Contacts of the strand formed by residues 457 - 465 (chain J) in PDB entry 1O18
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 J).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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166J MET* 3.6 42.8 - - + -
167J LEU* 4.9 14.9 + - + +
170J ARG* 3.9 52.4 + - + +
171J GLU 4.5 3.1 - - - +
172J ASN* 2.9 18.4 - - - +
253J HIS* 3.5 6.6 - - - +
254J PHE* 2.7 34.5 + - - +
255J GLY 3.8 19.1 - - - -
256J ALA 4.4 10.2 + - - -
258J GLY* 6.0 0.2 - - - -
455J ARG 3.8 0.4 - - - -
456J GLN* 1.3 117.3 + - + +
458J PHE* 1.3 58.3 + - - +
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Residues in contact with PHE 458 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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166J MET* 3.7 4.0 - - - +
172J ASN* 3.0 35.1 + - + +
173J GLN 3.2 28.6 + - - -
249J PHE* 4.7 5.8 - + - -
251J ARG* 3.7 40.8 - - + -
252J ILE 3.0 14.8 - - - +
253J HIS* 3.6 31.6 - + + +
457J TYR* 1.3 79.1 - - - +
459J ILE* 1.3 67.5 + - - +
460J GLY* 3.6 18.2 - - - -
663J ASN* 4.3 15.3 - - - -
666J SER* 5.0 3.6 - - - -
667J THR* 4.0 16.2 - - - -
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Residues in contact with ILE 459 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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162J ALA* 4.6 0.7 - - + -
163J TYR* 4.3 15.0 - - + +
166J MET* 3.7 16.6 - - + -
173J GLN* 3.6 23.1 - - + -
175J ILE* 4.2 15.9 - - + -
196J PHE* 3.7 42.6 - - + -
250J ILE 3.5 2.1 - - - +
252J ILE* 2.7 29.8 + - + +
254J PHE* 3.3 29.8 - - + -
458J PHE* 1.3 81.9 - - - +
460J GLY* 1.3 61.8 + - - +
461J VAL* 3.7 7.8 + - + +
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Residues in contact with GLY 460 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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173J GLN 3.0 14.6 + - - -
174J SER* 3.0 5.9 - - - -
175J ILE* 2.7 32.2 + - - +
249J PHE* 3.9 17.9 - - - -
250J ILE 3.3 8.5 - - - -
458J PHE* 3.6 11.7 - - - -
459J ILE* 1.3 74.0 - - - +
461J VAL* 1.3 59.3 - - - +
462J LEU 3.9 0.7 - - - -
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Residues in contact with VAL 461 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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175J ILE* 3.7 15.3 - - + +
177J ILE* 4.0 17.5 - - + -
189J THR* 3.7 30.6 - - + +
192J VAL* 4.8 11.9 - - + -
193J ILE* 4.7 13.5 - - + -
196J PHE* 4.9 1.1 - - + -
248J MLY 3.7 2.4 - - - +
249J PHE* 3.5 4.8 - - - -
250J ILE* 3.1 34.2 + - + +
252J ILE* 4.6 12.3 - - + -
459J ILE* 4.1 19.7 - - + +
460J GLY* 1.3 77.8 - - - +
462J LEU* 1.3 58.5 + - - +
463J ASP* 3.9 0.5 + - - +
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Residues in contact with LEU 462 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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174J SER* 6.3 0.4 - - - -
175J ILE 3.0 11.4 + - - +
176J LEU* 3.6 38.1 - - + -
177J ILE* 2.9 34.9 + - - +
178J THR* 5.7 2.7 - - - +
248J MLY 3.5 7.0 - - - +
249J PHE* 3.6 21.5 - - + -
268J TYR* 5.1 0.4 - - + -
461J VAL* 1.3 74.2 - - - +
463J ASP* 1.3 59.8 + - - +
464J ILE* 3.3 40.4 - - + +
487J LEU* 4.6 19.3 - - + -
660J LEU* 4.3 16.4 - - + -
664J LEU* 4.7 6.7 - - + -
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Residues in contact with ASP 463 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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177J ILE* 4.0 5.8 - - + -
185J LYS* 4.4 20.0 + - - +
186J THR* 3.8 15.2 + - - +
189J THR* 3.1 38.2 + - + +
244J SER* 4.7 7.7 + - - -
246J PHE 4.5 8.1 - - - +
247J GLY* 3.3 0.7 - - - -
248J MLY 2.4 63.3 + - + +
461J VAL 3.9 0.4 + - - +
462J LEU* 1.3 74.2 - - - +
464J ILE* 1.3 67.7 + - - +
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Residues in contact with ILE 464 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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177J ILE 3.7 7.3 + - - +
178J THR* 3.5 15.8 + - - +
185J LYS* 3.8 15.1 - - - +
246J PHE 5.6 0.4 - - - -
247J GLY* 4.2 11.7 - - - -
248J MLY 4.2 6.1 - - - +
268J TYR* 4.3 18.6 - - + -
269J LEU* 6.1 2.2 - - + -
462J LEU* 3.3 31.8 - - + +
463J ASP* 1.3 86.6 + - - +
465J ALA* 1.3 86.1 + - + +
480J ILE* 4.6 14.4 - - + -
483J THR* 4.4 24.9 - - + -
487J LEU* 5.2 5.2 - - + -
660J LEU* 4.5 6.5 - - + -
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Residues in contact with ALA 465 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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178J THR* 4.2 2.0 + - - -
179J GLY 4.2 9.2 - - - +
181J SER 6.3 0.7 - - - +
185J LYS* 4.6 7.8 - - - +
247J GLY* 5.7 0.2 - - - -
464J ILE* 1.3 92.0 - - - +
466J GLY* 1.3 58.8 + - - +
468J GLU* 5.3 6.3 - - - +
480J ILE* 4.4 21.8 - - + +
484J ASN* 2.5 28.1 + - - +
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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