Contacts of the helix formed by residues 624 - 631 (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 THR 624 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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173A SER* 4.2 7.0 - - - -
622A TYR* 4.1 4.7 - - + -
623A LEU* 1.3 80.0 - - - +
625A ASP* 1.3 69.5 + - - +
626A ASP* 2.7 6.0 + - - -
627A LYS* 2.6 34.6 + - - +
628A LEU* 2.8 22.1 + - - -
656A LYS* 5.5 0.4 - - - +
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Residues in contact with ASP 625 (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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624A THR* 1.3 72.7 - - - +
626A ASP* 1.3 57.1 + - - +
628A LEU* 3.7 9.5 - - - +
629A SER* 2.8 28.2 + - - -
656A LYS* 2.9 31.1 + - - -
659A THR* 5.1 5.0 - - - +
660A ASN* 2.9 36.5 + - - +
662A ARG* 5.8 0.7 + - - +
663A ILE* 4.2 9.0 - - - +
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Residues in contact with ASP 626 (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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171A VAL* 3.5 20.1 - - + +
172A GLU* 4.5 0.2 - - - -
173A SER* 3.5 26.4 + - - -
271A LYS* 3.2 31.0 + - - -
624A THR* 2.7 7.1 + - - +
625A ASP* 1.3 79.3 - - - +
627A LYS* 1.3 76.6 + - - +
628A LEU 3.0 4.0 + - - -
629A SER* 3.0 13.7 + - - -
630A GLN* 3.3 18.1 + - - +
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Residues in contact with LYS 627 (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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173A SER* 2.9 31.1 + - - +
623A LEU* 3.8 14.1 - - + -
624A THR* 2.6 36.1 + - - +
626A ASP* 1.3 86.3 + - - +
628A LEU* 1.3 59.4 + - - +
630A GLN* 3.6 16.3 - - - +
631A TYR* 2.7 66.3 + - + +
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Residues in contact with LEU 628 (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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623A LEU* 3.5 22.8 - - + +
624A THR 2.8 14.9 + - - +
625A ASP* 3.7 7.9 - - - +
626A ASP 3.0 0.4 + - - -
627A LYS* 1.3 78.5 - - - +
629A SER* 1.3 57.6 + - - +
631A TYR 3.3 1.7 + - - -
632A LEU* 2.8 34.1 + - + +
635A LEU* 3.4 30.5 - - + -
652A PHE* 4.4 10.5 - - + -
653A LEU* 4.5 11.2 - - + -
656A LYS* 3.5 37.9 - - + +
663A ILE* 3.6 24.9 - - + -
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Residues in contact with SER 629 (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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625A ASP 2.8 17.3 + - - -
626A ASP* 3.0 5.9 + - - -
628A LEU* 1.3 74.9 - - - +
630A GLN* 1.3 64.4 + - - +
632A LEU* 3.9 20.1 + - - +
662A ARG* 4.8 17.1 + - - -
663A ILE* 3.9 20.1 - - - +
666A PHE* 6.1 5.4 - - - -
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Residues in contact with GLN 630 (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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271A LYS* 5.7 1.2 + - - -
626A ASP* 3.3 21.8 + - - +
627A LYS* 3.6 21.7 - - - +
628A LEU 3.2 0.8 - - - -
629A SER* 1.3 81.7 - - - +
631A TYR* 1.3 70.5 + - + +
632A LEU 3.4 0.7 + - - -
633A ILE* 4.8 2.1 + - - +
815A GLN* 2.6 33.8 + - + +
818A ARG* 5.8 9.4 - - + -
819A ILE* 3.2 39.1 - - + +
822A ASN* 3.4 31.8 + - - +
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Residues in contact with TYR 631 (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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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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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