Contacts of the strand formed by residues 730 - 737 (chain A) in PDB entry 2XRG
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 VAL 730 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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633A TYR 4.2 0.3 - - - +
634A THR* 3.6 8.5 - - - +
635A ILE* 3.0 35.6 + - + +
720A VAL* 4.2 10.1 - - + +
723A TYR* 4.1 9.2 - - + +
724A ALA* 3.9 23.3 - - + +
727A ARG* 4.0 28.7 - - + +
729A GLY* 1.3 78.2 - - - +
731A ASN* 1.4 58.4 + - - +
732A VAL* 4.2 12.5 + - + +
771A ILE* 3.7 29.2 - - + -
772A THR 3.6 3.6 - - - +
773A SER* 4.2 3.6 - - - -
781A ALA* 4.2 2.7 - - - +
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Residues in contact with ASN 731 (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 HIS 3.3 17.4 + - - -
596A LEU* 5.5 0.2 - - - -
597A LEU* 3.5 17.9 + - + +
598A TYR* 3.5 34.7 - - + +
632A SER* 4.1 3.3 + - - -
633A TYR 3.8 4.7 + - - -
634A THR* 2.9 26.1 + - - -
730A VAL* 1.4 72.9 - - - +
732A VAL* 1.4 60.9 + - - +
733A ILE* 3.9 20.8 - - - +
770A ILE 3.1 6.8 - - - +
771A ILE* 3.4 1.7 - - - -
772A THR* 2.8 40.0 + - - +
781A ALA* 5.9 0.2 - - + -
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Residues in contact with VAL 732 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
631A THR 3.4 2.4 - - - +
632A SER* 3.4 4.9 + - - -
633A TYR* 3.0 78.8 + - + +
635A ILE* 5.6 1.8 - - + +
715A PHE* 5.1 5.2 - - + -
720A VAL* 4.6 17.5 - - + -
730A VAL* 4.7 12.3 - - + +
731A ASN* 1.4 77.1 - - - +
733A ILE* 1.4 63.4 + - - +
734A SER* 4.4 4.9 - - - +
769A SER* 3.6 22.9 - - - +
770A ILE 3.4 3.8 - - - +
771A ILE* 4.5 15.5 - - + -
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Residues in contact with ILE 733 (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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596A LEU* 4.8 11.0 - - + -
598A TYR* 5.3 7.9 - - + -
599A GLY 5.9 0.7 - - - +
601A PRO* 5.7 3.6 - - + -
630A TRP* 4.3 19.7 - - + -
631A THR 3.3 7.4 - - - +
632A SER* 3.6 20.6 - - - +
731A ASN* 3.9 16.2 - - - +
732A VAL* 1.4 78.8 - - - +
734A SER* 1.3 60.8 + - - +
768A TYR* 3.8 9.5 - - + -
769A SER* 3.4 1.6 - - - -
770A ILE* 2.9 48.2 + - + +
772A THR* 6.0 1.8 - - - +
837A PHE* 4.2 33.9 - - + -
838A TYR* 6.4 1.3 - - + -
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Residues in contact with SER 734 (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 TRP* 3.7 1.6 - - - -
631A THR* 3.2 33.8 + - - -
633A TYR* 4.4 6.2 + - - -
680A LEU* 3.8 24.5 + - - +
712A TRP* 4.4 14.9 - - - -
715A PHE* 6.1 0.2 - - - -
732A VAL* 4.4 8.3 - - - +
733A ILE* 1.3 72.8 - - - +
735A GLY* 1.3 58.0 + - - +
768A TYR* 3.3 24.0 - - - -
769A SER* 3.6 15.0 - - - -
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Residues in contact with GLY 735 (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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629A LEU 4.2 2.5 - - - -
680A LEU* 3.8 13.8 - - - +
734A SER* 1.3 76.4 - - - +
736A PRO* 1.4 68.3 - - - +
767A TYR* 3.5 13.8 - - - -
768A TYR* 3.2 43.2 + - - +
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Residues in contact with PRO 736 (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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627A MET* 4.0 18.2 - - + -
628A PRO 3.3 26.2 - - - +
629A LEU* 3.9 11.8 - - + +
680A LEU* 4.9 2.2 - - + -
702A VAL* 5.2 4.0 - - + -
735A GLY* 1.4 84.3 - - - +
737A ILE* 1.4 68.8 + - - +
738A PHE* 4.5 11.9 - - + -
764A PRO* 3.7 26.2 - - + -
766A HIS 3.9 4.7 - - - +
767A TYR* 4.0 10.3 - - + -
768A TYR* 3.8 6.8 - - - -
833A THR* 4.0 6.1 - - - +
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Residues in contact with ILE 737 (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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736A PRO* 1.4 79.1 - - - +
738A PHE* 1.4 62.2 + - - +
764A PRO* 3.4 2.3 - - - +
765A THR* 2.8 31.0 + - - +
766A HIS* 3.0 44.3 + - + +
768A TYR* 3.7 33.7 - - + +
794A ILE* 4.4 13.2 - - + -
829A ILE* 4.7 4.5 - - + -
832A LEU* 3.9 48.2 - - + +
833A THR* 3.8 17.7 - - + -
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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