Contacts of the strand formed by residues 80 - 86 (chain G) in PDB entry 3S4S
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 ASP 80 (chain G).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30G ASN* 3.3 14.9 - - - +
31G SER* 2.4 45.0 + - - -
78G ASP 3.4 3.4 + - - +
79G SER* 1.3 77.9 - - - +
81G THR* 1.3 77.4 + - - +
82G TYR* 3.6 22.3 - - + +
94G GLN* 3.5 5.3 - - - +
95G LEU 2.7 33.0 + - - -
96G LEU* 5.9 0.2 - - - +
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Residues in contact with THR 81 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30G ASN* 3.6 1.4 - - - -
31G SER* 2.9 36.1 + - - -
80G ASP* 1.3 86.3 + - - +
82G TYR* 1.3 62.3 + - - +
83G ILE* 3.6 5.4 - - + +
92G GLU* 3.7 37.7 - - + +
93G VAL 3.6 12.3 - - - +
94G GLN* 3.9 21.1 + - + +
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Residues in contact with TYR 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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14G LEU* 5.3 5.4 - - + -
28G TRP* 3.9 19.3 - - + -
29G LYS 3.3 6.1 - - - +
30G ASN* 4.4 9.4 - - + +
36G ILE* 3.3 35.7 - - + -
51G LEU* 3.7 22.0 - - + +
69G LEU* 3.7 11.0 - - + -
71G ILE* 4.1 10.7 - - + +
78G ASP* 2.6 33.9 + - - -
80G ASP* 3.6 30.3 + - + +
81G THR* 1.3 75.0 - - - +
83G ILE* 1.3 62.5 + - - +
84G CYS 4.1 0.2 - - - -
91G GLU 3.8 0.2 - - - +
92G GLU* 3.6 2.6 - - - -
93G VAL* 2.8 44.0 + - + +
95G LEU* 4.1 15.9 - - + -
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Residues in contact with ILE 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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27G HIS 3.8 0.9 - - - +
28G TRP* 3.4 4.1 - - - -
29G LYS* 2.8 52.0 + - + +
30G ASN 3.8 14.4 - - - +
31G SER* 4.1 6.3 - - - +
33G GLN* 4.8 10.3 - - - +
81G THR* 3.6 18.2 - - + +
82G TYR* 1.3 78.5 - - - +
84G CYS* 1.3 64.9 + - - +
85G GLU* 3.8 2.7 + - + +
90G LYS* 3.9 41.5 - - + +
91G GLU 3.4 10.3 - - - +
92G GLU* 3.7 25.6 - - + +
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Residues in contact with CYS 84 (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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16G CYS* 2.0 48.5 - - + -
26G PHE* 4.6 7.9 - - - -
27G HIS 3.3 9.9 - - - -
28G TRP* 3.6 37.3 - - + -
67G PHE 4.4 1.3 - - - -
83G ILE* 1.3 72.7 - - - +
85G GLU* 1.3 66.9 + - - +
86G VAL* 3.8 2.7 + - - +
89G GLN 3.8 0.5 - - - +
90G LYS* 3.6 3.3 - - - -
91G GLU* 3.0 34.8 + - + +
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Residues in contact with GLU 85 (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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25G GLN 4.1 1.0 - - - +
26G PHE* 3.5 6.1 - - - -
27G HIS* 2.9 59.4 + - + +
29G LYS* 3.4 28.7 + - - +
33G GLN* 4.5 0.2 + - - -
83G ILE* 4.4 6.4 - - + +
84G CYS* 1.3 75.1 - - - +
86G VAL* 1.3 60.6 + - - +
89G GLN 3.4 7.6 - - - +
90G LYS* 2.5 41.8 + - + +
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Residues in contact with VAL 86 (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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16G CYS* 3.8 25.4 - - - -
17G THR 4.1 5.8 - - - +
18G ALA* 3.8 12.3 - - + -
24G ILE* 3.5 27.6 - - + -
25G GLN 4.2 8.3 - - - +
26G PHE* 4.2 4.5 - - + -
67G PHE* 3.8 14.4 - - + -
84G CYS 3.8 0.9 + - - +
85G GLU* 1.3 75.2 - - - +
87G GLU* 1.3 61.3 + - + +
88G ASP 3.3 2.5 - - - -
89G GLN* 2.7 48.6 + - + +
91G GLU* 3.8 12.1 - - - +
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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