Contacts of the strand formed by residues 60 - 66 (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 ILE 60 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28B ARG* 3.5 27.6 - - - +
30B ILE* 4.2 12.3 - - + -
48B LEU* 4.3 11.7 - - + +
51B LEU* 3.8 37.5 - - + -
59B ASP* 1.3 75.6 - - - +
61B TYR* 1.3 70.5 + - - +
62B LEU* 4.7 0.7 - - + +
84B ILE* 3.8 28.9 - - + -
86B PRO* 4.0 13.9 - - + -
87B ASP 2.9 9.1 + - - +
88B VAL* 3.4 10.5 - - + -
89B GLN* 2.7 36.0 + - - +
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Residues in contact with TYR 61 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27B ASP 4.4 8.3 - - - -
28B ARG* 2.9 19.0 + - + +
29B ILE* 3.4 22.0 - - + +
30B ILE* 2.7 33.6 + - - +
59B ASP* 3.8 28.7 + - - -
60B ILE* 1.3 75.3 - - - +
62B LEU* 1.3 56.2 + - - +
63B TYR* 3.9 7.4 + + + -
89B GLN* 3.5 40.7 + - + -
91B ILE* 4.3 18.2 - - + -
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Residues in contact with LEU 62 (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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30B ILE* 3.5 37.7 - - + +
32B LEU* 4.4 14.1 - - + -
44B ILE* 4.6 10.3 - - + -
48B LEU* 5.9 2.7 - - + -
60B ILE* 4.0 2.0 + - + -
61B TYR* 1.3 71.3 - - - +
63B TYR* 1.3 67.3 + - - +
64B ILE* 3.7 24.2 + - + +
77B ILE* 5.0 8.7 - - + -
81B ILE* 4.1 26.0 - - + -
88B VAL* 4.0 11.2 - - + -
89B GLN 2.8 16.8 + - - +
90B THR* 3.4 8.5 - - + -
91B ILE* 3.0 24.0 + - - +
103B LEU* 5.5 3.1 - - + -
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Residues in contact with TYR 63 (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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45A VAL* 5.5 1.6 - - + -
49A LEU* 3.7 34.8 - - + +
80A THR* 6.1 0.4 - - - -
83A HIS* 5.3 8.3 - + - -
29B ILE* 3.7 30.8 - - + +
30B ILE 2.9 6.5 + - - +
31B MET* 3.8 26.2 - - + -
32B LEU* 2.9 31.0 + - - +
61B TYR* 4.4 9.7 - - + -
62B LEU* 1.3 74.6 - - - +
64B ILE* 1.3 59.5 + - - +
91B ILE* 3.3 52.8 - - + +
93B ILE* 4.1 23.1 - - + -
115B LEU* 6.1 0.9 - - + -
190B MET* 5.5 1.8 - - + -
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Residues in contact with ILE 64 (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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32B LEU* 3.6 13.7 - - + -
62B LEU* 3.8 20.6 - - + +
63B TYR* 1.3 80.5 - - - +
65B ASN* 1.3 61.1 + - - +
66B SER* 4.3 17.0 - - - +
90B THR* 4.1 19.1 - - + -
91B ILE 2.8 12.2 + - - +
92B CYS* 3.4 10.9 - - - -
93B ILE* 3.0 24.5 + - - +
96B ALA* 4.2 20.4 - - + -
100B GLY* 4.2 7.2 - - - +
103B LEU* 4.0 9.9 - - + -
104B LEU* 3.7 35.4 - - + +
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Residues in contact with ASN 65 (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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38A ASP* 3.6 31.4 + - - +
41A ALA* 4.5 7.9 - - - +
42A ASN* 5.5 3.6 - - - +
72A THR* 4.7 2.8 + - - -
73A ALA* 4.4 7.7 - - - +
76A ALA* 4.0 15.6 - - - +
32B LEU 2.9 11.2 + - - +
33B GLY* 3.3 28.8 + - - +
64B ILE* 1.3 70.5 - - - +
66B SER* 1.3 58.9 + - - +
93B ILE* 3.1 26.2 - - + +
94B GLY* 3.8 2.7 - - - -
95B MET* 3.0 28.0 + - - +
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Residues in contact with SER 66 (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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38A ASP* 4.7 0.7 - - - -
32B LEU* 4.3 16.2 - - - -
34B SER 3.0 20.8 + - - -
36B ILE* 3.8 10.4 - - - +
64B ILE* 4.0 11.3 - - - +
65B ASN* 1.3 75.1 + - - +
67B PRO* 1.3 64.0 - - - +
68B GLY* 3.0 18.9 + - - -
95B MET* 2.9 14.8 + - - +
96B ALA* 3.5 0.7 - - - -
97B ALA* 3.0 24.9 + - - +
100B GLY* 4.4 4.4 - - - -
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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
------------------------------------------------------------
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