Contacts of the strand formed by residues 457 - 465 (chain M) in PDB entry 1O1D
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 M).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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166M MET* 3.6 44.9 - - + -
167M LEU* 4.9 14.3 + - + +
170M ARG* 3.9 51.6 + - + +
171M GLU 4.5 3.1 - - - +
172M ASN* 2.9 18.2 - - - +
253M HIS* 3.5 6.9 - - - +
254M PHE* 2.7 34.9 + - - +
255M GLY 3.8 19.7 - - - -
256M ALA 4.4 10.2 + - - -
455M ARG* 3.8 0.6 - - - +
456M GLN* 1.3 118.7 + - + +
458M PHE* 1.3 60.6 + - - +
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Residues in contact with PHE 458 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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166M MET* 3.7 3.4 - - - +
172M ASN* 3.0 34.7 + - + +
173M GLN 3.2 28.9 + - - -
249M PHE* 4.7 5.6 - + - -
251M ARG* 3.7 40.6 - - + -
252M ILE 3.0 14.4 - - - +
253M HIS* 3.6 31.9 - + + +
457M TYR* 1.3 78.1 - - - +
459M ILE* 1.3 68.7 + - - +
460M GLY* 3.6 18.4 - - - -
663M ASN* 4.3 15.9 - - - -
666M SER* 5.0 3.8 - - - -
667M THR* 4.0 16.6 - - - -
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Residues in contact with ILE 459 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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162M ALA* 4.6 0.7 - - + -
163M TYR* 4.3 14.8 - - + +
166M MET* 3.7 15.7 - - + -
173M GLN* 3.6 22.9 - - + +
175M ILE* 4.2 15.9 - - + -
196M PHE* 3.7 42.0 - - + -
250M ILE 3.5 1.9 - - - +
252M ILE* 2.7 29.3 + - + +
254M PHE* 3.3 30.7 - - + -
458M PHE* 1.3 81.8 - - - +
460M GLY* 1.3 62.4 + - - +
461M VAL* 3.7 8.8 + - + +
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Residues in contact with GLY 460 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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173M GLN 3.0 14.8 + - - -
174M SER* 3.0 5.7 - - - -
175M ILE* 2.7 32.9 + - - +
249M PHE* 3.9 18.4 - - - -
250M ILE 3.3 8.3 - - - -
458M PHE* 3.6 11.5 - - - -
459M ILE* 1.3 72.1 - - - +
461M VAL* 1.3 60.3 + - - +
462M LEU 3.9 0.9 - - - -
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Residues in contact with VAL 461 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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175M ILE* 3.7 15.3 - - + +
177M ILE* 4.0 16.8 - - + -
189M THR* 3.7 30.0 - - + +
192M VAL* 4.8 12.3 - - + -
193M ILE* 4.7 15.0 - - + -
196M PHE* 4.9 0.7 - - + -
248M MLY 3.7 2.1 - - - +
249M PHE* 3.5 4.5 - - - -
250M ILE* 3.1 33.3 + - + +
252M ILE* 4.6 12.1 - - + -
459M ILE* 4.1 20.2 - - + +
460M GLY* 1.3 76.0 - - - +
462M LEU* 1.3 62.6 + - - +
463M ASP* 3.9 0.7 + - - +
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Residues in contact with LEU 462 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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174M SER* 6.3 0.2 - - - -
175M ILE 3.0 11.0 + - - +
176M LEU* 3.6 37.0 - - + -
177M ILE* 2.9 35.2 + - - +
178M THR* 5.7 2.5 - - - +
248M MLY 3.5 6.7 - - - +
249M PHE* 3.6 22.9 - - + -
268M TYR* 5.1 0.2 - - + -
460M GLY 3.9 0.4 - - - -
461M VAL* 1.3 74.1 - - - +
463M ASP* 1.3 59.7 + - - +
464M ILE* 3.3 39.9 - - + +
487M LEU* 4.6 20.2 - - + -
660M LEU* 4.3 15.7 - - + -
664M LEU* 4.7 5.6 - - + -
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Residues in contact with ASP 463 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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177M ILE* 4.0 5.6 - - + -
185M LYS* 4.4 19.5 + - - +
186M THR* 3.8 15.4 + - - +
189M THR* 3.1 38.0 + - + +
244M SER* 4.7 7.1 + - - -
246M PHE 4.5 8.2 - - - +
247M GLY* 3.3 0.9 - - - -
248M MLY 2.4 62.4 + - + +
461M VAL 3.9 0.4 + - - +
462M LEU* 1.3 74.3 - - - +
464M ILE* 1.3 67.1 + - - +
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Residues in contact with ILE 464 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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177M ILE 3.7 7.7 + - - +
178M THR* 3.5 15.0 + - - +
185M LYS* 3.8 15.1 - - - +
247M GLY* 4.2 11.4 - - - -
248M MLY 4.2 6.1 - - - +
268M TYR* 4.3 19.3 - - + -
269M LEU* 6.1 2.2 - - + -
462M LEU* 3.3 31.6 - - + +
463M ASP* 1.3 85.7 + - - +
465M ALA* 1.3 85.7 + - + +
480M ILE* 4.6 14.6 - - + -
483M THR* 4.4 25.1 - - + -
487M LEU* 5.2 4.9 - - + -
660M LEU* 4.5 7.0 - - + -
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Residues in contact with ALA 465 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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178M THR* 4.2 2.4 + - - -
179M GLY 4.2 8.7 - - - +
181M SER 6.3 0.4 - - - +
185M LYS* 4.6 7.8 - - - +
464M ILE* 1.3 91.9 - - - +
466M GLY* 1.3 59.5 + - - +
468M GLU* 5.3 6.5 - - - +
480M ILE* 4.4 20.6 - - + +
484M ASN* 2.5 27.7 + - - +
487M 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