Contacts of the helix formed by residues 631 - 639 (chain A) in PDB entry 2RD0
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 TYR 631 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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595A PRO* 5.9 1.3 - - + -
596A GLU* 5.5 8.6 - - + +
599A MET* 3.3 37.0 - - + -
623A LEU* 4.3 8.7 - - + -
627A LYS* 2.7 51.3 + - + +
628A LEU* 3.5 3.1 - - - +
630A GLN* 1.3 100.2 + - + +
632A LEU* 1.3 60.6 + - - +
633A ILE 3.2 4.2 + - - -
634A GLN* 3.2 14.8 + - + +
635A LEU* 3.1 23.0 + - + +
815A GLN* 4.7 0.2 - - - -
819A ILE* 4.3 12.4 - - + +
997A LEU* 4.6 16.7 - - + +
1001A LEU* 3.9 26.5 - - + -
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Residues in contact with LEU 632 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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628A LEU* 2.8 18.3 + - + +
629A SER* 3.9 17.0 - - - +
630A GLN 3.4 3.0 + - - -
631A TYR* 1.3 77.1 - - - +
633A ILE* 1.3 63.0 + - - +
635A LEU* 3.5 4.0 + - - -
636A VAL* 3.0 25.6 + - + +
653A LEU* 4.3 23.3 - - + -
663A ILE* 4.2 26.5 - - + +
666A PHE* 3.7 20.0 - - + -
667A PHE* 3.5 40.4 - - + +
670A HIS* 3.8 9.9 - - + +
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Residues in contact with ILE 633 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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630A GLN 4.9 1.8 - - - +
631A TYR 3.2 0.2 - - - -
632A LEU* 1.3 76.7 - - + +
634A GLN* 1.3 66.6 + - - +
636A VAL* 3.0 9.1 + - + +
637A GLN* 2.9 28.3 + - + +
670A HIS* 4.3 26.2 - - + +
811A MET* 4.4 38.4 - - + +
812A LEU* 4.8 4.9 - - - -
815A GLN* 3.3 39.7 - - + +
1005A MET* 3.6 25.6 - - + -
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Residues in contact with GLN 634 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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631A TYR* 3.2 12.4 + - + +
633A ILE* 1.3 73.1 - - - +
635A LEU* 1.3 55.9 + - - +
637A GLN* 3.0 3.1 + - - +
638A VAL* 2.9 33.1 + - - +
812A LEU* 3.7 17.6 - - - +
815A GLN* 2.9 42.5 + - - +
816A ILE* 5.7 0.2 - - - +
1001A LEU* 3.4 49.8 + - + +
1004A MET* 3.0 28.6 - - + +
1005A MET* 4.1 15.6 - - - -
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Residues in contact with LEU 635 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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599A MET* 3.9 29.8 - - + -
602A LEU* 4.4 13.2 - - + -
619A LEU* 4.3 19.5 - - + -
623A LEU* 4.9 3.4 - - + -
628A LEU* 3.4 34.1 - - + +
631A TYR* 3.1 20.7 + - + +
632A LEU* 3.8 4.3 - - - +
633A ILE 3.2 0.2 - - - -
634A GLN* 1.3 77.8 - - - +
636A VAL* 1.3 62.2 + - - +
638A VAL* 3.8 7.4 + - + +
639A LEU* 3.7 11.4 + - - +
649A LEU* 4.2 8.0 - - + +
652A PHE* 5.3 2.2 - - + -
653A LEU* 3.7 30.6 - - + +
1004A MET* 4.2 10.1 - - + -
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Residues in contact with VAL 636 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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632A LEU* 3.0 20.4 + - + +
633A ILE* 3.0 10.5 + - + +
635A LEU* 1.3 76.4 - - - +
637A GLN* 1.3 81.0 + - - +
639A LEU* 3.0 29.1 - - + +
653A LEU* 4.8 1.8 - - + -
667A PHE* 4.2 27.1 - - + -
670A HIS* 4.5 25.4 - - + +
671A LEU* 4.2 14.6 - - + -
684A PHE* 4.0 23.4 - - + -
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Residues in contact with GLN 637 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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633A ILE* 2.9 18.5 + - - +
634A GLN 3.0 4.2 + - - +
636A VAL* 1.3 89.9 - - - +
638A VAL* 1.3 53.5 + - - +
640A LYS* 2.6 72.9 + - + +
641A TYR* 4.7 3.5 - - - -
670A HIS* 5.2 2.8 + - - +
674A GLU* 3.4 21.7 + - - +
1004A MET 3.5 17.5 - - - +
1005A MET* 3.6 32.8 - - + -
1007A GLY* 5.4 2.7 - - - +
1008A SER* 3.2 18.6 + - - +
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Residues in contact with VAL 638 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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602A LEU* 3.2 43.6 - - + +
603A ASP 4.1 0.9 - - - +
612A ARG* 4.1 3.6 + - - +
634A GLN 2.9 16.7 + - - +
635A LEU* 3.9 5.2 - - - +
637A GLN* 1.3 75.6 - - - +
639A LEU* 1.3 55.3 + - - +
640A LYS 2.8 10.2 + - - -
641A TYR* 2.9 32.2 + - + -
642A GLU* 4.0 2.3 + - - +
649A LEU* 3.3 28.0 - - + -
1004A MET* 3.9 33.0 + - + +
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Residues in contact with LEU 639 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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635A LEU 3.7 6.2 + - - +
636A VAL* 3.0 29.4 + - + +
637A GLN 3.0 0.2 - - - -
638A VAL* 1.3 80.8 - - - +
640A LYS* 1.3 61.2 + - - +
641A TYR 3.3 0.2 - - - -
642A GLU* 3.3 18.4 + - + +
647A ASN* 4.8 2.0 - - - +
649A LEU* 4.6 6.5 - - + -
650A VAL* 3.6 43.1 - - + +
653A LEU* 4.1 20.0 - - + -
667A PHE* 5.1 0.7 - - + -
671A LEU* 4.8 0.4 - - + -
683A ARG* 3.1 28.1 + - + +
684A PHE* 4.3 14.8 - - + -
687A LEU* 3.8 25.4 - - + -
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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