Contacts of the strand formed by residues 115 - 125 (chain B) in PDB entry 4WNB
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 115 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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82B VAL* 3.9 2.0 - - - -
111B ARG* 3.3 4.9 - - - -
112B ASN* 2.8 39.3 + - - +
113B THR 3.2 2.1 - - - -
114B LEU* 1.3 79.8 - - - +
116B ASP* 1.3 66.8 + - - -
117B HIS 3.4 0.5 + - - -
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Residues in contact with ASP 116 (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 GLY* 3.4 5.9 - - - -
82B VAL* 3.0 23.6 + - - +
109B VAL* 4.1 14.3 - - + +
110B GLY 3.8 5.2 - - - +
111B ARG* 3.3 32.9 + - - +
115B GLY* 1.3 71.4 - - - -
117B HIS* 1.3 61.7 - - - +
118B VAL 3.5 1.6 - - - +
119B THR* 4.8 11.8 + - - +
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Residues in contact with HIS 117 (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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50B VAL* 4.9 8.5 - - - +
55B ASP* 2.6 40.0 + - - +
80B LEU* 4.4 1.2 - - - +
81B GLY* 2.9 20.5 + - - -
82B VAL* 2.8 29.1 + - - +
83B PRO* 4.8 1.1 - - + -
84B TRP* 3.5 44.1 + + + -
90B VAL* 4.1 11.7 - - + -
92B PHE* 5.6 0.9 - + - -
110B GLY 2.7 15.7 + - - +
112B ASN* 3.8 17.7 - - - +
115B GLY 3.4 2.8 + - - -
116B ASP* 1.3 74.1 - - - +
118B VAL* 1.3 70.8 + - + +
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Residues in contact with VAL 118 (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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55B ASP* 4.6 12.6 - - + +
59B VAL* 4.9 5.4 - - + -
78B LEU* 3.9 36.8 - - + -
79B ARG 3.7 13.0 - - - +
80B LEU* 4.7 3.4 - - + -
81B GLY* 4.4 0.7 - - - +
92B PHE* 4.2 15.3 - - + -
108B VAL* 6.0 0.9 - - + -
109B VAL* 3.5 4.4 - - - +
110B GLY* 2.9 41.6 + - - +
116B ASP 3.5 1.7 - - - -
117B HIS* 1.3 101.2 - - + +
119B THR* 1.3 67.5 + - - +
120B ALA* 4.9 1.6 - - + +
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Residues in contact with THR 119 (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 GLY 3.7 0.3 - - - +
78B LEU* 3.5 2.4 - - - -
79B ARG* 2.8 74.9 + - - +
107B LYS* 3.8 31.6 - - + +
108B VAL 3.4 8.5 - - - +
109B VAL* 4.3 10.7 - - + +
116B ASP* 4.8 10.4 + - - +
118B VAL* 1.3 76.2 + - - +
120B ALA* 1.3 64.9 + - - +
121B THR* 5.9 0.7 - - - +
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Residues in contact with ALA 120 (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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59B VAL* 3.8 26.9 - - + -
76B ILE* 5.1 0.2 - - + -
77B GLY 3.1 9.6 - - - +
78B LEU* 3.7 19.1 - - + -
106B VAL 3.5 0.2 - - - +
107B LYS* 3.4 7.4 - - - +
108B VAL* 2.7 48.3 + - + +
118B VAL* 4.9 2.0 - - + -
119B THR* 1.3 76.2 - - - +
121B THR* 1.3 64.2 + - - +
122B VAL* 4.1 1.8 - - + -
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Residues in contact with THR 121 (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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75B SER* 3.9 3.5 + - - +
76B ILE* 3.6 1.9 - - - -
77B GLY* 2.9 36.7 + - - -
105B THR* 3.6 26.7 - - + -
106B VAL 3.4 3.8 - - - +
107B LYS* 5.3 5.0 - - - +
119B THR* 5.9 0.9 - - - +
120B ALA* 1.3 76.4 + - - +
122B VAL* 1.3 64.5 + - - +
123B GLU* 5.1 5.6 - - + -
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Residues in contact with VAL 122 (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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59B VAL* 3.4 32.1 - - + -
60B GLN* 6.1 0.4 - - - -
63B VAL* 4.0 34.1 - - + -
73B ILE* 4.4 12.8 - - + -
75B SER 3.4 9.0 - - - +
76B ILE* 4.4 13.2 - - + -
104B ILE 3.5 1.0 - - - +
105B THR* 3.2 6.1 - - - +
106B VAL* 2.9 42.9 + - + +
108B VAL* 4.5 4.3 - - + -
121B THR* 1.3 79.3 - - - +
123B GLU* 1.3 73.1 + - - +
124B LEU* 4.3 2.6 - - + +
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Residues in contact with GLU 123 (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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73B ILE* 3.7 1.4 - - - -
74B LYS* 2.7 40.7 + - + +
75B SER* 2.8 39.7 + - - +
103B LEU* 6.2 3.1 - - + -
104B ILE 3.3 4.7 - - - +
105B THR* 4.1 20.6 + - + +
121B THR* 5.1 5.2 - - + -
122B VAL* 1.3 76.3 - - - +
124B LEU* 1.3 57.1 + - - +
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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
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63B VAL* 4.1 22.9 - - + -
66B TRP* 4.6 4.0 - - + -
67B ALA* 3.8 17.7 - - + -
71B ALA* 3.6 20.2 - - + -
72B LEU 3.1 17.5 - - - +
73B ILE* 4.1 9.6 - - + -
74B LYS* 3.9 7.1 - - - +
103B LEU* 3.7 6.6 - - - +
104B ILE* 3.0 60.6 + - + +
106B VAL* 4.2 13.0 - - + -
122B VAL* 4.3 5.2 - - + +
123B GLU* 1.3 77.1 - - - +
125B SER* 1.3 73.0 + - - +
126B MET 5.3 0.4 - - - +
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Residues in contact with SER 125 (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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72B LEU* 2.9 40.1 + - - +
74B LYS* 3.4 19.4 + - - +
102B GLY 3.9 12.6 + - - -
103B LEU* 5.6 0.5 - - - +
104B ILE* 3.8 4.4 - - - +
124B LEU* 1.3 92.8 + - - +
126B MET* 1.3 67.8 + - - +
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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