Contacts of the strand formed by residues 60 - 66 (chain E) 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 E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28E ARG* 3.7 29.4 - - - +
30E ILE* 4.1 15.9 - - + -
48E LEU* 4.2 12.1 - - + +
51E LEU* 3.7 37.5 - - + -
59E ASP* 1.3 77.4 - - - +
61E TYR* 1.3 67.5 + - - +
62E LEU* 4.0 0.9 - - + -
84E ILE* 3.8 28.5 - - + -
86E PRO* 4.0 9.6 - - + -
87E ASP 2.8 10.0 + - - +
88E VAL* 3.5 9.8 - - + -
89E GLN* 2.7 36.0 + - - +
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Residues in contact with TYR 61 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27E ASP 4.4 8.3 - - - -
28E ARG* 3.0 18.7 + - + +
29E ILE* 3.4 22.2 - - + +
30E ILE* 2.7 35.0 + - - +
59E ASP* 3.7 28.4 + - - -
60E ILE* 1.3 75.4 - - - +
62E LEU* 1.3 55.1 + - - +
63E TYR* 3.8 6.1 + + + -
89E GLN* 3.5 42.0 + - + -
91E ILE* 4.3 18.2 - - + -
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Residues in contact with LEU 62 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30E ILE* 3.6 38.8 - - + +
32E LEU* 4.4 14.6 - - + -
44E ILE* 4.6 10.5 - - + -
48E LEU* 5.8 2.2 - - + -
60E ILE* 4.0 2.2 + - + -
61E TYR* 1.3 70.1 - - - +
63E TYR* 1.3 67.1 + - - +
64E ILE* 3.8 23.8 + - + +
77E ILE* 5.0 8.3 - - + -
81E ILE* 4.1 26.9 - - + -
88E VAL* 3.9 11.7 - - + -
89E GLN 2.8 17.0 + - - +
90E THR* 3.3 9.2 - - + -
91E ILE* 2.9 25.5 + - - +
103E LEU* 5.5 2.2 - - + -
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Residues in contact with TYR 63 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45D VAL* 5.6 1.3 - - + -
49D LEU* 3.8 35.5 - - + +
80D THR* 6.1 0.4 - - - -
83D HIS* 5.4 7.1 - + - -
29E ILE* 3.8 32.6 - - + +
30E ILE 2.9 7.3 + - - +
31E MET* 3.8 25.1 - - + -
32E LEU* 2.9 31.6 + - - +
61E TYR* 4.4 9.3 - + + +
62E LEU* 1.3 74.8 - - - +
64E ILE* 1.3 59.8 + - - +
65E ASN 4.2 0.2 - - - -
91E ILE* 3.3 50.7 - - + +
93E ILE* 4.1 25.4 - - + -
115E LEU* 6.0 1.3 - - + -
190E MET* 5.4 4.8 - - + +
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Residues in contact with ILE 64 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32E LEU* 3.7 21.1 - - + -
62E LEU* 3.8 19.1 - - + +
63E TYR* 1.3 79.0 - - - +
65E ASN* 1.3 61.8 + - - +
66E SER* 4.3 10.3 - - - +
90E THR* 4.1 17.0 - - + -
91E ILE 2.8 13.1 + - - +
92E CYS* 3.4 10.3 - - + -
93E ILE* 3.0 25.7 + - - +
95E MET 4.0 0.2 - - - +
96E ALA* 4.1 13.2 - - + -
100E GLY 4.0 15.3 - - - +
103E LEU* 4.0 12.3 - - + -
104E LEU* 3.6 35.0 - - + +
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Residues in contact with ASN 65 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38D ASP* 3.7 32.4 + - - +
41D ALA* 4.6 6.5 - - - +
42D ASN* 5.6 3.2 - - - +
72D THR* 4.8 2.4 + - - -
73D ALA* 4.4 7.7 - - - +
76D ALA* 4.0 17.6 - - - +
32E LEU 2.9 12.5 + - - +
33E GLY* 3.3 29.6 + - - -
64E ILE* 1.3 71.0 - - - +
66E SER* 1.3 59.3 + - - +
93E ILE* 3.2 25.8 - - + +
94E GLY* 3.9 1.8 - - - -
95E MET* 3.1 26.6 + - - +
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Residues in contact with SER 66 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38D ASP* 5.1 0.2 - - - -
32E LEU* 4.3 15.7 - - - -
34E SER 3.0 21.1 + - - -
36E ILE* 3.6 14.2 - - - +
64E ILE* 4.0 11.3 - - - +
65E ASN* 1.3 75.2 - - - +
67E PRO* 1.4 63.8 - - - +
68E GLY* 3.0 15.3 + - - -
95E MET* 2.9 14.3 + - - +
96E ALA* 3.5 0.9 - - - -
97E ALA* 3.0 24.6 + - - +
100E GLY* 4.4 5.1 - - - -
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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