Contacts of the strand formed by residues 457 - 465 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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166D MET* 3.6 43.3 - - + -
167D LEU* 4.9 15.4 + - + -
170D ARG* 3.9 53.5 + - + +
171D GLU 4.5 3.8 - - - +
172D ASN* 2.9 17.5 - - - +
253D HIS* 3.5 6.6 - - - +
254D PHE* 2.7 35.0 + - - +
255D GLY 3.8 19.3 - - - -
256D ALA 4.4 11.3 + - - -
455D ARG* 3.8 0.4 - - - +
456D GLN* 1.3 117.0 + - + +
458D PHE* 1.3 57.1 + - - +
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Residues in contact with PHE 458 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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166D MET* 3.7 3.7 - - - +
172D ASN* 3.0 33.3 + - + +
173D GLN 3.2 28.6 + - - -
249D PHE* 4.7 5.8 - + - -
251D ARG* 3.7 40.8 - - + -
252D ILE 3.0 14.6 - - - +
253D HIS* 3.6 31.4 - + + +
457D TYR* 1.3 79.2 - - - +
459D ILE* 1.3 70.2 + - - +
460D GLY* 3.6 17.9 - - - -
663D ASN* 4.3 16.2 - - - -
666D SER* 5.0 3.8 - - - -
667D THR* 4.0 17.0 - - - -
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Residues in contact with ILE 459 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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162D ALA* 4.6 0.7 - - + -
163D TYR* 4.3 14.1 - - + +
166D MET* 3.7 16.6 - - + -
173D GLN* 3.6 24.2 - - + -
175D ILE* 4.2 16.2 - - + -
196D PHE* 3.7 42.0 - - + -
250D ILE 3.5 1.7 - - - +
252D ILE* 2.7 29.4 + - + +
254D PHE* 3.3 30.5 - - + -
458D PHE* 1.3 79.9 - - - +
460D GLY* 1.3 62.3 - - - +
461D VAL* 3.7 8.6 + - + +
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Residues in contact with GLY 460 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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173D GLN 3.0 14.2 + - - -
174D SER* 3.0 5.3 - - - -
175D ILE 2.7 32.6 + - - +
249D PHE* 3.9 19.5 - - - -
250D ILE 3.3 9.0 - - - -
458D PHE* 3.6 12.1 - - - -
459D ILE* 1.3 72.1 - - - +
461D VAL* 1.3 59.0 + - - +
462D LEU 3.9 0.7 - - - -
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Residues in contact with VAL 461 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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175D ILE* 3.7 14.8 - - + +
177D ILE* 4.0 17.0 - - + -
189D THR* 3.7 30.0 - - + +
192D VAL* 4.8 11.9 - - + -
193D ILE* 4.7 15.3 - - + -
196D PHE* 4.9 0.7 - - + -
248D MLY 3.7 2.3 - - - +
249D PHE* 3.5 4.7 - - - -
250D ILE* 3.1 34.3 + - + +
252D ILE* 4.6 12.8 - - + -
459D ILE* 4.1 20.0 - - + +
460D GLY* 1.3 77.4 - - - +
462D LEU* 1.3 61.8 + - - +
463D ASP* 3.9 0.7 + - - +
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Residues in contact with LEU 462 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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174D SER* 6.3 0.4 - - - -
175D ILE 3.0 11.9 + - - +
176D LEU* 3.6 37.7 - - + -
177D ILE* 2.9 35.4 + - - +
178D THR* 5.7 3.1 - - - +
248D MLY 3.5 6.7 - - - +
249D PHE* 3.6 22.7 - - + -
268D TYR* 5.1 0.4 - - + -
460D GLY 3.9 0.6 - - - +
461D VAL* 1.3 74.4 - - - +
463D ASP* 1.3 59.8 + - - +
464D ILE* 3.3 39.7 - - + +
487D LEU* 4.6 19.7 - - + -
660D LEU* 4.3 16.2 - - + -
664D LEU* 4.7 5.8 - - + -
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Residues in contact with ASP 463 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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177D ILE* 4.0 5.6 - - + -
185D LYS* 4.4 19.4 + - - +
186D THR* 3.8 15.2 + - - +
189D THR* 3.1 37.8 + - + +
244D SER* 4.7 6.9 + - - -
246D PHE 4.5 8.6 - - - +
247D GLY* 3.3 1.0 - - - -
248D MLY 2.4 63.1 + - + +
461D VAL 5.2 0.2 - - - +
462D LEU* 1.3 74.6 - - - +
464D ILE* 1.3 67.2 + - - +
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Residues in contact with ILE 464 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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177D ILE 3.7 7.9 + - - +
178D THR* 3.5 14.2 + - - +
185D LYS* 3.8 15.4 - - - +
247D GLY* 4.2 11.7 - - - -
248D MLY 4.2 6.5 - - - +
268D TYR* 4.3 18.6 - - + -
269D LEU* 6.1 2.2 - - + -
462D LEU* 3.3 31.6 - - + +
463D ASP* 1.3 85.8 + - - +
465D ALA* 1.3 84.7 + - + +
480D ILE* 4.6 15.0 - - + -
483D THR* 4.4 24.9 - - + -
487D LEU* 5.2 4.9 - - + -
660D LEU* 4.5 6.7 - - + -
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Residues in contact with ALA 465 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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178D THR* 4.2 2.4 + - - -
179D GLY 4.2 8.3 - - - +
180D GLU* 6.2 0.2 - - - -
181D SER 6.3 0.7 - - - +
185D LYS* 4.6 6.9 - - - +
247D GLY* 5.7 0.2 - - - -
464D ILE* 1.3 91.0 - - - +
466D GLY* 1.3 59.7 + - - +
468D GLU* 5.3 6.7 - - - +
480D ILE* 4.4 21.0 - - + +
484D ASN* 2.5 27.5 + - - +
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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