Contacts of the strand formed by residues 108 - 113 (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 PRO 108 (chain p).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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7p VAL* 4.5 17.5 - - + +
8p TYR 4.5 2.7 - - - +
9p LYS 4.8 6.7 - - - +
10p ASP 5.0 1.3 - - - -
11p GLY* 3.8 41.1 - - - +
12p ILE* 4.1 4.0 - - + -
102p GLY 3.3 9.0 - - - +
103p VAL* 4.2 6.3 - - + -
106p THR 4.5 1.3 - - - +
107p GLY* 1.3 84.9 - - - +
109p HIS* 1.3 74.2 + - - +
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Residues in contact with HIS 109 (chain p).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
216g SER 4.1 20.4 - - - -
7p VAL* 5.3 1.3 - - - -
12p ILE* 3.1 3.3 - - - +
76p VAL* 3.9 13.3 - - + +
100p LEU 3.8 0.9 - - - +
101p GLY* 3.5 2.4 - - - -
102p GLY 2.9 30.5 + - - -
104p ASP* 4.1 9.0 - - - -
106p THR* 3.4 34.2 + - - -
107p GLY 3.6 12.3 - - - -
108p PRO* 1.3 88.4 + - + +
110p LEU* 1.3 60.5 + - - +
111p TYR* 3.9 23.6 - - + -
121p LYS* 4.1 27.1 + - - +
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Residues in contact with LEU 110 (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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5p GLY* 3.4 30.1 - - - +
6p VAL* 3.8 3.4 - - - +
7p VAL* 3.8 12.8 - - + +
12p ILE* 4.0 8.5 - - + +
14p LEU* 4.0 15.5 - - + -
99p VAL* 3.9 20.4 - - + -
100p LEU 3.4 12.8 - - - +
101p GLY* 4.0 5.8 - - - -
109p HIS* 1.3 76.7 - - - +
111p TYR* 1.3 62.8 + - - +
121p LYS* 3.6 8.3 - - - +
122p LEU 3.1 42.3 + - - +
123p PRO 3.6 12.1 - - - +
124p TYR* 3.8 2.0 - - - -
125p VAL* 3.7 16.8 - - + -
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Residues in contact with TYR 111 (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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76p VAL* 3.6 35.0 - - + -
77p VAL* 3.5 23.9 + - + +
80p ASN* 3.3 46.2 - - + +
99p VAL* 3.6 3.6 - - - +
100p LEU* 2.9 41.9 + - + +
109p HIS* 3.9 15.7 - - + +
110p LEU* 1.3 76.9 - - - +
112p SER* 1.3 63.0 + - - +
113p ILE* 4.6 0.2 - - + -
119p THR* 4.5 4.5 - - - -
120p ASP 3.3 9.6 - - - +
121p LYS* 3.3 53.5 + - + -
125p VAL* 4.2 9.0 - - - +
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Residues in contact with SER 112 (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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98p LEU 3.4 8.1 - - - -
99p VAL* 4.7 0.4 - - - +
111p TYR* 1.3 75.0 - - - +
113p ILE* 1.3 61.5 + - - +
114p TYR* 3.7 14.4 + - - -
118p SER 4.0 0.2 - - - +
119p THR* 3.0 6.4 - - - -
120p ASP* 2.9 48.1 + - - +
122p LEU* 4.4 2.6 - - - +
125p VAL* 3.7 26.4 - - - +
126p THR 5.5 0.2 - - - -
127p MET* 4.2 17.3 - - - -
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Residues in contact with ILE 113 (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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80p ASN* 3.6 17.7 - - - +
83p LEU* 3.4 40.6 - - + -
84p LYS* 5.1 2.7 - - - -
87p LEU* 3.8 26.7 - - + -
96p ALA 3.7 0.5 - - - +
97p ALA* 3.5 5.4 - - - -
98p LEU* 2.9 49.1 + - + +
100p LEU* 4.0 16.6 - - + -
111p TYR* 4.6 2.0 - - + -
112p SER* 1.3 74.2 - - - +
114p TYR* 1.3 65.8 + - - +
117p GLY* 5.3 0.4 - - - -
118p SER 3.6 2.7 - - - +
119p THR* 3.6 22.4 - - + -
127p MET* 4.0 2.9 - - - +
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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