Contacts of the strand formed by residues 457 - 465 (chain G) in PDB entry 1O1F
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 457 (chain G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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166G MET* 3.6 43.7 - - + -
167G LEU* 4.9 14.3 + - + +
170G ARG* 3.9 51.6 + - + +
171G GLU 4.5 3.1 - - - +
172G ASN* 2.9 18.2 - - - +
253G HIS* 3.5 6.4 - - - +
254G PHE* 2.7 35.0 + - - +
255G GLY 3.8 19.1 - - - -
256G ALA 4.4 10.8 + - - -
258G GLY* 6.4 0.2 - - - -
455G ARG 3.8 0.2 - - - -
456G GLN* 1.3 117.0 + - + +
458G PHE* 1.3 56.6 + - - +
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Residues in contact with PHE 458 (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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166G MET* 3.7 3.1 - - - +
172G ASN* 3.0 35.1 + - + +
173G GLN 3.2 28.7 + - - -
249G PHE* 4.7 6.1 - + - -
251G ARG* 3.7 41.1 - - + -
252G ILE 3.0 14.4 - - - +
253G HIS* 3.6 31.2 - + + +
457G TYR* 1.3 77.7 - - - +
459G ILE* 1.3 68.7 + - - +
460G GLY* 3.6 18.4 - - - -
663G ASN* 4.3 15.5 - - - -
666G SER* 5.0 3.6 - - - -
667G THR* 4.0 16.6 - - - -
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Residues in contact with ILE 459 (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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162G ALA* 4.6 1.1 - - + -
163G TYR* 4.3 13.9 - - + +
166G MET* 3.7 16.6 - - + -
173G GLN* 3.6 23.1 - - + -
175G ILE* 4.2 16.4 - - + -
196G PHE* 3.7 43.1 - - + -
250G ILE 3.5 1.9 - - - +
252G ILE* 2.7 29.2 + - + +
254G PHE* 3.3 29.4 - - + -
458G PHE* 1.3 81.2 - - - +
460G GLY* 1.3 62.4 + - - +
461G VAL* 3.7 7.6 + - + +
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Residues in contact with GLY 460 (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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173G GLN 3.0 14.2 + - - -
174G SER* 3.0 5.7 - - - -
175G ILE 2.7 33.3 + - - +
249G PHE* 3.9 19.1 - - - -
250G ILE 3.3 9.0 - - - -
458G PHE* 3.6 11.3 - - - -
459G ILE* 1.3 72.3 - - - +
461G VAL* 1.3 58.9 + - - +
462G LEU 3.9 0.7 - - - -
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Residues in contact with VAL 461 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
175G ILE* 3.7 14.8 - - + +
177G ILE* 4.0 17.3 - - + -
189G THR* 3.7 30.4 - - + +
192G VAL* 4.8 12.1 - - + -
193G ILE* 4.7 14.8 - - + -
196G PHE* 4.9 1.1 - - + -
248G MLY 3.7 1.7 - - - +
249G PHE* 3.5 4.8 - - - -
250G ILE* 3.1 34.9 + - + +
252G ILE* 4.6 12.1 - - + -
459G ILE* 4.1 19.1 - - + +
460G GLY* 1.3 78.4 - - - +
462G LEU* 1.3 61.0 + - - +
463G ASP* 3.9 0.9 + - - +
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Residues in contact with LEU 462 (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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174G SER* 6.3 0.7 - - - -
175G ILE 3.0 11.8 + - - +
176G LEU* 3.6 38.8 - - + -
177G ILE* 2.9 35.0 + - - +
178G THR* 5.7 2.7 - - - +
248G MLY 3.5 6.5 - - - +
249G PHE* 3.6 22.0 - - + -
268G TYR* 5.1 0.2 - - + -
460G GLY 3.9 0.4 - - - -
461G VAL* 1.3 74.1 - - - +
463G ASP* 1.3 60.5 + - - +
464G ILE* 3.3 40.2 - - + +
487G LEU* 4.6 19.3 - - + -
660G LEU* 4.3 15.7 - - + -
664G LEU* 4.7 5.6 - - + -
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Residues in contact with ASP 463 (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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177G ILE* 4.0 6.1 - - + -
185G LYS* 4.4 19.0 + - - +
186G THR* 3.8 15.1 + - - +
189G THR* 3.1 38.4 + - + +
244G SER* 4.7 7.1 + - - -
246G PHE 4.5 8.6 - - - +
247G GLY* 3.3 0.7 - - - -
248G MLY 2.4 62.7 + - + +
461G VAL 3.9 0.2 + - - -
462G LEU* 1.3 74.4 - - - +
464G ILE* 1.3 66.8 + - - +
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Residues in contact with ILE 464 (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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177G ILE 3.7 8.3 + - - +
178G THR* 3.5 14.4 + - - +
185G LYS* 3.8 15.6 - - - +
246G PHE 5.6 0.2 - - - -
247G GLY* 4.2 12.3 - - - -
248G MLY 4.2 6.5 - - - +
268G TYR* 4.3 19.5 - - + -
269G LEU* 6.1 2.5 - - + -
462G LEU* 3.3 31.6 - - + +
463G ASP* 1.3 84.2 + - - +
465G ALA* 1.3 85.8 + - + +
480G ILE* 4.6 13.9 - - + -
483G THR* 4.4 25.6 - - + -
487G LEU* 5.2 4.9 - - + -
660G LEU* 4.5 6.1 - - + -
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Residues in contact with ALA 465 (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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178G THR* 4.2 2.0 + - - -
179G GLY 4.2 8.1 - - - +
181G SER 6.3 0.9 - - - +
185G LYS* 4.6 7.4 - - - +
464G ILE* 1.3 92.4 - - - +
466G GLY* 1.3 60.3 + - - +
468G GLU* 5.3 6.3 - - - +
480G ILE* 4.4 21.4 - - + +
484G ASN* 2.5 27.1 + - - +
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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