Contacts of the strand formed by residues 756 - 761 (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 ASN 756 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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-27A SER* 5.5 5.4 - - - -
-26A TYR* 6.2 0.2 - - - -
259A GLU* 5.7 0.7 - - - +
666A PHE* 4.8 1.6 - - - -
753A SER* 2.6 9.9 + - - +
755A LEU* 1.3 83.2 - - + +
757A PRO* 1.3 68.2 - - - +
758A ALA* 2.6 30.5 - - - +
759A HIS* 2.9 55.2 + - + +
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Residues in contact with PRO 757 (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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258A ASP* 5.1 1.6 - - - +
661A GLN 5.9 0.2 - - - +
662A ARG* 5.8 10.1 - - + -
665A HIS* 3.9 35.7 - - + +
666A PHE* 4.5 7.2 - - + -
698A TYR* 3.9 18.8 - - + +
752A LEU* 3.6 40.5 - - + +
753A SER 3.0 11.8 - - - +
756A ASN* 1.3 84.4 - - - +
758A ALA* 1.3 65.1 + - - +
759A HIS 3.0 1.9 + - - +
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Residues in contact with ALA 758 (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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257A CYS* 3.9 8.5 - - + -
258A ASP* 3.2 60.3 + - - +
259A GLU* 4.7 8.1 - - + +
756A ASN* 2.6 28.0 - - - +
757A PRO* 1.3 73.7 - - - +
759A HIS* 1.3 62.3 + - + +
760A GLN* 3.3 4.0 + - - +
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Residues in contact with HIS 759 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
-27A SER* 3.0 34.9 + - - -
-26A TYR* 5.2 5.7 - + - -
256A GLY 5.9 0.2 - - - -
257A CYS* 4.7 16.3 - - + +
752A LEU* 3.8 0.2 - - - -
753A SER* 3.1 34.3 + - - -
756A ASN* 2.9 49.3 + - + +
757A PRO 3.7 3.8 - - - +
758A ALA* 1.3 79.1 - - + +
760A GLN* 1.3 61.6 + - - +
794A PHE* 5.3 0.7 - + - -
795A GLN* 3.1 25.9 + - - -
797A ASN* 3.5 19.5 + - - +
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Residues in contact with GLN 760 (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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256A GLY 5.9 0.2 + - - -
257A CYS* 5.8 0.8 - - - +
258A ASP* 3.6 27.3 + - - +
751A PHE 3.9 4.7 - - - +
752A LEU* 3.7 23.3 - - + +
758A ALA 3.3 2.9 + - - +
759A HIS* 1.3 76.2 - - - +
761A LEU* 1.3 58.9 + - - +
785A ASN* 4.4 8.8 + - - +
786A PRO* 3.7 36.0 - - + +
787A ASP* 4.8 11.4 + - - +
788A ILE* 5.9 2.4 - - - +
797A ASN* 3.6 16.6 + - - -
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Residues in contact with LEU 761 (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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749A GLN 2.4 21.3 - - - +
750A GLY* 3.8 1.6 - - - -
751A PHE* 2.9 57.6 + - + +
752A LEU 3.9 0.4 - - - -
753A SER* 3.7 32.8 - - - +
754A PRO* 4.9 0.7 - - + -
760A GLN* 1.3 75.1 - - - +
762A GLY* 1.3 57.0 + - - +
783A TRP* 3.5 45.8 - - + +
784A GLU 4.3 0.2 - - - -
786A PRO* 4.1 2.3 - - - +
797A ASN* 3.6 31.0 - - + +
799A ILE* 5.3 7.2 - - + -
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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