Contacts of the strand formed by residues 77 - 83 (chain B) in PDB entry 3Q2S
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 ARG 77 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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57B ASP* 5.1 0.8 + - - -
63B ARG* 4.1 19.8 + - - +
66B ARG* 3.7 24.2 - - - +
67B MET* 3.4 45.6 - - + +
70B GLU* 3.6 27.1 + - + +
71B PHE* 4.7 0.2 - - - -
74B ILE* 6.4 0.4 - - - -
75B GLY 3.3 4.2 + - - +
76B MET* 1.3 74.9 - - - +
78B ARG* 1.3 59.6 + - - +
79B THR* 3.8 5.8 - - - +
110B GLU* 3.6 38.5 + - + +
169B LYS 2.8 16.0 + - - +
170B GLU* 3.4 27.6 + - + -
171B HIS* 2.7 31.4 + - - -
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Residues in contact with ARG 78 (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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76B MET* 3.8 13.8 + - + +
77B ARG* 1.3 80.4 - - - +
79B THR* 1.3 60.4 + - - +
80B VAL* 5.9 0.2 - - + -
111B LEU* 2.9 58.3 + - + +
112B ASN 2.6 32.9 + - - -
113B PRO* 4.1 1.8 - - - +
114B GLY* 3.4 9.7 - - - +
115B GLU 3.0 31.7 + - - +
117B GLU* 5.1 6.7 - - - +
171B HIS* 3.4 16.8 - - + +
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Residues in contact with THR 79 (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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77B ARG* 3.8 9.9 - - - -
78B ARG* 1.3 70.4 - - - +
80B VAL* 1.3 80.7 + - - +
81B GLU* 4.3 5.2 - - + +
109B GLY* 3.7 17.5 - - - +
110B GLU* 4.4 4.4 - - - +
170B GLU* 2.5 29.3 + - - +
171B HIS 2.7 12.7 + - - +
172B LYS* 3.6 29.6 - - + -
173B LYS* 2.9 23.4 + - - +
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Residues in contact with VAL 80 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78B ARG* 5.9 0.2 - - + -
79B THR* 1.3 82.8 - - - +
81B GLU* 1.3 66.6 + - - +
108B GLY* 3.1 3.3 - - - -
109B GLY 2.9 29.2 + - - +
111B LEU* 3.9 29.2 - - + -
117B GLU* 4.6 7.9 - - + +
121B LEU* 3.7 17.5 - - + +
124B LEU* 3.6 27.4 - - + -
173B LYS* 3.3 18.2 - - + +
175B PHE* 4.0 18.8 - - + -
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Residues in contact with GLU 81 (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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79B THR* 4.3 5.1 - - + +
80B VAL* 1.3 80.4 - - - +
82B GLY* 1.3 60.2 + - - +
106B LEU* 3.1 40.9 + - + +
107B PRO 3.3 7.2 - - - +
108B GLY* 4.1 2.7 - - - -
109B GLY 5.2 0.2 - - - +
121B LEU* 4.2 4.3 - - - -
172B LYS* 3.3 38.6 + - + +
173B LYS 3.1 6.2 + - - +
174B LEU* 3.0 25.9 - - + +
175B PHE* 3.1 27.9 + - - -
211B ILE* 4.4 6.8 - - - +
212B ILE* 5.8 0.3 - - - +
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Residues in contact with GLY 82 (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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81B GLU* 1.3 73.0 - - - +
83B VAL* 1.3 62.9 + - - -
84B LEU* 3.3 15.9 - - - +
95B LEU 5.2 0.2 - - - +
106B LEU* 3.8 7.1 - - - +
107B PRO* 2.7 31.9 + - - +
121B LEU* 4.2 5.2 - - - +
125B MET* 4.3 6.1 - - - -
175B PHE 3.7 1.1 - - - -
177B VAL* 3.7 19.7 - - - -
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Residues in contact with VAL 83 (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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81B GLU 5.0 0.2 - - - +
82B GLY* 1.3 75.0 - - - +
84B LEU* 1.3 59.4 + - - +
85B ILE* 4.1 21.8 - - + -
94B VAL* 4.2 20.9 - - + -
106B LEU* 4.1 23.6 - - + -
145B ILE* 3.6 31.2 - - + -
174B LEU* 4.8 5.4 - - + -
175B PHE 2.8 17.1 + - - +
176B LEU* 3.7 9.6 - - + +
177B VAL* 2.7 28.6 + - - +
215B LEU* 4.3 9.6 - - + -
219B LEU* 4.8 4.7 - - + -
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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