Contacts of the strand formed by residues 64 - 71 (chain A) in PDB entry 4OUH
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 LEU 64 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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61A ASN* 3.2 38.8 + - - +
62A LYS 3.6 0.8 - - - -
63A ASP* 1.3 82.7 - - + +
65A TYR* 1.3 66.1 + - - +
66A VAL* 3.8 27.4 + - + +
81A LYS* 4.5 10.5 - - + +
82A ALA 3.5 2.7 - - - +
83A ILE* 3.9 28.7 - - + -
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Residues in contact with TYR 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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19A GLN* 3.3 30.1 - - + +
20A ASP* 2.5 30.0 + - - -
23A VAL* 3.6 25.8 - - + -
58A TRP* 3.2 33.7 - + - +
59A ASN* 4.0 5.2 - - - -
61A ASN 3.5 19.5 - - - -
62A LYS* 3.6 26.1 - - - +
64A LEU* 1.3 74.3 - - - +
66A VAL* 1.3 62.5 + - - +
67A LEU* 4.1 6.5 - - + -
80A VAL* 3.6 0.7 - - - +
81A LYS* 3.2 6.6 - - - +
82A ALA* 2.8 53.3 + - + -
89A MET* 3.7 12.3 - - + -
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Residues in contact with VAL 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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40A VAL* 3.3 9.9 - - - +
41A GLY* 2.9 47.7 + - - +
42A ASP* 3.5 25.6 - - - +
58A TRP 5.6 0.4 + - - -
64A LEU* 3.8 31.9 + - + +
65A TYR* 1.3 77.5 - - - +
67A LEU* 1.3 64.7 + - - +
79A LEU* 3.7 13.7 - - + -
80A VAL 3.4 3.8 - - - +
81A LYS* 4.3 12.1 - - + -
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Residues in contact with LEU 67 (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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23A VAL* 3.8 29.2 - - + -
26A LEU* 6.2 1.6 - - + -
27A HIS* 4.9 5.8 - - + +
39A GLY 3.6 1.6 - - - +
40A VAL* 3.7 22.9 - - + -
54A LEU* 5.0 3.8 - - + -
55A PRO* 3.8 16.4 - - + -
58A TRP* 3.8 18.8 - - + +
65A TYR* 5.0 4.5 - - + -
66A VAL* 1.3 86.8 - - - +
68A ARG* 1.3 63.7 + - - +
69A TYR* 3.6 32.3 - - + +
79A LEU* 3.7 2.5 - - - +
80A VAL* 2.8 48.4 + - + +
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Residues in contact with ARG 68 (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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37A GLY* 3.7 1.7 - - - -
38A LEU* 2.8 40.2 + - + +
39A GLY 2.9 13.1 + - - +
40A VAL 3.0 27.1 + - - +
41A GLY 2.8 25.6 + - - +
42A ASP 3.7 15.3 - - - -
43A GLN 3.3 17.7 + - - -
44A PRO* 3.6 11.8 - - - +
48A ASP* 2.6 44.2 + - - -
55A PRO* 5.8 0.5 - - - +
67A LEU* 1.3 72.8 - - - +
69A TYR* 1.3 69.4 + - - +
78A LEU 3.4 6.5 - - - +
79A LEU* 3.6 18.8 - - + -
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Residues in contact with TYR 69 (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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26A LEU* 5.9 0.7 - - - +
27A HIS* 2.7 49.2 + + - -
30A VAL* 3.6 29.1 - - + +
31A VAL* 4.5 2.9 - - + -
35A TYR* 4.1 12.8 - - + -
36A CYS 3.2 20.6 - - - +
37A GLY* 3.5 11.0 - - - -
38A LEU* 3.9 6.3 - - - +
55A PRO* 6.1 0.7 - - + -
67A LEU* 3.6 35.6 - - + +
68A ARG* 1.3 76.4 - - - +
70A GLU* 1.3 60.0 + - - +
77A LYS* 3.4 8.7 - - - +
78A LEU* 2.8 44.0 + - + +
80A VAL* 3.7 32.4 - - + +
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Residues in contact with GLU 70 (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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35A TYR* 3.9 4.0 - - - -
36A CYS* 2.8 33.0 + - - +
38A LEU* 3.5 28.3 - - + +
50A LYS* 3.1 33.2 + - - +
69A TYR* 1.3 74.8 - - - +
71A TYR* 1.3 66.3 + - - +
74A GLY 3.7 14.1 - - - +
75A SER* 4.2 3.6 + - - -
76A ARG 3.3 11.4 - - - +
77A LYS* 2.5 32.7 + - - +
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Residues in contact with TYR 71 (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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33A HIS 4.1 10.8 + - - -
34A GLY* 3.8 17.5 - - - -
35A TYR* 3.5 39.8 - + + -
50A LYS* 3.0 17.3 + - - -
70A GLU* 1.3 69.9 - - - +
72A LYS* 1.3 66.3 + - + +
73A ASP* 3.1 50.5 + - + +
74A GLY 3.4 8.3 - - - +
76A ARG* 2.8 60.1 + - + +
143A HIS* 5.8 2.4 + - - -
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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
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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