Contacts of the strand formed by residues 60 - 66 (chain A) 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 A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28A ARG* 3.6 30.1 - - - +
30A ILE* 4.2 12.6 - - + -
48A LEU* 4.3 12.6 - - + +
51A LEU* 3.8 35.9 - - + -
59A ASP* 1.3 73.7 - - - +
61A TYR* 1.3 70.5 + - - +
62A LEU* 4.6 0.4 - - - +
84A ILE* 3.8 29.6 - - + -
86A PRO* 3.8 14.1 - - + -
87A ASP 2.9 9.6 + - - +
88A VAL* 3.5 8.9 - - + -
89A GLN* 2.7 36.9 + - - +
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Residues in contact with TYR 61 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27A ASP 4.4 9.2 - - - -
28A ARG* 2.9 16.9 + - + +
29A ILE* 3.4 21.2 - - + +
30A ILE* 2.7 34.0 + - - +
59A ASP* 3.6 30.4 + - - -
60A ILE* 1.3 73.7 - - - +
62A LEU* 1.3 55.5 + - - +
63A TYR* 4.0 7.6 - + + -
89A GLN* 3.5 41.6 + - + -
91A ILE* 4.3 17.5 - - + -
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Residues in contact with LEU 62 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30A ILE* 3.5 35.4 - - + +
32A LEU* 4.4 15.0 - - + -
44A ILE* 4.7 11.0 - - + -
48A LEU* 5.9 2.9 - - + -
60A ILE* 4.0 1.7 + - + -
61A TYR* 1.3 70.3 - - - +
63A TYR* 1.3 67.3 + - - +
64A ILE* 3.8 23.5 + - + +
77A ILE* 4.9 9.6 - - + -
81A ILE* 4.1 24.9 - - + -
88A VAL* 4.0 11.4 - - + -
89A GLN 2.8 17.0 + - - +
90A THR* 3.3 9.2 - - + -
91A ILE* 2.9 26.0 + - - +
103A LEU* 5.4 2.5 - - + -
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Residues in contact with TYR 63 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29A ILE* 3.7 35.1 - - + +
30A ILE 2.9 6.7 + - - +
31A MET* 3.8 26.0 - - + -
32A LEU* 2.9 31.1 + - - +
61A TYR* 4.4 10.0 - - + +
62A LEU* 1.3 75.5 - - - +
64A ILE* 1.3 59.6 - - - +
65A ASN 4.1 0.7 - - - -
91A ILE* 3.3 50.9 - - + +
93A ILE* 4.1 24.0 - - + -
115A LEU* 6.1 0.9 - - + -
190A MET* 5.4 4.0 - - + +
45G VAL* 5.6 1.3 - - + -
49G LEU* 3.9 30.7 - - + +
83G HIS* 5.3 7.8 - - - -
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Residues in contact with ILE 64 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32A LEU* 3.7 19.3 - - + -
62A LEU* 3.9 18.8 - - + +
63A TYR* 1.3 78.5 - - - +
65A ASN* 1.3 61.5 + - - +
66A SER* 4.2 11.7 - - - +
90A THR* 4.1 17.9 - - + -
91A ILE 2.8 12.0 + - - +
92A CYS* 3.4 12.2 - - + -
93A ILE* 3.0 27.7 + - - +
95A MET 4.0 0.2 - - - +
96A ALA* 4.1 20.0 - - + -
100A GLY* 4.1 7.6 - - - +
103A LEU* 4.0 13.0 - - + -
104A LEU* 3.6 36.1 - - + +
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Residues in contact with ASN 65 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32A LEU 2.9 20.0 + - - +
33A GLY* 3.2 21.5 + - - +
63A TYR 4.1 0.2 - - - -
64A ILE* 1.3 71.9 - - - +
66A SER* 1.3 57.5 + - - +
93A ILE* 3.1 27.3 - - + +
94A GLY* 3.9 1.9 - - - -
95A MET* 3.1 27.3 + - - +
38G ASP* 3.7 34.4 + - - +
41G ALA* 4.7 4.8 - - - +
42G ASN* 5.6 3.8 - - - +
72G THR* 4.8 2.6 + - - -
73G ALA* 4.6 5.9 - - - +
76G ALA* 4.2 15.4 - - - +
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Residues in contact with SER 66 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32A LEU* 4.2 16.6 - - - -
34A SER 3.0 22.0 + - - -
36A ILE* 3.8 7.4 - - - +
64A ILE* 4.0 11.2 - - - +
65A ASN* 1.3 75.5 + - - +
67A PRO* 1.4 62.4 - - - +
68A GLY* 2.9 22.1 + - - -
95A MET* 2.9 14.2 + - - +
96A ALA* 3.6 0.9 - - - -
97A ALA 3.0 24.9 + - - +
100A GLY* 4.4 4.3 - - - -
38G ASP* 5.3 0.2 - - - -
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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