Contacts of the strand formed by residues 457 - 465 (chain P) 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 P).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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166P MET* 3.6 43.5 - - + -
167P LEU* 4.9 13.9 + - + +
170P ARG* 3.9 52.0 + - + +
171P GLU 4.5 3.1 - - - +
172P ASN* 2.9 19.1 - - - +
253P HIS* 3.5 6.7 - - - +
254P PHE* 2.7 34.8 + - - +
255P GLY 3.8 19.5 - - - -
256P ALA 4.4 10.6 + - - -
258P GLY* 6.0 0.2 - - - -
455P ARG 3.8 0.2 - - - -
456P GLN* 1.3 118.6 + - + +
458P PHE* 1.3 57.6 + - - +
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Residues in contact with PHE 458 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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166P MET* 3.7 3.0 - - - +
172P ASN* 3.0 35.6 + - + +
173P GLN 3.2 29.0 + - - -
249P PHE* 4.7 6.7 - + - -
251P ARG* 3.7 40.2 - - + -
252P ILE 3.0 14.6 - - - +
253P HIS* 3.6 31.2 - + + +
457P TYR* 1.3 78.9 - - - +
459P ILE* 1.3 69.7 + - - +
460P GLY* 3.6 17.7 - - - -
663P ASN* 4.3 16.2 - - - -
666P SER* 5.0 3.6 - - - -
667P THR* 4.0 16.4 - - - -
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Residues in contact with ILE 459 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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162P ALA* 4.6 0.4 - - + -
163P TYR* 4.3 14.8 - - + +
166P MET* 3.7 16.2 - - + -
173P GLN* 3.6 23.3 - - + -
175P ILE* 4.2 16.2 - - + -
196P PHE* 3.7 42.2 - - + -
250P ILE 3.5 2.1 - - - +
252P ILE* 2.7 29.8 + - + +
254P PHE* 3.3 29.4 - - + -
458P PHE* 1.3 81.8 - - - +
460P GLY* 1.3 61.9 + - - +
461P VAL* 3.7 8.1 + - + +
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Residues in contact with GLY 460 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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173P GLN 3.0 13.7 + - - -
174P SER* 3.0 5.3 - - - -
175P ILE 2.7 33.4 + - - +
249P PHE* 3.9 19.3 - - - -
250P ILE 3.3 9.0 - - - -
458P PHE* 3.6 11.2 - - - -
459P ILE* 1.3 73.1 - - - +
461P VAL* 1.3 58.8 + - - +
462P LEU 3.9 0.7 - - - -
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Residues in contact with VAL 461 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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175P ILE* 3.7 14.4 - - + +
177P ILE* 4.0 17.5 - - + -
189P THR* 3.7 30.0 - - + +
192P VAL* 4.8 11.9 - - + -
193P ILE* 4.7 14.6 - - + -
196P PHE* 4.9 1.1 - - + -
248P MLY 3.7 2.1 - - - +
249P PHE* 3.5 4.7 - - - -
250P ILE* 3.1 35.2 + - + +
252P ILE* 4.6 12.3 - - + -
459P ILE* 4.1 19.5 - - + +
460P GLY* 1.3 78.2 - - - +
462P LEU* 1.3 60.0 + - - +
463P ASP* 3.9 0.9 + - - +
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Residues in contact with LEU 462 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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174P SER* 6.3 0.4 - - - -
175P ILE 3.0 12.1 + - - +
176P LEU* 3.6 38.6 - - + -
177P ILE* 2.9 35.4 + - - +
178P THR* 5.7 2.7 - - - +
248P MLY 3.5 6.1 - - - +
249P PHE* 3.6 23.1 - - + -
268P TYR* 5.1 0.4 - - + -
460P GLY 3.9 0.2 - - - -
461P VAL* 1.3 74.2 - - - +
463P ASP* 1.3 59.5 + - - +
464P ILE* 3.3 39.3 - - + +
487P LEU* 4.6 19.3 - - + -
660P LEU* 4.3 16.2 - - + -
664P LEU* 4.7 6.1 - - + -
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Residues in contact with ASP 463 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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177P ILE* 4.0 6.3 - - + -
185P LYS* 4.4 18.9 + - - +
186P THR* 3.8 16.0 + - - +
189P THR* 3.1 38.0 + - + +
244P SER* 4.7 7.4 + - - -
246P PHE 4.5 8.6 - - - +
247P GLY* 3.3 0.5 - - - -
248P MLY 2.4 63.8 + - + +
461P VAL 3.9 0.6 + - - +
462P LEU* 1.3 73.3 - - - +
464P ILE* 1.3 67.4 + - - +
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Residues in contact with ILE 464 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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177P ILE 3.7 8.1 + - - +
178P THR* 3.5 15.5 + - - +
185P LYS* 3.8 14.6 - - - +
246P PHE 5.6 0.2 - - - -
247P GLY* 4.2 11.9 - - - -
248P MLY 4.2 6.3 - - - +
268P TYR* 4.3 19.3 - - + -
269P LEU* 6.1 2.9 - - + -
462P LEU* 3.3 31.6 - - + +
463P ASP* 1.3 85.1 + - - +
465P ALA* 1.3 85.9 + - + +
480P ILE* 4.6 14.4 - - + -
483P THR* 4.4 25.4 - - + -
487P LEU* 5.2 4.9 - - + -
660P LEU* 4.5 6.3 - - + -
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Residues in contact with ALA 465 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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178P THR* 4.2 2.4 + - - -
179P GLY 4.2 8.5 - - - +
181P SER 6.3 0.7 - - - +
185P LYS* 4.6 7.8 - - - +
464P ILE* 1.3 92.4 - - - +
466P GLY* 1.3 59.7 + - - +
468P GLU* 5.3 6.7 - - - +
480P ILE* 4.4 21.5 - - + +
484P ASN* 2.5 27.7 + - - +
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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