Contacts of the strand formed by residues 173 - 179 (chain p) 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 ILE 173 (chain p).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16p ALA 3.7 8.3 - - - +
156p SER* 3.5 33.2 - - - +
159p ILE* 4.0 12.8 - - + -
160p ALA* 4.0 21.8 - - + +
163p ILE* 3.7 13.9 - - + -
172p ASN* 1.3 79.0 - - - +
174p ASP* 1.3 72.9 + - - +
175p LEU* 4.1 17.9 - - + -
188p PRO* 3.8 0.5 - - - +
189p TYR* 2.9 30.4 + - + +
190p THR* 2.9 34.0 + - + +
192p PRO* 4.7 7.4 - - + -
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Residues in contact with ASP 174 (chain p).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15p GLY* 3.3 5.0 - - - -
16p ALA* 2.9 36.9 + - + +
17p ASP 5.4 0.4 - - - +
18p THR* 3.7 20.9 - - - +
30p ASN* 5.1 1.4 - - - +
31p CYS 4.6 2.6 - - - +
32p SER* 4.9 4.5 + - - -
33p LYS 5.4 1.4 + - - +
34p ILE* 3.8 16.8 - - + +
172p ASN* 4.5 1.9 - - - +
173p ILE* 1.3 80.3 + - - +
175p LEU* 1.3 64.0 + - - +
185p PHE* 5.4 3.1 - - + -
186p LEU 4.1 1.1 - - - +
187p ARG* 2.3 61.7 + - - +
188p PRO* 3.7 4.2 - - - +
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Residues in contact with LEU 175 (chain p).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13p VAL* 4.4 7.6 - - + -
14p LEU 3.1 6.7 - - - +
15p GLY* 3.8 1.6 - - - -
34p ILE* 4.4 3.6 - - - -
152p LYS* 3.9 23.1 - - + +
155p VAL* 3.5 31.2 - - + -
156p SER* 4.5 2.5 - - - +
173p ILE* 4.1 12.8 + - + -
174p ASP* 1.3 84.5 - - - +
176p CYS* 1.3 62.6 + - - +
177p VAL* 5.4 0.7 - - + -
184p ASP 4.5 0.4 - - - -
185p PHE* 3.8 8.0 - - - -
186p LEU* 3.0 44.8 + - + +
189p TYR* 3.4 49.6 - - + +
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Residues in contact with CYS 176 (chain p).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12p ILE 3.6 1.6 - - - +
13p VAL* 3.4 3.4 - - - -
14p LEU* 2.9 45.9 + - + +
34p ILE* 4.4 3.4 - - + -
42p TYR* 3.8 33.0 - - - -
175p LEU* 1.3 75.4 - - - +
177p VAL* 1.3 64.5 + - - +
178p ILE* 4.1 13.5 - - - +
183p LEU* 4.1 9.2 - - - -
184p ASP 3.4 6.3 - - - -
185p PHE* 3.6 28.3 - - + -
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Residues in contact with VAL 177 (chain p).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8p TYR* 3.6 22.7 - - + +
12p ILE 3.5 2.5 - - - +
13p VAL* 4.1 18.6 - - + +
148p GLU* 3.8 19.1 - - + +
152p LYS* 3.9 33.0 - - + -
175p LEU* 5.4 0.9 - - + -
176p CYS* 1.3 74.8 - - - +
178p ILE* 1.3 65.8 + - - +
179p SER 4.2 0.2 - - - -
182p LYS* 3.7 6.2 - - - +
183p LEU* 3.3 10.0 - - - +
184p ASP* 2.9 50.3 + - + +
186p LEU* 4.6 5.6 - - + -
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Residues in contact with ILE 178 (chain p).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8p TYR* 4.2 2.8 + - - -
11p GLY* 3.2 3.5 - - - -
12p ILE* 2.9 44.2 + - + +
14p LEU* 4.6 5.8 - - + -
39p PRO 5.4 0.2 - - - +
40p ASN* 3.7 19.3 - - + +
42p TYR* 4.0 31.4 - - + +
101p GLY 3.8 25.4 - - - +
103p VAL* 3.5 23.4 - - + +
176p CYS* 4.1 8.3 - - - +
177p VAL* 1.3 80.0 - - - +
179p SER* 1.3 64.8 + - - +
182p LYS 3.7 2.5 - - - +
183p LEU* 3.8 14.8 - - + -
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Residues in contact with SER 179 (chain p).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8p TYR* 3.7 13.5 - - - -
10p ASP* 3.3 20.4 - - - -
103p VAL* 4.0 11.7 - - - +
148p GLU* 5.4 0.7 - - - -
177p VAL 4.2 0.4 - - - -
178p ILE* 1.3 78.9 - - - +
180p LYS* 1.3 61.6 + - - +
181p ASN* 2.9 14.3 + - - -
182p LYS* 2.9 47.7 + - - +
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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
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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