Contacts of the strand formed by residues 672 - 683 (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 GLN 672 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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646A TYR* 3.0 25.6 + - - -
667A ASN* 2.9 46.6 + - - +
669A LEU* 3.4 29.8 - - + +
670A ASN 3.5 0.8 - - - -
671A ASP* 1.3 84.5 - - - +
673A THR* 1.3 64.7 + - - +
674A LEU* 3.7 18.1 - - + +
700A TYR* 4.0 5.7 + - - +
730A PHE* 5.5 0.2 - - - -
732A VAL* 3.8 21.9 - - + +
733A LYS 3.3 11.0 - - - +
734A ASP* 4.9 1.6 - - - +
735A CYS* 3.5 7.5 - - - -
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Residues in contact with THR 673 (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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672A GLN* 1.3 75.4 + - - +
674A LEU* 1.3 75.8 + - - +
675A GLU* 4.1 10.1 + - + +
697A SER* 4.0 11.2 - - - +
698A LEU 3.8 2.9 - - - -
699A PRO* 3.7 32.3 - - + +
700A TYR 4.8 0.7 + - - -
731A THR 3.8 0.2 - - - +
732A VAL* 3.8 1.0 - - - -
733A LYS* 2.9 42.2 + - - +
735A CYS* 3.9 12.7 - - - +
742A THR* 4.7 9.5 + - - -
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Residues in contact with LEU 674 (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* 3.8 29.2 - - + +
667A ASN* 4.4 7.4 - - + +
672A GLN* 3.7 31.6 - - - +
673A THR* 1.3 79.0 - - - +
675A GLU* 1.3 65.8 + - - +
677A VAL* 3.9 15.9 - - + -
697A SER* 3.5 0.3 - - - -
698A LEU* 2.8 43.5 + - + -
728A MET* 4.2 8.1 - - + -
730A PHE* 3.7 41.7 - - + -
731A THR 3.2 6.5 - - - +
732A VAL* 4.0 5.2 - - + -
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Residues in contact with GLU 675 (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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673A THR* 4.7 12.3 - - + +
674A LEU* 1.3 79.9 - - - +
676A ASN* 1.3 72.4 + - + +
677A VAL* 3.4 3.7 + - - -
696A ARG 3.3 13.9 - - - +
697A SER* 4.7 6.5 + - - +
730A PHE* 3.7 1.9 - - - +
731A THR* 2.8 41.0 + - - +
733A LYS* 3.2 43.1 + - + +
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Residues in contact with ASN 676 (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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675A GLU* 1.3 76.7 - - + +
677A VAL* 1.3 60.9 + - - +
678A THR* 3.8 4.1 + - - +
694A PRO* 3.6 12.4 - - - +
695A ALA 3.3 4.7 + - - -
696A ARG* 2.7 48.3 + - - +
729A LYS 3.4 10.0 - - - +
730A PHE* 3.7 4.0 - - - -
731A THR* 4.6 11.1 + - - +
748A GLU* 5.7 3.0 + - - -
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Residues in contact with VAL 677 (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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665A CYS* 5.0 5.4 - - - -
674A LEU* 3.9 11.7 - - + -
675A GLU* 3.9 9.4 - - - +
676A ASN* 1.3 72.3 - - - +
678A THR* 1.3 69.3 + - - +
679A VAL* 5.8 0.2 - - + -
694A PRO* 3.2 5.2 - - - +
695A ALA* 2.9 41.2 + - + +
698A LEU* 3.7 38.6 - - + -
706A CYS* 3.4 11.6 - - - +
728A MET* 4.3 17.3 - - + -
729A LYS 3.2 8.5 - - - +
730A PHE* 3.8 19.7 - - + -
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Residues in contact with THR 678 (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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676A ASN* 4.9 4.0 + - - +
677A VAL* 1.3 80.5 - - - +
679A VAL* 1.3 63.1 + - - +
680A GLN* 3.8 3.7 + - - +
692A TYR* 3.8 34.9 - - + -
693A VAL 4.5 1.3 - - - +
694A PRO* 3.7 24.9 - - + -
706A CYS* 4.0 8.1 - - + -
707A TYR 5.5 1.3 - - - +
728A MET* 3.3 5.7 - - - +
729A LYS* 2.8 45.3 + - - +
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Residues in contact with VAL 679 (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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648A ILE* 4.6 3.4 - - + -
663A PHE* 3.6 52.3 - - + -
665A CYS* 4.9 2.2 - - - -
677A VAL* 5.8 0.4 - - + -
678A THR* 1.3 77.0 - - - +
680A GLN* 1.3 63.6 + - - +
681A MET* 3.5 3.0 - - + +
692A TYR* 3.2 5.7 - - - -
706A CYS* 4.0 10.7 - - - -
708A THR* 3.0 24.0 + - - -
726A CYS* 4.0 17.5 - - + -
727A MET 3.5 4.9 - - - +
728A MET* 4.4 8.5 - - + -
753A LEU* 3.8 28.9 - - + -
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Residues in contact with GLN 680 (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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678A THR* 3.8 4.7 + - - +
679A VAL* 1.3 73.7 - - - +
681A MET* 1.3 65.3 + - - +
682A GLU* 3.7 25.7 + - + +
692A TYR* 3.5 19.9 - - + +
725A SER 3.5 1.1 - - - +
726A CYS* 3.2 6.2 - - - -
727A MET* 2.9 58.7 + - + +
729A LYS* 3.6 35.4 + - + +
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Residues in contact with MET 681 (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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661A PHE* 3.6 35.0 - - + -
663A PHE* 3.8 10.5 - - + -
679A VAL* 3.5 12.6 - - + +
680A GLN* 1.3 81.2 - - - +
682A GLU* 1.3 63.7 + - - +
683A PRO* 3.9 1.4 - - - +
689A VAL* 3.4 27.3 - - + +
692A TYR* 3.1 9.7 + - - -
708A THR* 3.6 19.7 - - + -
710A VAL* 5.0 0.7 - - - -
724A PHE* 3.5 39.9 - - + -
725A SER 3.3 4.5 - - - +
726A CYS* 4.2 12.8 - - - -
756A LEU* 3.8 20.4 - - + -
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Residues in contact with GLU 682 (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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680A GLN* 3.7 25.8 + - + +
681A MET* 1.3 77.2 - - - +
683A PRO* 1.3 68.4 - - + +
684A THR* 5.3 0.9 - - - +
723A THR 3.7 0.7 - - - +
724A PHE* 3.4 2.5 - - - -
725A SER* 2.9 52.4 + - - +
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Residues in contact with PRO 683 (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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681A MET 3.9 6.7 - - - +
682A GLU* 1.3 87.6 - - + +
684A THR* 1.3 62.9 + - - +
685A GLU 3.3 14.8 - - - +
687A TYR* 3.3 25.6 - - + +
688A GLU* 5.3 1.1 - - - -
689A VAL* 4.8 7.6 - - + +
722A CYS* 3.5 14.1 - - - -
723A THR 3.4 6.3 - - - +
724A PHE* 3.6 17.0 - - + -
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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