Contacts of the helix formed by residues 630 - 643 (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 SER 630 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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628B TYR 3.4 2.9 + - - +
629B SER* 1.3 74.6 - - - +
631B ARG* 1.3 64.4 + - - +
632B GLN 3.9 0.3 + - - -
633B HIS* 3.2 9.3 + - - +
634B ALA* 3.0 23.4 + - - +
652B TRP* 3.8 1.1 - - - -
821B HIS 4.3 7.0 + - - -
822B MET* 3.6 17.8 - - - +
850B THR 2.9 27.7 + - - -
851B ILE* 4.2 0.2 - - - -
852B SER 3.0 33.6 + - - -
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Residues in contact with ARG 631 (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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629B SER 3.6 2.0 + - - -
630B SER* 1.3 70.5 + - - +
632B GLN* 1.3 58.3 + - - +
634B ALA* 3.9 1.4 - - - +
635B THR* 2.7 42.5 + - - +
648B LEU* 4.1 14.5 - - + +
652B TRP* 3.4 30.7 - - + -
653B LEU* 3.9 32.3 - - - +
780B ASP 4.6 5.1 + - - -
821B HIS 4.7 4.9 + - - +
823B TYR* 4.0 32.0 + - + +
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Residues in contact with GLN 632 (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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630B SER* 3.3 1.6 + - - -
631B ARG* 1.3 75.6 - - - +
633B HIS* 1.3 61.3 + - - +
635B THR* 4.1 14.8 - - - +
636B ASN* 2.8 68.9 + - - +
639B ILE* 5.8 0.8 - - - +
852B SER* 3.6 12.1 + - - +
853B GLY 2.9 31.2 - - - +
854B SER* 4.0 18.3 + - - +
859B PHE* 4.0 5.4 - - + -
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Residues in contact with HIS 633 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
628B TYR* 3.6 21.1 - + - -
630B SER* 3.2 12.9 + - - +
632B GLN* 1.3 79.9 - - - +
634B ALA* 1.3 62.5 + - - +
636B ASN* 3.2 1.2 + - - +
637B VAL* 3.0 47.6 + - + +
699B GLU* 4.3 8.4 + - - -
737B ARG* 5.3 2.0 - - - -
850B THR* 3.4 42.0 + - + +
852B SER* 3.7 7.9 - - - +
861B SER* 4.4 4.7 - - - -
863B LEU* 5.9 0.4 - - + -
864B GLU* 2.9 34.7 + - - -
1009B FUM 4.2 5.4 + - - -
1011B AAE 3.2 29.6 + - - -
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Residues in contact with ALA 634 (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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628B TYR* 3.8 30.2 + - + +
630B SER 3.0 13.7 + - - +
631B ARG 3.9 1.6 - - - +
633B HIS* 1.3 76.3 - - - +
635B THR* 1.3 57.6 + - - +
638B GLY* 2.9 26.2 + - - -
642B ARG* 4.8 0.5 + - - -
647B ALA 4.2 1.6 - - - +
648B LEU* 3.6 20.2 - - + +
652B TRP* 3.5 30.3 - - + +
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Residues in contact with THR 635 (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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631B ARG* 2.7 30.6 + - - +
632B GLN* 3.8 16.6 - - - +
634B ALA* 1.3 73.4 - - - +
636B ASN* 1.3 59.7 + - - +
638B GLY* 3.2 1.4 + - - -
639B ILE* 2.8 51.8 + - + +
647B ALA* 3.7 13.1 - - + +
648B LEU* 3.9 19.7 - - + +
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Residues in contact with ASN 636 (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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632B GLN* 2.8 40.6 + - - +
633B HIS 3.6 0.7 - - - +
635B THR* 1.3 73.1 - - - +
637B VAL* 1.3 63.2 + - - +
639B ILE* 3.2 7.7 + - - +
640B MET* 3.0 29.1 + - - +
859B PHE* 3.4 37.2 - - - -
864B GLU* 2.9 32.6 + - + +
867B TRP* 3.7 29.5 - - + -
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Residues in contact with VAL 637 (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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628B TYR* 4.0 8.7 - - - +
633B HIS* 3.0 44.2 + - + +
636B ASN* 1.3 75.6 - - - +
638B GLY* 1.3 64.3 + - - +
640B MET* 3.2 8.3 + - - +
641B PHE* 3.0 49.8 + - + -
737B ARG* 6.1 0.2 - - - +
863B LEU* 4.3 15.7 - - + -
864B GLU* 4.9 5.2 - - + -
1009B FUM 3.6 33.2 - - + +
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Residues in contact with GLY 638 (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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634B ALA 2.9 12.0 + - - -
635B THR 3.6 2.9 - - - -
637B VAL* 1.3 78.2 - - - +
639B ILE* 1.3 52.4 + - - +
642B ARG* 2.7 48.7 + - - +
643B GLY 3.3 4.5 + - - +
647B ALA* 3.3 30.1 - - - -
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Residues in contact with ILE 639 (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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632B GLN* 5.8 0.4 - - - +
635B THR* 2.8 40.4 + - + +
636B ASN* 3.6 10.8 - - - +
638B GLY* 1.3 71.2 - - - +
640B MET* 1.3 64.8 + - - +
643B GLY* 3.0 25.4 + - - -
644B LYS* 3.9 33.4 - - + +
647B ALA* 3.8 6.5 - - + +
867B TRP* 4.0 23.1 - - + +
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Residues in contact with MET 640 (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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636B ASN 3.0 29.1 + - - +
637B VAL* 3.2 11.0 + - - +
639B ILE* 1.3 78.2 - - - +
641B PHE* 1.3 64.1 + - + +
643B GLY 4.9 0.2 - - - -
863B LEU* 3.8 28.0 - - + +
864B GLU* 3.9 24.2 - - + -
867B TRP* 3.8 34.3 - - + +
868B LYS* 3.4 64.2 + - + +
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Residues in contact with PHE 641 (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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637B VAL* 3.0 44.1 + - + +
638B GLY 4.6 0.2 - - - +
640B MET* 1.3 83.0 - - + +
642B ARG* 1.3 74.5 + - + +
643B GLY 3.9 0.4 - - - -
737B ARG* 5.8 5.4 - - + -
741B GLN* 3.3 30.7 - - - -
744B TYR* 5.2 7.2 - - - +
863B LEU* 4.3 28.3 - - + -
868B LYS* 3.8 24.9 - - + +
1009B FUM 5.0 13.0 - - + -
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Residues in contact with ARG 642 (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* 4.7 2.4 - - - +
628B TYR* 4.4 4.0 + - - -
634B ALA 4.8 0.4 + - - -
638B GLY* 2.7 28.8 + - - +
641B PHE* 1.3 84.0 - - + +
643B GLY* 1.3 59.4 + - - +
646B ASN* 3.1 51.1 + - + +
647B ALA 3.1 18.4 + - - -
648B LEU* 5.3 0.2 - - - +
649B LEU* 4.0 36.3 - - - +
744B TYR* 4.6 3.2 + - - -
1009B FUM 2.8 42.2 + - - -
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Residues in contact with GLY 643 (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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638B GLY 3.3 0.8 + - - -
639B ILE* 3.0 20.6 + - - -
641B PHE 3.9 0.2 - - - -
642B ARG* 1.3 79.0 - - - +
644B LYS* 1.3 69.5 + - - -
645B GLU* 3.2 3.6 - - - -
646B ASN* 3.0 13.3 + - - -
647B ALA* 3.1 11.6 + - - -
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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