Contacts of the strand formed by residues 729 - 734 (chain B) in PDB entry 1QAS
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 729 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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240B GLN 3.2 23.4 + - - -
241B GLN* 3.3 3.4 - - - -
242B ARG* 4.8 0.4 - - - +
728B GLN* 1.3 74.8 - - - +
730B TYR* 1.3 63.5 + - - -
731B ARG* 3.5 4.5 + - - +
750B VAL 3.7 0.2 - - - +
751B LYS* 3.2 18.8 - - - -
752B ILE 2.9 34.0 + - - -
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Residues in contact with TYR 730 (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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216B ARG* 5.6 1.9 + - - -
217B ALA* 4.3 15.1 - - + +
220B GLU* 2.9 25.6 + - - -
236B PHE* 4.0 21.1 - + + -
240B GLN* 3.3 23.3 - - + -
241B GLN* 2.9 30.9 - - - +
279B LEU* 3.3 20.1 - - + +
636B ILE* 4.1 17.3 - - + -
729B GLY* 1.3 71.9 - - - -
731B ARG* 1.3 66.1 + - - +
749B PHE* 3.3 35.7 - + + -
750B VAL 3.5 3.4 - - - -
751B LYS* 3.1 36.1 + - + +
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Residues in contact with ARG 731 (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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241B GLN* 3.2 23.5 + - - +
243B GLU* 3.0 27.7 + - - -
278B TYR* 3.9 8.7 + - - -
279B LEU 4.9 0.7 - - - -
283B ASP 2.9 26.5 + - - -
284B GLY* 3.1 21.9 - - - +
285B ASN 3.6 7.2 + - - -
286B ALA* 3.7 20.4 - - + -
727B LYS* 3.1 41.3 - - - +
728B GLN 2.7 29.2 + - - +
729B GLY 3.9 3.4 - - - +
730B TYR* 1.3 81.6 + - - +
732B HIS* 1.3 66.1 + - - +
749B PHE* 3.7 3.5 - - - -
750B VAL* 2.9 41.9 + - + +
752B ILE* 4.4 1.1 - - + -
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Residues in contact with HIS 732 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
211B ARG* 2.8 33.6 + - - -
214B ILE* 4.4 0.4 - - + -
276B LEU* 4.2 4.0 - - + -
279B LEU* 3.0 34.5 + - + +
280B LEU* 3.2 30.7 - - + +
284B GLY 3.2 5.5 + - - -
285B ASN* 3.4 2.8 - - - -
286B ALA 3.2 17.0 + - - -
639B GLN* 3.6 20.6 - - - -
731B ARG* 1.3 72.9 - - - +
733B VAL* 1.3 61.8 + - - +
734B HIS* 3.2 28.6 + - + -
747B THR* 3.8 6.1 - - + -
748B LEU 3.4 2.5 - - - -
749B PHE* 3.3 28.3 - + - -
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Residues in contact with VAL 733 (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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285B ASN* 5.3 0.7 - - - -
286B ALA* 4.0 16.2 - - + -
702B PHE* 4.1 33.9 - - + -
719B SER* 3.7 29.4 - - - +
721B ILE* 4.9 2.2 - - + -
732B HIS* 1.3 70.5 - - - +
734B HIS* 1.3 62.1 + - - +
735B LEU* 3.5 9.7 + - + +
747B THR* 3.0 7.3 - - - -
748B LEU* 2.8 38.1 + - + +
750B VAL* 3.9 31.2 - - + -
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Residues in contact with HIS 734 (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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280B LEU* 3.0 31.4 + - - +
281B SER 4.4 4.7 - - - -
285B ASN* 3.0 31.8 + - - +
719B SER* 3.7 16.5 + - - -
732B HIS* 3.2 28.0 + - + -
733B VAL* 1.3 70.8 - - - +
735B LEU* 1.3 65.9 + - - +
736B LEU* 3.8 9.2 + - - +
742B GLN* 3.5 33.0 + - + +
743B HIS 5.7 1.8 - - - +
744B PRO 5.7 4.5 - - - -
745B SER* 6.4 0.7 - - - -
746B ALA 3.8 5.2 - - - +
747B THR* 3.6 16.6 - - + +
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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