Contacts of the strand formed by residues 695 - 698 (chain A) in PDB entry 1R4X
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 ALA 695 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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665A CYS* 6.0 0.7 - - - -
676A ASN 3.3 0.5 + - - -
677A VAL* 2.9 42.2 + - + +
694A PRO* 1.3 71.6 - - - +
696A ARG* 1.3 65.5 + - - +
697A SER 3.3 1.7 + - - +
698A LEU* 4.1 25.8 - - + -
704A GLY* 4.3 2.2 - - - +
705A THR 3.4 28.5 - - - +
706A CYS* 3.5 6.1 - - + +
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Residues in contact with ARG 696 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
675A GLU* 3.3 10.6 - - - +
676A ASN* 2.7 55.1 + - - +
694A PRO* 3.5 32.8 + - - +
695A ALA* 1.3 72.5 - - - +
697A SER* 1.3 62.6 + - - +
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Residues in contact with SER 697 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
673A THR* 4.0 9.4 - - - +
674A LEU 3.5 6.1 - - - -
675A GLU* 4.8 7.3 + - - +
695A ALA* 3.3 2.7 + - - +
696A ARG* 1.3 83.4 - - - +
698A LEU* 1.3 72.2 + - - +
699A PRO* 3.4 24.1 - - - +
702A GLN 4.7 1.2 - - - +
703A PRO 5.6 0.2 - - - +
704A GLY* 5.0 3.3 - - - -
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Residues in contact with LEU 698 (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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646A TYR* 6.2 0.2 - - + -
665A CYS* 3.7 30.7 - - + +
666A THR 5.1 0.4 - - - -
667A ASN* 3.2 23.6 + - + +
673A THR* 3.9 3.6 - - - -
674A LEU* 2.8 40.8 + - + +
677A VAL* 3.7 33.0 - - + -
695A ALA* 4.1 10.8 - - + -
697A SER* 1.3 81.0 + - - +
699A PRO* 1.3 67.9 - - - +
702A GLN 4.2 4.3 - - - +
704A GLY* 3.5 35.0 - - - +
728A MET* 5.2 2.9 - - + -
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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
------------------------------------------------------------
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