Contacts of the helix formed by residues 678 - 690 (chain B) in PDB entry 1XR2
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 SER 678 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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676B VAL 3.4 4.4 + - - -
677B PRO* 1.3 75.4 - - - +
679B ILE* 1.3 66.0 + - - +
680B ASN* 3.6 9.3 + - - +
681B GLU* 3.0 51.2 + - - +
682B MET* 3.1 14.3 + - - +
720B ASN* 5.1 1.6 - - - +
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Residues in contact with ILE 679 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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677B PRO 4.0 0.6 + - - -
678B SER* 1.3 73.8 - - - +
680B ASN* 1.3 59.8 + - - +
682B MET* 3.3 10.9 + - - +
683B ARG* 2.9 39.0 + - - +
720B ASN* 4.0 29.5 - - + +
723B ALA* 3.7 24.0 - - + -
724B LEU* 3.9 18.0 - - + +
727B GLU* 3.6 28.3 - - - +
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Residues in contact with ASN 680 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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678B SER* 3.1 8.4 + - - +
679B ILE* 1.3 76.3 - - - +
681B GLU* 1.3 64.2 + - - +
683B ARG* 2.6 42.1 + - - +
684B GLU* 3.2 22.0 + - - +
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Residues in contact with GLU 681 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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647B LYS* 5.4 12.3 + - - +
668B VAL 6.0 0.2 - - - +
676B VAL 5.1 1.4 - - - +
677B PRO* 3.8 17.4 - - + +
678B SER* 3.0 38.2 + - - +
680B ASN* 1.3 79.3 - - - +
682B MET* 1.3 63.5 + - + +
684B GLU* 3.5 15.1 + - - +
685B ILE* 3.6 16.1 - - + +
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Residues in contact with MET 682 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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668B VAL* 3.4 47.5 - - + +
669B TRP* 5.0 4.3 - - - -
677B PRO* 3.9 19.7 - - + +
678B SER 3.1 17.8 + - - +
679B ILE* 3.8 9.6 - - - +
681B GLU* 1.3 74.4 - - - +
683B ARG* 1.3 65.2 + - - +
685B ILE* 3.0 17.7 + - - +
686B VAL* 3.1 15.8 + - - +
717B SER 4.5 2.7 - - - +
720B ASN* 3.3 46.7 - - + +
721B MET* 3.9 15.7 - - - -
724B LEU* 4.1 11.9 - - + -
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Residues in contact with ARG 683 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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679B ILE* 2.9 27.5 + - - +
680B ASN* 2.6 37.7 + - - +
681B GLU 3.3 0.2 - - - -
682B MET* 1.3 76.4 - - - +
684B GLU* 1.3 62.8 + - - +
686B VAL* 3.2 3.6 + - - +
687B GLU* 2.9 54.9 + - + +
724B LEU* 3.8 20.9 - - + +
727B GLU* 2.5 36.1 + - - +
728B MET* 4.3 10.2 - - - -
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Residues in contact with GLU 684 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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691A ARG* 3.2 29.3 + - - +
647B LYS* 4.0 30.0 + - + +
680B ASN 3.2 9.4 + - - +
681B GLU* 3.7 12.4 - - - +
682B MET 3.2 0.4 - - - -
683B ARG* 1.3 77.8 - - - +
685B ILE* 1.3 64.4 + - + +
687B GLU* 3.5 11.0 + - - +
688B ARG* 3.1 23.9 + - + +
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Residues in contact with ILE 685 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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643B ALA* 4.0 12.8 - - + +
644B SER* 3.8 22.4 - - - +
647B LYS* 4.1 24.7 - - + +
648B GLY* 4.0 7.4 - - - +
666B VAL* 3.9 15.7 - - + -
667B GLY 3.9 4.9 - - - +
668B VAL* 3.6 45.8 - - + +
681B GLU 3.6 17.3 - - - +
682B MET* 3.0 5.8 + - - +
684B GLU* 1.3 74.3 - - + +
686B VAL* 1.3 65.9 + - - +
688B ARG* 3.2 4.2 + - - +
689B VAL* 3.1 22.2 + - - +
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Residues in contact with VAL 686 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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404B PHE* 4.8 7.4 - - + -
666B VAL* 5.3 4.7 - - + -
668B VAL* 3.9 15.9 - - + -
682B MET 3.1 13.1 + - - +
683B ARG 3.2 4.9 + - - +
685B ILE* 1.3 75.4 - - - +
687B GLU* 1.3 58.1 + - - +
689B VAL* 3.2 9.0 + - - +
690B LEU* 3.0 36.2 + - + +
698B ILE* 4.9 8.1 - - + -
700B ILE* 4.0 16.2 - - + -
724B LEU* 3.7 23.1 - - + -
728B MET* 3.4 30.7 - - + -
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Residues in contact with GLU 687 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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683B ARG* 2.9 49.7 + - + +
684B GLU* 3.8 8.5 + - - +
686B VAL* 1.3 72.8 - - - +
688B ARG* 1.3 67.4 + - - +
690B LEU* 3.2 16.2 + - - +
691B ARG* 3.4 9.7 + - - +
728B MET* 4.1 14.5 - - + +
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Residues in contact with ARG 688 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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647B LYS 3.8 11.0 - - - +
648B GLY 3.7 21.8 - - - +
649B GLU* 2.8 38.2 + - - +
651B ILE* 3.5 11.8 - - - +
652B SER* 4.6 2.2 - - - +
655B GLU* 2.9 41.2 + - - -
684B GLU* 3.1 19.0 + - + +
685B ILE 3.2 5.4 + - - +
687B GLU* 1.3 76.5 - - - +
689B VAL* 1.3 64.0 + - - +
691B ARG* 3.1 58.7 + - - +
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Residues in contact with VAL 689 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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641B ILE* 6.5 0.2 - - + -
643B ALA* 5.3 1.8 - - + -
648B GLY* 4.4 11.0 - - - +
651B ILE* 3.9 37.5 - - + +
655B GLU* 5.2 1.2 - - - +
666B VAL* 3.7 33.2 - - + -
685B ILE 3.1 13.6 + - - +
686B VAL* 3.2 9.2 + - - +
688B ARG* 1.3 77.1 - - - +
690B LEU* 1.3 56.6 + - - +
691B ARG 3.2 3.4 + - - -
692B VAL 4.3 0.7 + - - -
693B LEU* 3.9 22.1 + - + +
698B ILE* 3.4 32.8 - - + -
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Residues in contact with LEU 690 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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404B PHE* 3.6 22.7 - - + -
686B VAL* 3.0 21.2 + - + +
687B GLU* 3.7 9.2 - - - +
688B ARG 3.1 0.8 - - - -
689B VAL* 1.3 75.6 - - - +
691B ARG* 1.3 63.0 + - - +
692B VAL 3.4 2.0 - - - -
693B LEU 4.0 14.2 - - - +
695B LYS* 3.6 34.8 - - + +
698B ILE* 3.8 18.6 - - + -
728B MET* 3.8 25.4 - - + -
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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