Contacts of the strand formed by residues 77 - 83 (chain A) in PDB entry 3UZP
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 TYR 77 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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5A VAL* 6.4 1.3 - - + -
39A LEU* 3.8 43.1 - - + -
40A GLU 3.3 4.5 - - - -
41A CYS* 3.9 32.5 - - - -
42A VAL* 4.2 3.8 - - - -
73A ALA* 3.0 2.4 - - - +
74A GLU 2.7 41.6 + - - +
75A GLY 3.3 0.8 + - - -
76A ASP* 1.3 105.6 - - + +
78A ASN* 1.3 69.3 + - - +
79A VAL* 3.7 2.9 + - + +
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Residues in contact with ASN 78 (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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39A LEU* 3.6 0.9 - - - -
40A GLU* 2.6 56.1 + - - +
42A VAL* 4.2 19.5 - - - +
47A PRO* 5.4 3.1 - - - +
49A LEU* 3.5 17.4 - - + +
50A HIS* 3.5 30.9 + - + +
72A GLY 3.4 4.0 + - - +
73A ALA* 3.1 23.0 - - - +
77A TYR* 1.3 76.6 - - - +
79A VAL* 1.3 58.3 + - - +
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Residues in contact with VAL 79 (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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5A VAL* 4.0 14.1 - - + -
37A ILE* 3.7 22.4 - - + -
38A LYS 3.4 5.2 - - - -
39A LEU* 3.8 14.4 - - + -
49A LEU* 3.7 2.9 - - - +
70A TRP* 3.7 23.7 - - + +
71A CYS* 3.3 4.5 - - - -
72A GLY 2.6 48.1 + - - +
73A ALA* 4.1 2.2 - - - -
74A GLU* 4.1 7.4 - - + +
77A TYR* 3.8 10.1 - - + +
78A ASN* 1.3 77.7 - - - +
80A MET* 1.3 63.9 + - - +
81A VAL* 3.9 16.6 - - + -
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Residues in contact with MET 80 (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 ILE* 3.5 1.9 - - - -
38A LYS* 3.0 32.0 + - + +
49A LEU* 4.0 27.8 - - + +
52A GLU* 4.5 7.4 - - + +
53A SER* 3.7 32.8 - - - -
56A TYR* 3.7 17.0 - - + -
68A ILE* 3.3 32.8 - - + -
70A TRP 3.3 2.9 - - - -
71A CYS* 4.0 7.0 - - - +
79A VAL* 1.3 77.5 - - - +
81A VAL* 1.3 61.5 + - - +
295A 0CK 3.2 41.9 - - + -
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Residues in contact with VAL 81 (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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5A VAL* 5.3 0.2 - - + -
9A TYR* 3.6 47.6 - - + -
35A VAL* 3.6 28.5 - - + -
36A ALA 3.6 3.8 - - - +
37A ILE* 4.2 11.2 - - + -
68A ILE* 3.5 6.6 - - - +
69A ARG* 2.8 32.3 + - + -
70A TRP* 2.7 24.0 + - + +
79A VAL* 3.9 17.5 - - + -
80A MET* 1.3 75.9 - - - +
82A MET* 1.3 62.3 + - - +
295A 0CK 4.3 0.9 - - - -
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Residues in contact with MET 82 (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 VAL* 3.3 10.2 - - - +
36A ALA* 2.8 26.9 + - + +
56A TYR* 3.6 17.0 - - + +
66A PRO* 3.3 43.7 - - + -
67A THR 3.8 7.6 - - - +
68A ILE* 3.6 13.0 - - + -
69A ARG* 4.6 2.2 - - - +
80A MET 4.0 0.2 + - - -
81A VAL* 1.3 74.7 - - - +
83A GLU* 1.3 77.7 + - - +
85A LEU* 4.8 0.4 - - - -
148A ILE* 4.8 1.1 - - - -
295A 0CK 3.4 71.1 - - + -
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Residues in contact with GLU 83 (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 GLU* 3.7 22.0 - - - +
34A GLU 4.6 0.2 - - - -
65A ILE 4.4 0.7 - - - +
66A PRO* 3.5 7.7 - - + +
67A THR* 2.9 40.9 + - - +
69A ARG* 4.0 21.3 + - - +
82A MET* 1.3 89.7 - - + +
84A LEU* 1.3 67.3 + - - +
85A LEU* 3.4 21.8 + - + +
141A LYS* 5.5 1.6 - - - +
146A TYR* 3.9 18.6 + - - -
295A 0CK 3.6 4.9 - - - -
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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