Contacts of the helix formed by residues 737 - 744 (chain B) in PDB entry 1QCO
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 ARG 737 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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633B HIS* 5.3 2.6 - - - -
637B VAL* 6.1 0.2 - - - +
641B PHE* 5.8 5.2 - - + -
695B LEU* 3.0 30.0 + - + +
697B ASP* 2.9 38.2 + - + +
699B GLU* 3.0 44.6 + - - +
735B SER* 3.9 10.5 + - - +
736B ALA* 1.3 71.6 - - - +
738B ASP* 1.3 57.5 + - - +
740B GLN* 3.8 13.7 + - - +
741B GLN* 3.0 30.3 + - - +
753B LYS* 4.0 9.5 - - - +
861B SER* 3.7 9.7 + - - -
863B LEU* 3.8 32.2 - - + +
883B PHE* 4.3 11.2 - - + -
1009B FUM 4.4 12.3 + - - -
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Residues in contact with ASP 738 (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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680B MET* 3.2 35.1 - - + +
681B ARG 5.1 0.9 + - - -
682B PRO* 6.5 0.2 - - + -
693B CYS* 3.5 23.9 - - - +
694B ARG* 2.8 30.0 + - - +
695B LEU* 3.5 24.6 + - + +
736B ALA 3.9 1.0 - - - -
737B ARG* 1.3 71.8 - - - +
739B ILE* 1.3 69.6 + - - +
740B GLN 3.4 0.2 + - - -
741B GLN* 3.5 15.4 + - - +
742B TRP* 3.5 13.0 + - - +
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Residues in contact with ILE 739 (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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336A ASN* 5.2 3.8 - - + -
676B PRO* 4.2 7.6 - - + -
677B MET 3.9 23.1 - - - +
678B GLY* 4.0 8.1 - - - +
679B GLN 3.8 25.6 - - - +
680B MET* 4.1 11.0 - - + -
693B CYS* 4.1 14.6 - - + -
736B ALA* 3.3 24.1 + - + +
738B ASP* 1.3 82.2 + - - +
740B GLN* 1.3 63.7 + - - +
742B TRP* 3.5 3.1 + - - +
743B GLU* 3.3 25.4 + - + +
751B LEU* 4.1 17.0 - - + +
752B GLY 4.0 18.4 - - - +
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Residues in contact with GLN 740 (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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735B SER* 5.2 1.7 - - - -
736B ALA 3.0 16.2 + - - +
737B ARG* 3.8 14.5 + - - +
739B ILE* 1.3 77.8 - - - +
741B GLN* 1.3 59.1 + - - +
743B GLU* 3.2 17.1 + - - +
744B TYR* 2.8 63.4 + - + -
749B PRO* 4.1 17.4 - - + +
752B GLY* 4.2 7.4 - - - +
753B LYS* 3.5 26.0 + - - +
1009B FUM 2.7 30.9 + - - +
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Residues in contact with GLN 741 (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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641B PHE* 3.3 37.8 - - + -
681B ARG 5.5 3.1 - - - +
737B ARG 3.0 18.5 + - - +
738B ASP* 3.8 8.7 - - - +
739B ILE 3.4 0.2 - - - -
740B GLN* 1.3 77.4 - - - +
742B TRP* 1.3 62.3 + - - +
744B TYR* 3.7 23.6 - - + -
745B VAL* 5.0 4.3 - - - +
868B LYS* 5.1 4.8 - - - +
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Residues in contact with TRP 742 (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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150A PRO* 3.7 11.4 - - + -
151A ASN* 2.9 54.5 + - + +
154A HIS* 3.8 21.1 - + + -
155A LEU* 3.6 19.4 - - + +
679B GLN* 2.8 42.4 + - - -
680B MET* 4.2 4.3 - - - -
681B ARG* 3.3 60.6 - - + +
688B PRO* 3.6 15.0 - - + +
738B ASP 3.5 7.9 + - - +
739B ILE 3.5 7.1 + - - +
740B GLN 3.2 0.4 - - - -
741B GLN* 1.3 79.4 - - - +
743B GLU* 1.3 58.9 + - + +
745B VAL* 4.9 0.9 + - - +
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Residues in contact with GLU 743 (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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151A ASN* 3.2 13.1 + - - +
155A LEU* 4.5 21.9 - - + +
157A VAL* 4.8 10.9 - - - +
332A HIS* 5.1 2.1 + - - +
739B ILE* 3.3 15.2 + - + +
740B GLN* 3.2 15.3 + - - +
742B TRP* 1.3 80.9 - - - +
744B TYR* 1.3 70.1 + - + +
745B VAL 3.2 6.0 + - - +
747B LEU 5.5 0.3 + - - -
748B GLY 4.6 1.8 - - - +
749B PRO 4.0 0.2 - - - -
750B PHE* 2.9 28.2 + - + +
751B LEU* 2.9 34.7 + - - +
752B GLY* 2.9 27.7 + - - -
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Residues in contact with TYR 744 (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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246A PRO* 3.8 25.1 - - + +
247A LEU* 5.0 1.1 - - + -
641B PHE* 5.2 8.5 - + - +
642B ARG* 4.6 2.9 + - - -
740B GLN* 2.8 50.0 + - + +
741B GLN* 3.7 23.3 - - + -
742B TRP 3.7 0.4 - - - -
743B GLU* 1.3 73.0 - - + +
745B VAL* 1.3 73.7 + - + +
746B PRO* 3.7 1.4 - - - +
747B LEU 3.5 0.9 + - - -
748B GLY* 2.8 51.0 + - - +
749B PRO* 3.9 5.4 - - + -
1009B FUM 2.9 42.1 + - + +
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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