Contacts of the helix formed by residues 678 - 690 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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676A VAL 3.9 1.4 + - - -
677A PRO* 1.3 73.7 - - - +
679A ILE* 1.3 57.9 + - - +
680A ASN* 3.9 9.8 + - - +
681A GLU* 2.7 44.7 + - - +
682A MET* 3.1 11.6 + - - +
720A ASN* 4.3 4.0 - - - +
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Residues in contact with ILE 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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678A SER* 1.3 71.5 - - - +
680A ASN* 1.3 57.5 + - - +
682A MET* 3.4 10.9 + - - +
683A ARG* 2.9 28.3 + - + +
720A ASN* 3.6 30.7 - - - +
723A ALA* 3.9 21.1 - - + -
724A LEU* 3.5 34.0 - - + +
727A GLU* 5.6 3.8 - - + -
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Residues in contact with ASN 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 SER* 2.9 10.0 + - - +
679A ILE* 1.3 81.0 - - - +
681A GLU* 1.3 59.9 + - - +
683A ARG* 3.5 8.3 + - - +
684A GLU* 3.3 19.8 + - - +
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Residues in contact with GLU 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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647A LYS* 5.3 7.8 - - - +
668A VAL 5.5 0.2 - - - -
677A PRO* 4.9 7.0 - - + -
678A SER* 2.7 33.7 + - - +
680A ASN* 1.3 72.4 - - - +
682A MET* 1.3 63.3 + - - +
684A GLU* 3.3 18.6 + - - +
685A ILE* 3.5 13.2 + - - +
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Residues in contact with MET 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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668A VAL* 3.4 50.4 - - + +
669A TRP* 3.8 21.3 - - + -
677A PRO* 4.2 15.3 - - + -
678A SER 3.1 11.6 + - - +
679A ILE* 3.8 6.7 - - - +
681A GLU* 1.3 74.3 - - - +
683A ARG* 1.3 66.0 + - - +
685A ILE* 3.1 15.0 + - - +
686A VAL* 3.1 17.7 + - - +
717A SER 4.0 9.4 - - - +
720A ASN* 4.0 17.9 - - + +
721A MET* 3.8 36.8 - - + -
724A LEU* 4.3 11.0 - - + -
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Residues in contact with ARG 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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679A ILE* 2.9 18.4 + - + +
680A ASN* 3.6 10.5 - - - +
681A GLU 3.2 0.4 - - - -
682A MET* 1.3 78.1 - - - +
684A GLU* 1.3 55.1 + - - +
686A VAL* 3.8 3.6 - - - +
687A GLU* 2.9 32.3 + - - +
724A LEU* 3.8 22.1 - - + +
728A MET* 5.0 8.5 - - + +
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Residues in contact with GLU 684 (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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647A LYS* 4.5 13.6 - - + +
680A ASN 3.3 9.5 + - - +
681A GLU* 3.5 12.6 - - - +
683A ARG* 1.3 79.7 - - - +
685A ILE* 1.3 62.5 + - + +
687A GLU* 3.4 5.5 + - - +
688A ARG* 3.1 23.7 + - - +
691B ARG* 6.1 2.5 - - - +
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Residues in contact with ILE 685 (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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643A ALA* 4.0 7.0 - - + +
644A SER* 3.4 34.5 - - - +
647A LYS* 4.0 25.4 - - + -
648A GLY* 3.9 15.0 - - - +
666A VAL* 3.8 24.9 - - + -
668A VAL* 3.6 28.7 - - + +
681A GLU 3.6 15.3 - - - +
682A MET* 3.1 6.9 + - - +
684A GLU* 1.3 78.3 - - + +
686A VAL* 1.3 62.1 + - - +
688A ARG* 3.2 4.7 + - - +
689A VAL* 3.1 22.2 + - - +
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Residues in contact with VAL 686 (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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404A PHE* 4.8 1.8 - - + -
666A VAL* 5.2 2.2 - - + -
668A VAL* 3.9 11.9 - - + -
682A MET 3.1 15.2 + - - +
683A ARG 4.0 3.4 - - - +
685A ILE* 1.3 73.5 - - - +
687A GLU* 1.3 67.0 + - - +
689A VAL* 3.1 21.2 - - + +
690A LEU* 3.0 31.5 - - + +
698A ILE* 4.7 4.7 - - + -
700A ILE* 3.4 33.7 - - + -
724A LEU* 4.1 11.0 - - + -
728A MET* 4.1 24.5 - - + -
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Residues in contact with GLU 687 (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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683A ARG 2.9 18.4 + - - +
684A GLU* 3.7 6.5 - - - +
686A VAL* 1.3 78.3 - - - +
688A ARG* 1.3 63.4 + - - +
690A LEU* 3.5 20.9 + - + +
691A ARG* 3.6 12.1 + - - +
728A MET* 5.5 7.4 - - + +
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Residues in contact with ARG 688 (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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647A LYS 3.6 20.2 - - - +
648A GLY 3.7 13.2 - - - +
649A GLU* 2.8 38.0 + - - +
651A ILE* 3.4 11.0 - - - +
652A SER* 4.6 2.0 - - - -
655A GLU* 2.9 36.8 + - - -
684A GLU 3.1 14.5 + - - +
685A ILE 3.4 9.4 - - - +
687A GLU* 1.3 78.1 - - - +
689A VAL* 1.3 63.0 + - - +
690A LEU 3.3 0.5 + - - -
691A ARG* 3.4 57.0 + - - +
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Residues in contact with VAL 689 (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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643A ALA* 5.1 1.8 - - + -
648A GLY* 4.2 11.0 - - - +
651A ILE* 4.0 34.5 - - + +
655A GLU* 4.5 2.3 - - - +
666A VAL* 3.9 31.2 - - + -
685A ILE 3.1 11.6 + - - +
686A VAL* 3.1 26.7 - - + +
688A ARG* 1.3 75.7 - - - +
690A LEU* 1.3 58.4 + - + +
691A ARG 3.3 2.8 + - - -
692A VAL 4.3 0.9 + - - -
693A LEU* 3.9 25.6 + - - +
698A ILE* 4.0 25.2 - - + +
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Residues in contact with LEU 690 (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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404A PHE* 3.7 36.1 - - + -
686A VAL* 3.0 29.8 + - + +
687A GLU* 3.8 15.5 - - + +
688A ARG 3.2 0.4 - - - -
689A VAL* 1.3 82.9 - - + +
691A ARG* 1.3 61.8 + - - +
692A VAL 3.2 2.6 + - - -
693A LEU* 3.9 17.9 - - - +
695A LYS* 4.8 9.0 - - + -
698A ILE* 4.9 7.2 - - + -
728A MET* 5.2 6.3 - - + -
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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