0 15.8 + - - +
136s TYR* 3.8 32.3 - - + +
138s VAL* 1.3 79.8 - - - +
140s ASP* 1.3 57.2 + - - +
142s GLY 3.3 0.5 + - - -
143s TYR* 2.8 36.7 + - + +
155s LEU* 4.1 12.4 - - + +
159s ALA* 4.5 7.4 - - + -
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Residues in contact with ASP 140 (chain s).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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166d GLU* 3.1 27.0 - - - +
169d LYS* 4.0 16.2 - - + +
170d ARG* 2.8 51.4 + - - +
125s THR* 4.2 6.6 + - - +
136s TYR* 2.9 28.6 + - - +
139s MET* 1.3 77.8 - - - +
141s ARG* 1.3 72.4 + - - +
142s GLY 3.5 0.3 + - - -
143s TYR* 3.8 16.0 + - - +
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Residues in contact with ARG 141 (chain s).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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142d ILE* 3.8 16.2 - - + -
146d TYR* 4.1 26.3 + - + +
162d LYS* 4.3 35.6 + - + +
165d GLU* 3.8 26.3 + - - +
166d GLU* 3.8 25.2 + - - +
169d LYS* 4.8 13.3 - - - +
137s GLY 3.3 19.2 + - - +
138s VAL* 3.2 7.0 + - - +
140s ASP* 1.3 88.2 + - - +
142s GLY* 1.3 59.5 + - - +
143s TYR 5.1 0.6 - - - +
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Residues in contact with GLY 142 (chain s).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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146d TYR* 5.3 3.4 - - - -
138s VAL 2.9 14.1 + - - -
141s ARG* 1.3 78.5 - - - +
143s TYR* 1.3 61.0 + - - +
144s SER* 3.7 1.7 + - - -
147s LEU* 3.7 14.4 - - - +
155s LEU* 3.5 25.2 - - - +
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Residues in contact with TYR 143 (chain s).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6s PHE* 3.6 39.3 - + + -
7s LYS 2.3 33.9 + - - -
8s PHE* 4.5 0.9 - - + -
124s ALA* 4.1 14.5 - - + +
125s THR* 4.0 23.1 - - + -
139s MET* 2.8 20.2 + - + +
140s ASP* 3.8 12.6 + - - +
141s ARG 3.6 1.5 - - - +
142s GLY* 1.3 79.1 - - - +
144s SER* 1.3 86.0 + - - +
145s TYR* 3.8 16.4 - - + -
147s LEU* 4.2 2.2 - - + -
155s LEU* 3.9 4.9 - - + -
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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
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Atomic class I II III IV V VI VII VIII
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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