Contacts of the strand formed by residues 329 - 333 (chain B) in PDB entry 2W9M
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 GLY 329 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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327B LEU 4.6 0.2 - - - -
328B ARG* 1.3 77.2 - - - +
330B MET* 1.3 65.6 + - - +
331B ILE* 3.6 5.2 - - - -
358B PHE* 3.3 32.4 - - - -
545B ASN* 2.9 42.5 + - - +
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Residues in contact with MET 330 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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327B LEU* 3.8 31.0 - - + -
329B GLY* 1.3 79.5 - - - +
331B ILE* 1.3 62.8 + - - +
333B THR* 3.6 10.7 - - + +
351B THR* 4.4 11.2 - - + -
356B HIS* 3.5 49.4 - - + -
358B PHE 2.9 12.4 + - - +
359B LEU* 3.7 1.6 - - - -
360B GLY 2.8 19.1 + - - -
513B ILE 4.2 12.3 - - - +
515B THR* 4.4 23.6 - - + +
523B LEU* 4.4 22.0 - - + +
526B ALA* 4.6 4.5 - - - -
545B ASN* 4.4 0.4 - - - +
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Residues in contact with ILE 331 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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329B GLY 3.6 6.7 + - - -
330B MET* 1.3 78.9 - - - +
332B HIS* 1.3 72.5 + - - +
333B THR* 3.6 2.1 - - - +
358B PHE* 4.2 20.9 - - + -
360B GLY* 3.6 16.4 - - - -
422B TYR* 3.6 25.8 - - + +
453B VAL* 4.4 13.7 - - + -
512B ALA* 4.5 6.1 - - + -
514B ASN* 3.2 43.7 - - - +
515B THR* 4.3 3.1 + - - -
544B VAL* 5.0 3.6 - - + -
545B ASN* 4.0 9.6 - - - +
552B PHE* 4.4 25.6 - - + -
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Residues in contact with HIS 332 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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331B ILE* 1.3 81.1 - - - +
333B THR* 1.3 57.4 + - - +
334B HIS* 3.8 5.4 - - - -
360B GLY 3.3 0.2 + - - -
362B ALA* 3.6 22.2 - - + -
401B GLU* 3.0 19.6 + - + -
422B TYR* 3.0 10.7 + - - -
424B VAL* 4.5 17.6 - - + +
426B SER* 5.0 0.7 - - - -
456B HIS* 4.5 1.8 - + - -
487B GLU* 2.7 33.1 + - - +
489B ASN* 4.0 1.3 + - - -
514B ASN* 3.7 17.0 - - + +
516B ASP* 3.1 37.5 + - - +
1566B ZN 2.3 34.6 - - - -
1567B ZN 4.4 1.3 - - - -
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Residues in contact with THR 333 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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330B MET 3.6 20.9 - - - +
331B ILE 4.1 2.9 - - - +
332B HIS* 1.3 81.3 - - - +
334B HIS* 1.3 64.2 + - - +
347B MET* 3.9 16.2 - - + +
359B LEU* 3.3 22.9 - - + +
360B GLY 2.8 18.8 + - - -
361B THR* 4.1 2.9 - - - -
362B ALA* 3.1 27.6 + - - +
363B ASP* 4.1 0.9 + - - +
515B THR* 4.2 5.8 - - - +
517B ALA* 3.7 5.8 - - + +
523B LEU* 3.9 20.6 - - + -
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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