Contacts of the strand formed by residues 88 - 97 (chain B) in PDB entry 3V5I
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 VAL 88 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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48B LEU* 4.2 10.1 - - + -
60B ILE* 3.4 19.1 - - + +
62B LEU* 4.0 18.8 - - + -
81B ILE* 3.8 37.1 - - + +
84B ILE* 3.9 26.9 - - + -
86B PRO 3.7 2.4 + - - +
87B ASP* 1.3 78.9 - - - +
89B GLN* 1.3 72.6 + - - +
90B THR* 4.5 6.1 - - + -
107B GLY* 3.3 4.7 - - - -
108B ALA* 2.9 30.0 + - - +
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Residues in contact with GLN 89 (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 ASP* 3.6 18.8 + - - +
60B ILE 2.7 16.9 + - - +
61B TYR* 3.5 37.3 + - + -
62B LEU* 2.8 33.6 + - - +
87B ASP 5.1 0.2 - - - +
88B VAL* 1.3 73.7 - - - +
90B THR* 1.3 56.9 + - - +
91B ILE* 4.8 6.1 - - + +
111B LYS* 3.3 46.2 - - + +
113B PHE* 3.2 23.6 - - + -
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Residues in contact with THR 90 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62B LEU* 3.4 16.4 - - + -
64B ILE* 4.1 13.0 - - + -
81B ILE* 5.3 1.8 - - + -
88B VAL* 3.7 4.9 + - + +
89B GLN* 1.3 74.0 - - - +
91B ILE* 1.3 61.4 + - - +
92B CYS 4.2 0.4 - - - -
103B LEU 3.7 14.8 - - - +
104B LEU* 2.6 31.0 + - - +
107B GLY* 3.5 20.2 - - - +
111B LYS 3.2 5.4 + - - +
112B ARG* 3.4 14.2 - - - +
113B PHE* 2.7 33.8 + - - +
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Residues in contact with ILE 91 (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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61B TYR* 4.3 24.5 - - + -
62B LEU 3.0 9.1 + - - +
63B TYR* 3.3 55.8 - - + +
64B ILE* 2.8 25.4 + - - -
89B GLN* 4.8 5.8 - - + +
90B THR* 1.3 79.7 - - - +
92B CYS* 1.3 63.1 + - - +
93B ILE* 3.5 10.0 + - + -
104B LEU* 4.3 1.6 - - - -
113B PHE* 3.5 22.4 - - + -
115B LEU* 4.5 6.5 - - + -
190B MET* 4.0 24.2 - - + -
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Residues in contact with CYS 92 (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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64B ILE* 3.4 8.5 - - + +
91B ILE* 1.3 71.8 - - - +
93B ILE* 1.3 62.8 + - - +
95B MET 4.1 2.7 - - - -
96B ALA* 3.6 35.7 - - + -
104B LEU* 3.6 29.5 - - + +
113B PHE 3.0 13.1 + - - +
114B ALA* 4.0 4.9 - - + -
115B LEU* 3.1 25.1 + - - +
118B ALA* 3.4 21.2 - - - +
119B GLU 3.9 5.4 - - - -
120B VAL* 4.6 3.4 - - - -
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Residues in contact with ILE 93 (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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42A ASN* 5.3 4.0 - - - +
45A VAL* 3.9 37.7 - - + -
76A ALA* 4.0 14.6 - - + -
79A ASP* 5.9 0.4 - - + -
80A THR* 4.4 5.8 - - - +
31B MET* 4.5 8.3 - - + -
63B TYR* 4.1 26.5 - - + -
64B ILE 3.0 12.9 + - - +
65B ASN* 3.1 27.2 - - + +
91B ILE* 3.5 2.4 + - + -
92B CYS* 1.3 76.6 - - - +
94B GLY* 1.3 61.7 + - - +
95B MET 3.0 8.4 + - - -
115B LEU* 3.8 31.0 - - + -
118B ALA* 4.2 1.3 - - - -
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Residues in contact with GLY 94 (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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72A THR* 3.4 32.0 - - - +
75A PHE* 4.5 4.6 - - - +
76A ALA* 3.7 15.0 - - - +
79A ASP* 5.7 1.8 + - - +
65B ASN* 3.8 4.3 - - - -
93B ILE* 1.3 69.1 - - - +
95B MET* 1.3 58.6 + - - +
117B ASN 4.4 1.7 - - - +
118B ALA* 3.4 12.4 - - - +
119B GLU* 3.0 25.0 + - - +
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Residues in contact with MET 95 (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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72A THR* 3.7 26.5 - - + +
142A HIS* 4.6 3.4 - - + -
65B ASN* 3.0 13.1 + - - +
66B SER 2.9 30.6 + - - +
67B PRO* 5.2 2.7 - - + -
92B CYS* 4.1 3.1 - - - -
93B ILE 3.0 4.9 + - - -
94B GLY* 1.3 73.9 - - - +
96B ALA* 1.3 68.5 + - - +
97B ALA* 4.0 25.4 - - + +
119B GLU* 3.1 48.0 - - + +
121B MET* 4.3 6.3 - - - -
174B PHE* 3.9 24.5 - - + -
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Residues in contact with ALA 96 (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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64B ILE* 4.2 11.9 - - + -
66B SER 3.5 3.8 - - - +
92B CYS* 3.6 19.3 - - - -
95B MET* 1.3 74.1 - - - +
97B ALA* 1.3 60.0 + - - +
100B GLY* 4.0 7.9 - - - +
101B SER* 3.2 28.1 - - - +
104B LEU* 4.2 11.0 - - + -
119B GLU 2.9 9.8 + - - +
120B VAL* 3.4 3.4 - - + -
121B MET 3.1 19.5 + - - -
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Residues in contact with ALA 97 (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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66B SER 3.0 8.2 + - - +
67B PRO* 3.7 19.1 - - + +
68B GLY* 3.4 8.1 - - - -
95B MET* 4.0 12.1 - - + -
96B ALA* 1.3 75.6 - - - +
98B ALA* 1.3 62.1 + - - +
99B MET 3.2 0.7 + - - -
100B GLY* 2.7 27.4 + - - -
101B SER 3.8 0.2 - - - +
121B MET* 3.4 35.0 - - + +
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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