Contacts of the strand formed by residues 84 - 93 (chain G) in PDB entry 1OPT
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 VAL 84 (chain G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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83G GLU* 1.3 85.1 - - - +
85G VAL* 1.3 78.0 + - - +
86G LEU 4.8 1.6 - - - +
227G LYS* 6.1 3.8 - - - +
229G ASN* 5.2 5.4 - - - +
243G SER* 4.0 18.6 - - - +
244G THR 3.8 4.9 - - - +
245G VAL* 4.5 9.9 - - + -
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Residues in contact with VAL 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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83G GLU* 6.3 1.1 - - + -
84G VAL* 1.3 87.2 - - - +
86G LEU* 1.3 65.8 + - - +
87G VAL* 3.4 5.3 - - + +
243G SER* 3.1 15.7 - - - -
244G THR* 3.1 41.3 + - + +
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Residues in contact with LEU 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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84G VAL* 4.4 3.4 - - + +
85G VAL* 1.3 74.3 - - - +
87G VAL* 1.3 66.5 + - - +
88G ASN 4.4 0.4 + - - +
229G ASN* 4.0 8.7 - - - +
241G ASN* 3.7 29.4 - - - +
242G VAL 3.7 12.8 - - - +
243G SER* 3.6 4.6 - - - -
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Residues in contact with VAL 87 (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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85G VAL* 3.4 18.6 - - + +
86G LEU* 1.3 81.2 - - - +
88G ASN* 1.3 61.0 + - - +
89G VAL* 3.1 31.6 + - + +
240G THR 4.3 2.1 - - - +
241G ASN* 5.4 0.2 - - - -
242G VAL* 2.9 37.6 + - + +
243G SER* 4.0 0.9 - - - -
244G THR* 4.0 22.4 - - - +
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Residues in contact with ASN 88 (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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86G LEU* 4.3 1.2 + - - +
87G VAL* 1.3 70.1 - - - +
89G VAL* 1.3 63.6 + - - +
240G THR 5.4 0.8 - - - +
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Residues in contact with VAL 89 (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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87G VAL* 3.1 27.9 + - + -
88G ASN* 1.3 75.1 + - - +
90G THR* 1.3 79.7 + - + +
91G GLU* 5.2 6.3 - - + -
239G CYS 3.6 0.2 - - - +
240G THR* 3.1 21.0 + - - +
242G VAL* 3.3 20.9 - - + +
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Residues in contact with THR 90 (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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89G VAL* 1.3 82.7 - - + +
91G GLU* 1.3 68.1 + - - +
238G PRO* 3.9 15.8 - - - +
239G CYS 3.6 10.2 + - - -
240G THR* 4.3 13.0 + - - +
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Residues in contact with GLU 91 (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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89G VAL* 3.8 7.5 + - + -
90G THR* 1.3 76.4 + - - +
92G ASN* 1.3 83.5 + - - +
93G PHE* 3.9 19.3 - - + -
226G LEU* 3.7 28.6 - - + +
238G PRO* 3.2 7.3 - - - +
239G CYS 2.9 32.3 + - - +
242G VAL* 4.5 13.0 - - + -
487G LYS* 2.9 24.2 + - - -
489G VAL* 5.1 6.9 - - - +
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Residues in contact with ASN 92 (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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91G GLU* 1.3 83.6 + - - +
93G PHE* 1.3 72.2 + - - +
237G GLY* 3.6 14.3 + - - +
238G PRO* 5.0 8.3 - - - +
487G LYS* 2.7 29.3 + - - +
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Residues in contact with PHE 93 (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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91G GLU* 3.9 17.0 - - + -
92G ASN* 1.3 87.2 - - - +
94G ASN* 1.3 67.9 + - - +
226G LEU* 4.0 2.7 - - + -
227G LYS 4.1 4.0 - - - -
228G CYS* 3.7 17.9 - - + -
233G PHE* 3.5 12.6 - + + -
235G GLY* 3.3 24.1 - - - +
236G THR* 3.7 1.0 - - - -
237G GLY 3.0 18.2 + - - -
239G CYS* 3.5 32.5 - - + -
242G VAL* 4.2 9.2 - - + -
484G TYR 4.6 3.1 - - - +
485G LYS 3.3 26.7 - - - -
486G TYR 3.8 11.9 - - - -
487G LYS* 3.5 33.4 - - + +
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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