Contacts of the strand formed by residues 78 - 83 (chain G) in PDB entry 4UN7
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 78 (chain G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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41G THR* 3.2 8.1 - - - -
42G GLN 2.8 38.5 + - - +
43G LYS 3.3 24.9 - - - -
45G GLU* 2.5 62.1 + - + -
48G ILE* 3.6 15.2 - - + +
49G LYS* 5.1 0.2 - - - -
71G ILE* 4.3 17.9 - - + -
72G VAL 3.6 3.6 - - - -
73G LYS* 3.5 38.6 - - + +
77G ARG* 1.3 77.3 - - - +
79G GLU* 1.3 60.2 + - - +
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Residues in contact with GLU 79 (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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37G ARG* 5.0 0.3 + - - -
39G VAL* 3.3 43.3 - - + +
40G ILE 3.7 2.5 - - - -
41G THR* 4.2 2.2 - - + -
48G ILE* 4.5 0.9 - - - -
70G GLN 3.4 0.9 - - - +
71G ILE* 3.3 6.3 - - - -
72G VAL* 2.9 47.1 + - + +
77G ARG* 3.3 34.5 + - - +
78G TYR* 1.3 73.3 - - - +
80G LEU* 1.3 65.5 + - - +
81G ARG* 3.0 39.0 + - + +
16H T 4.4 5.1 - - - +
17H T 4.7 3.1 - - - +
9I A 3.7 5.9 + - - +
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Residues in contact with LEU 80 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38G VAL 4.9 1.1 - - - +
39G VAL* 3.4 5.0 - - - -
40G ILE* 2.8 54.4 + - + +
48G ILE* 4.0 24.0 - - + +
52G ILE* 4.2 9.9 - - + -
53G ALA* 3.6 41.5 - - + +
56G MET* 4.2 33.0 - - + -
69G ILE* 3.9 17.9 - - + -
70G GLN 3.4 4.3 - - - +
71G ILE* 4.6 3.6 - - + +
79G GLU* 1.3 73.6 - - - +
81G ARG* 1.3 62.8 + - - +
82G VAL* 4.4 7.0 - - + +
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Residues in contact with ARG 81 (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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35G GLU* 4.8 1.3 - - - -
37G ARG* 3.2 52.8 - - + +
38G VAL 3.6 4.7 - - - +
39G VAL* 4.6 1.1 - - + -
68G LYS 3.6 0.9 - - - +
69G ILE 3.7 0.7 - - - -
70G GLN* 2.7 69.2 + - + +
72G VAL* 4.3 11.7 - - + +
79G GLU* 3.0 40.4 + - + +
80G LEU* 1.3 76.4 - - - +
82G VAL* 1.3 69.0 + - - +
83G SER* 5.1 0.2 - - - -
7I G 3.2 14.3 + - - -
8I G 2.9 35.3 + - - -
9I A 3.3 14.6 + - - +
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Residues in contact with VAL 82 (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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37G ARG* 3.6 1.6 - - - -
38G VAL* 2.9 35.3 + - - +
56G MET* 4.0 15.9 - - + -
60G ILE* 3.9 25.8 - - + -
65G VAL* 4.4 1.3 - - + -
67G SER* 3.9 16.6 - - - -
68G LYS 3.6 13.7 - - - +
69G ILE* 4.4 5.8 - - + -
80G LEU* 4.4 6.3 - - + -
81G ARG* 1.3 80.6 - - - +
83G SER* 1.3 60.3 + - - +
84G SER* 3.4 12.9 + - - -
87G LEU* 3.8 29.4 - - + -
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Residues in contact with SER 83 (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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35G GLU* 2.5 43.5 + - - +
36G TYR 3.5 4.3 - - - -
37G ARG* 4.7 2.7 - - - -
67G SER* 2.8 24.3 + - - -
68G LYS 4.2 4.4 + - - -
70G GLN* 3.9 19.5 - - - +
81G ARG* 4.0 2.5 + - - -
82G VAL* 1.3 72.1 - - - +
84G SER* 1.3 52.2 + - - +
5I C 3.4 32.2 - - - +
6I C 4.4 2.0 + - - -
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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