Contacts of the strand formed by residues 363 - 367 (chain M) in PDB entry 3HOU
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 GLN 363 (chain M).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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358M ASN 4.9 0.9 - - - +
359M LEU* 3.6 25.0 - - + +
360M GLU* 2.8 45.0 + - + +
361M LEU 4.0 3.3 - - - +
362M ASP* 1.3 74.1 - - - +
364M VAL* 1.3 61.8 + - - +
439M ASN* 4.5 4.4 + - - -
458M HIS* 2.9 19.6 + - - -
459M ARG* 3.2 41.5 + - - +
460M VAL 4.3 6.9 + - - -
461M LYS* 3.2 32.7 + - + +
469M ARG 4.7 0.9 - - - +
470M LEU* 4.9 5.5 - - - -
471M ASN 5.0 0.7 + - - -
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Residues in contact with VAL 364 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
359M LEU* 4.2 0.4 - - - -
363M GLN* 1.3 80.2 - - - +
365M GLY* 1.3 70.7 + - - +
366M VAL* 3.1 11.2 + - + +
442M VAL* 4.0 15.3 - - + -
444M PHE* 3.9 43.1 - - + -
458M HIS* 3.5 17.9 - - + +
459M ARG 2.9 21.8 + - - +
460M VAL* 4.0 4.7 - - - -
461M LYS* 3.5 13.5 + - - +
468M PHE* 4.7 5.4 - - + -
469M ARG 3.4 8.5 - - - +
470M LEU* 5.1 0.7 - - + +
489M LEU* 5.0 1.8 - - + -
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Residues in contact with GLY 365 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
359M LEU* 3.4 12.9 - - - +
364M VAL* 1.3 69.9 - - - +
366M VAL* 1.3 58.2 + - - -
367M PRO* 3.6 0.7 - - - +
461M LYS* 3.5 6.7 - - - -
463M ILE* 3.4 24.9 - - - -
467M THR 3.8 0.2 - - - +
468M PHE* 3.1 15.4 - - - +
469M ARG 2.6 36.3 + - - -
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Residues in contact with VAL 366 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
364M VAL* 3.1 17.9 + - + +
365M GLY* 1.3 73.9 - - - +
367M PRO* 1.3 79.0 - - + +
368M LYS 3.2 0.2 + - - -
370M ILE* 3.9 21.8 - - + -
371M ALA* 3.9 13.9 - - + +
374M LEU* 5.6 1.1 - - + -
436M ILE* 5.6 3.1 - - + -
460M VAL* 3.9 25.8 - - + -
461M LYS 2.9 10.5 + - - +
462M VAL* 3.4 3.5 - - - -
463M ILE* 2.8 28.6 + - - +
468M PHE* 4.5 3.4 - - + -
489M LEU* 3.8 26.2 - - + -
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Residues in contact with PRO 367 (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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351M THR* 4.8 0.9 - - - +
365M GLY 3.6 8.1 - - - +
366M VAL* 1.3 84.2 - - + +
368M LYS* 1.3 57.4 + - - +
369M SER 4.5 0.2 - - - +
370M ILE* 2.8 52.1 + - + +
371M ALA 3.0 9.7 + - - -
463M ILE* 3.2 9.6 - - + +
465M TYR 3.0 21.5 - - - +
466M SER* 3.9 14.4 - - - +
467M THR 4.0 16.2 - - - +
468M PHE* 4.1 7.9 - - + +
1103N ILE* 4.0 14.4 - - + -
2W ASN* 4.4 4.5 - - - +
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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