Contacts of the strand formed by residues 60 - 66 (chain G) 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 G).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28G ARG* 3.6 25.6 - - - +
30G ILE* 4.2 12.8 - - + -
48G LEU* 4.3 11.9 - - + +
51G LEU* 3.8 38.1 - - + -
59G ASP* 1.3 76.7 - - - +
61G TYR* 1.3 70.6 + - - +
62G LEU* 5.4 0.4 - - + -
84G ILE* 3.8 29.6 - - + -
86G PRO* 3.9 14.1 - - + -
87G ASP 2.8 10.2 + - - +
88G VAL* 3.4 8.9 - - + -
89G GLN* 2.7 36.0 + - - +
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Residues in contact with TYR 61 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27G ASP 4.4 8.7 - - - -
28G ARG* 3.0 15.4 + - + +
29G ILE* 3.4 24.4 - - + +
30G ILE* 2.7 33.8 + - - +
59G ASP* 3.7 28.8 + - - -
60G ILE* 1.3 74.0 - - - +
62G LEU* 1.3 55.0 + - - +
63G TYR* 4.0 14.1 + + + -
89G GLN* 3.5 41.6 + - + -
91G ILE* 4.3 11.0 - - + -
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Residues in contact with LEU 62 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30G ILE* 3.4 37.5 - - + +
32G LEU* 4.4 14.1 - - + -
44G ILE* 4.6 10.5 - - + -
48G LEU* 6.0 2.5 - - + -
60G ILE* 4.0 1.9 + - + -
61G TYR* 1.3 70.9 - - - +
63G TYR* 1.3 65.7 + - - +
64G ILE* 3.8 18.9 + - + +
77G ILE* 5.0 8.5 - - + -
81G ILE* 4.1 25.6 - - + -
88G VAL* 4.0 10.5 - - + -
89G GLN 2.8 16.3 + - - +
90G THR* 3.3 16.3 - - + -
91G ILE* 2.9 25.4 + - - +
103G LEU* 5.4 3.1 - - + -
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Residues in contact with TYR 63 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45F VAL* 5.5 0.9 - - + -
49F LEU* 3.7 32.1 - - + +
83F HIS* 5.4 5.1 - + - -
29G ILE* 3.7 34.7 - - + +
30G ILE 3.0 6.9 + - - +
31G MET* 3.7 26.0 - - + -
32G LEU* 2.9 30.9 + - - +
61G TYR* 4.4 9.4 - - + -
62G LEU* 1.3 74.7 - - - +
64G ILE* 1.3 59.6 + - - +
65G ASN 4.2 0.4 - - - -
91G ILE* 3.3 49.6 - - + +
93G ILE* 4.0 25.1 - - + -
115G LEU* 5.9 1.1 - - + -
190G MET* 5.4 6.3 - - + +
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Residues in contact with ILE 64 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32G LEU* 3.6 14.8 - - + -
62G LEU* 3.9 20.6 - - + +
63G TYR* 1.3 80.2 - - - +
65G ASN* 1.3 61.3 + - - +
66G SER* 4.2 19.5 - - - +
90G THR* 4.1 17.5 - - + -
91G ILE 2.8 12.0 + - - +
92G CYS* 3.4 7.9 - - + -
93G ILE* 3.1 24.6 + - - +
95G MET 3.9 3.3 - - - +
96G ALA* 4.2 11.7 - - + -
100G GLY 4.0 13.9 - - - +
103G LEU* 4.0 10.3 - - + -
104G LEU* 3.7 36.1 - - + +
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Residues in contact with ASN 65 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38F ASP* 3.8 34.9 + - - +
41F ALA* 4.7 4.4 - - - +
42F ASN* 5.4 5.3 - - - +
72F THR* 5.0 2.1 + - - -
73F ALA* 4.7 5.5 - - - +
76F ALA* 4.1 16.4 - - - +
32G LEU 2.8 10.4 + - - +
33G GLY* 3.2 30.2 + - - +
63G TYR 4.2 0.2 - - - -
64G ILE* 1.3 70.7 - - - +
66G SER* 1.3 59.6 + - - +
93G ILE* 3.1 27.5 + - + +
94G GLY* 3.8 3.5 - - - -
95G MET* 3.1 27.0 + - - +
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Residues in contact with SER 66 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38F ASP* 5.1 0.2 - - - -
32G LEU* 4.3 11.7 - - - -
34G SER 2.7 23.4 + - - -
36G ILE* 3.8 13.0 - - - +
64G ILE* 3.9 15.5 - - - +
65G ASN* 1.3 76.5 + - - +
67G PRO* 1.4 62.5 - - - +
68G GLY 3.1 15.2 + - - -
95G MET* 2.9 14.0 + - - +
96G ALA* 3.5 0.9 - - - -
97G ALA* 2.9 25.1 + - - +
100G GLY* 4.4 5.7 - - - -
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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