Contacts of the strand formed by residues 77 - 83 (chain B) in PDB entry 5A72
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 MET 77 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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49B PHE* 3.7 15.0 - - + -
50B GLN 3.3 38.6 - - - +
51B SER* 3.8 4.3 - - - -
52B THR* 3.0 11.7 + - - -
73B ARG* 2.9 45.6 + - + +
75B ASP* 3.1 22.3 + - - +
76B GLY* 1.3 78.9 - - - +
78B SER* 1.3 59.2 + - - +
613D A 3.7 28.0 - - + -
614D C 3.5 39.0 - - + +
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Residues in contact with SER 78 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49B PHE* 3.6 1.4 - - - -
50B GLN 2.6 37.6 + - - -
52B THR* 3.0 26.4 + - - +
55B HIS* 3.2 26.7 + - - -
58B LEU* 3.5 18.2 - - - -
71B ARG 3.3 9.0 - - - -
72B LYS* 3.9 4.3 - - - -
73B ARG* 4.5 0.4 - - - -
77B MET* 1.3 73.7 + - - +
79B GLU* 1.3 70.5 + - - +
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Residues in contact with GLU 79 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47B THR* 4.1 10.0 - - + +
48B VAL 3.5 4.5 - - - +
49B PHE* 3.1 24.9 - - + -
58B LEU* 3.6 4.9 - - - -
69B THR 3.7 0.7 - - - +
70B VAL* 3.3 4.7 - - - +
71B ARG* 2.8 73.0 + - + +
73B ARG* 2.8 33.1 + - - -
78B SER* 1.3 81.0 - - - +
80B PHE* 1.3 60.3 + - - +
81B CYS* 5.5 4.7 - - + +
507C C 4.9 3.1 + - - -
508C G 4.6 0.2 - - - +
616D A 2.9 18.7 + - - -
617D C 5.0 2.1 + - - -
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Residues in contact with PHE 80 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46B LEU* 4.0 11.2 - - + -
47B THR* 3.1 10.1 - - - +
48B VAL* 3.0 46.8 + - + +
58B LEU* 3.8 25.1 - - + +
61B ILE* 3.7 24.2 - - + -
62B GLN* 3.5 26.7 - - + -
65B LEU* 3.8 15.9 - - + -
67B CYS 3.5 21.5 - - - -
68B GLY* 4.0 7.9 - - - -
69B THR 3.2 14.8 - - - -
70B VAL* 4.0 6.3 - - + +
79B GLU* 1.3 74.1 - - - +
81B CYS* 1.3 59.7 + - - +
82B VAL* 3.5 30.7 - - + -
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Residues in contact with CYS 81 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45B SER* 4.2 7.9 - - - -
46B LEU 3.4 2.9 - - - -
47B THR* 3.5 20.4 - - + +
68B GLY* 3.3 1.4 - - - -
69B THR* 2.8 50.9 + - - +
71B ARG* 6.5 0.9 - - + -
79B GLU* 5.5 5.6 - - + +
80B PHE* 1.3 79.4 - - - +
82B VAL* 1.3 67.6 + - - +
83B VAL* 3.4 28.5 + - + +
505C A 4.8 0.9 + - - -
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Residues in contact with VAL 82 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45B SER* 3.2 5.5 - - - -
46B LEU* 3.0 35.2 + - + +
65B LEU* 4.5 3.6 - - + -
67B CYS* 4.1 10.8 - - - -
68B GLY* 3.9 11.7 - - - -
80B PHE* 3.5 32.5 - - + -
81B CYS* 1.3 72.5 - - - +
83B VAL* 1.3 60.6 + - - +
87B SER* 3.5 43.3 - - - +
88B LEU* 3.8 18.3 - - + +
91B THR* 4.1 9.4 - - + +
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Residues in contact with VAL 83 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43B ARG* 3.8 29.4 - - + +
44B VAL 3.6 10.1 - - - +
45B SER* 4.5 3.1 - - - -
69B THR* 5.5 0.7 - - - +
81B CYS* 3.4 27.5 + - + -
82B VAL* 1.3 75.1 - - - +
84B GLY* 1.3 68.9 + - - +
87B SER* 4.4 10.2 + - - -
88B LEU* 5.0 0.2 - - - -
504C G 3.6 43.3 - - + +
505C A 3.7 25.3 + - + +
506C A 6.1 1.6 - - - +
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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