Contacts of the strand formed by residues 457 - 465 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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166A MET* 3.6 43.5 - - + -
167A LEU* 4.9 13.9 + - + +
170A ARG* 3.9 52.0 + - + +
171A GLU 4.5 3.6 - - - +
172A ASN* 2.9 18.6 - - - +
253A HIS* 3.5 7.2 - - - +
254A PHE* 2.7 35.2 + - - +
255A GLY 3.8 19.5 - - - -
256A ALA 4.4 10.6 + - - -
455A ARG 3.8 0.2 - - - -
456A GLN* 1.3 118.9 + - + +
458A PHE* 1.3 60.1 + - - +
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Residues in contact with PHE 458 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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166A MET* 3.7 3.2 - - - +
172A ASN* 3.0 35.3 + - + +
173A GLN 3.2 28.5 + - - -
249A PHE* 4.7 5.8 - + - -
251A ARG* 3.7 40.8 - - + -
252A ILE 3.0 14.4 - - - +
253A HIS* 3.6 31.6 - + + +
457A TYR* 1.3 77.7 - - - +
459A ILE* 1.3 70.0 + - - +
460A GLY* 3.6 18.4 - - - -
663A ASN* 4.3 16.2 - - - -
666A SER* 5.0 3.8 - - - -
667A THR* 4.0 16.8 - - - -
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Residues in contact with ILE 459 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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162A ALA* 4.6 0.9 - - + -
163A TYR* 4.3 14.4 - - + +
166A MET* 3.7 15.9 - - + -
173A GLN* 3.6 23.3 - - + +
175A ILE* 4.2 15.9 - - + -
196A PHE* 3.7 42.6 - - + -
250A ILE 3.5 2.1 - - - +
252A ILE* 2.7 29.6 + - + +
254A PHE* 3.3 30.1 - - + -
458A PHE* 1.3 82.0 - - - +
460A GLY* 1.3 62.1 + - - +
461A VAL* 3.7 8.7 + - + +
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Residues in contact with GLY 460 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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173A GLN 3.0 14.2 + - - -
174A SER* 3.0 6.4 - - - -
175A ILE* 2.7 32.2 + - - +
249A PHE* 3.9 18.2 - - - -
250A ILE 3.3 8.3 - - - -
458A PHE* 3.6 12.1 - - - -
459A ILE* 1.3 72.6 - - - +
461A VAL* 1.3 59.1 + - - +
462A LEU 3.9 0.9 - - - -
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Residues in contact with VAL 461 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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175A ILE* 3.7 15.3 - - + +
177A ILE* 4.0 16.8 - - + -
189A THR* 3.7 30.0 - - + +
192A VAL* 4.8 11.9 - - + -
193A ILE* 4.7 15.7 - - + -
196A PHE* 4.9 0.7 - - + -
248A MLY 3.7 1.9 - - - +
249A PHE* 3.5 4.9 - - - -
250A ILE* 3.1 33.3 + - + +
252A ILE* 4.6 12.1 - - + -
459A ILE* 4.1 19.3 - - + +
460A GLY* 1.3 77.3 - - - +
462A LEU* 1.3 61.8 + - - +
463A ASP* 3.9 0.9 + - - +
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Residues in contact with LEU 462 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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174A SER* 6.3 0.2 - - - -
175A ILE 3.0 11.0 + - - +
176A LEU* 3.6 37.5 - - + -
177A ILE* 2.9 34.3 + - - +
178A THR* 5.7 2.9 - - - +
248A MLY 3.5 6.5 - - - +
249A PHE* 3.6 21.8 - - + -
268A TYR* 5.1 0.4 - - + -
460A GLY 3.9 0.6 - - - +
461A VAL* 1.3 75.3 - - - +
463A ASP* 1.3 59.7 + - - +
464A ILE* 3.3 39.5 - - + +
487A LEU* 4.6 20.0 - - + -
660A LEU* 4.3 16.4 - - + -
664A LEU* 4.7 5.6 - - + -
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Residues in contact with ASP 463 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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177A ILE* 4.0 5.6 - - + -
185A LYS* 4.4 19.3 + - - +
186A THR* 3.8 15.6 + - - +
189A THR* 3.1 37.9 + - + +
244A SER* 4.7 6.6 + - - -
246A PHE 4.5 8.3 - - - +
247A GLY* 3.3 0.7 - - - -
248A MLY 2.4 62.6 + - + +
461A VAL 3.9 0.2 + - - -
462A LEU* 1.3 73.2 - - - +
464A ILE* 1.3 67.2 + - - +
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Residues in contact with ILE 464 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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177A ILE 3.7 7.3 + - - +
178A THR* 3.5 14.7 + - - +
185A LYS* 3.8 15.1 - - - +
247A GLY* 4.2 11.4 - - - -
248A MLY 4.2 6.5 - - - +
268A TYR* 4.3 19.3 - - + -
269A LEU* 6.1 2.5 - - + -
462A LEU* 3.3 31.6 - - + +
463A ASP* 1.3 86.8 + - - +
465A ALA* 1.3 84.6 + - + +
480A ILE* 4.6 14.8 - - + -
483A THR* 4.4 24.9 - - + -
487A LEU* 5.2 4.9 - - + -
660A LEU* 4.5 6.7 - - + -
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Residues in contact with ALA 465 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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178A THR* 4.2 2.6 + - - -
179A GLY 4.2 9.2 - - - +
181A SER 6.3 0.4 - - - +
185A LYS* 4.6 7.6 - - - +
464A ILE* 1.3 92.3 - - - +
466A GLY* 1.3 59.9 + - - +
468A GLU* 5.3 6.3 - - - +
480A ILE* 4.4 20.6 - - + +
484A ASN* 2.5 27.4 + - - +
487A LEU* 5.6 0.2 - - - +
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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