Contacts of the helix formed by residues 680 - 692 (chain A) in PDB entry 1R1H
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 ASN 680 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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670A GLU* 6.0 2.0 - - - +
673A LEU* 4.0 14.1 - - + -
679A LEU* 1.3 75.5 - - - +
681A HIS* 1.3 63.4 + - - +
682A LYS* 3.2 13.9 + - - +
683A GLN* 2.8 49.8 + - - +
684A LEU* 2.9 27.1 + - - +
731A ALA 5.2 1.4 + - - -
733A HIS* 6.0 2.2 - - - -
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Residues in contact with HIS 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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569A SER* 3.6 24.7 - - - -
571A SER* 2.7 36.8 + - - -
661A TYR* 3.2 22.2 - - + +
665A ILE* 5.2 4.5 - - + -
670A GLU* 6.0 2.5 - - + -
671A GLU* 3.4 35.8 - - + +
672A LYS 2.7 24.3 + - - -
673A LEU* 4.0 12.4 - - + +
674A LEU* 4.7 2.9 - - + -
680A ASN* 1.3 73.8 - - - +
682A LYS* 1.3 62.6 + - + +
684A LEU* 3.6 18.8 - - + +
685A PHE* 2.9 25.8 + - - +
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Residues in contact with LYS 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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658A TYR* 2.8 35.9 + - + +
661A TYR* 4.5 8.7 - - + -
662A GLN* 3.6 31.2 - - - +
665A ILE* 5.4 13.9 - - + -
670A GLU* 6.0 1.8 - - - +
680A ASN* 3.6 12.1 - - + +
681A HIS* 1.3 78.3 - - + +
683A GLN* 1.3 60.4 + - - +
685A PHE* 3.4 14.0 - - - +
686A PHE* 3.2 22.9 - - - -
730A GLU* 4.8 13.2 + - - +
731A ALA* 4.6 11.7 - - + -
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Residues in contact with GLN 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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678A ASP 4.1 1.6 - - - +
679A LEU* 3.0 31.3 - - + +
680A ASN* 2.8 54.1 + - - +
682A LYS* 1.3 75.4 - - - +
684A LEU* 1.3 58.5 + - - +
686A PHE* 3.1 5.5 + - - +
687A LEU* 2.9 26.5 + - - +
731A ALA* 3.1 30.2 + - + +
732A PHE* 3.6 34.0 - - + +
733A HIS* 4.3 11.7 + - - -
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Residues in contact with LEU 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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68A LEU* 4.2 13.2 - - + -
571A SER* 3.8 9.0 - - - +
572A LEU* 4.0 8.0 - - + +
673A LEU* 5.6 0.4 - - + -
674A LEU* 3.9 25.4 - - + +
677A LEU* 4.1 23.6 - - + -
679A LEU* 4.1 29.6 - - + +
680A ASN 2.9 21.2 + - - +
681A HIS* 3.3 35.4 + - + +
683A GLN* 1.3 72.7 - - - +
685A PHE* 1.3 67.0 + - - +
687A LEU* 3.5 7.4 - - + +
688A ASN* 2.9 27.4 + - - +
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Residues in contact with PHE 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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571A SER* 3.5 19.9 - - - +
574A TYR* 3.5 17.3 - - + -
575A GLY* 3.2 41.1 - - - -
579A MET* 5.8 0.2 - - + -
654A LEU* 3.8 26.2 - - + -
657A ALA* 4.0 6.7 - - + -
658A TYR* 3.6 51.1 - + + -
661A TYR* 4.2 13.7 - + + -
681A HIS 2.9 13.4 + - - +
682A LYS* 3.4 12.3 - - - +
684A LEU* 1.3 75.7 - - - +
686A PHE* 1.3 69.9 + + - +
688A ASN* 4.0 1.0 - - - +
689A PHE* 3.1 29.1 + - + +
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Residues in contact with PHE 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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82A PHE* 3.5 12.8 - - + -
654A LEU* 4.0 19.1 - - + -
658A TYR* 3.9 31.4 - + + -
682A LYS 3.2 19.2 + - - -
683A GLN 3.1 6.7 + - - +
685A PHE* 1.3 85.7 - + - +
687A LEU* 1.3 65.5 + - - +
689A PHE* 3.3 6.6 - + - +
690A ALA* 2.9 18.7 + - - +
722A LEU* 3.3 31.6 - - + -
725A SER* 4.1 5.8 - - - -
727A GLU* 3.9 10.1 - - + -
728A PHE* 3.5 40.8 - + + -
731A ALA* 4.0 14.1 - - + -
732A PHE* 4.0 11.7 - + + -
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Residues in contact with LEU 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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68A LEU* 4.0 29.4 - - + -
72A MET* 4.2 15.5 - - + -
82A PHE* 3.9 7.2 - - + -
85A TYR* 4.6 11.2 - - + -
86A ALA* 3.8 22.9 - - + -
677A LEU* 4.6 1.1 - - + -
679A LEU* 3.9 25.6 - - + -
683A GLN 2.9 13.8 + - - +
684A LEU* 3.5 15.3 - - + +
686A PHE* 1.3 76.9 - - - +
688A ASN* 1.3 62.9 + - - +
690A ALA* 3.2 2.4 + - - +
691A GLN* 3.1 42.6 + - - +
732A PHE* 5.8 0.2 - - + -
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Residues in contact with ASN 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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67A ARG* 2.7 48.6 - - - +
68A LEU* 3.9 7.3 - - + +
562A PRO* 3.0 24.6 - - - +
572A LEU* 3.0 39.1 - - + +
575A GLY 4.6 0.9 - - - -
576A GLY* 4.2 5.5 + - - -
684A LEU 2.9 17.3 + - - +
685A PHE 4.0 2.7 - - - +
687A LEU* 1.3 72.5 - - - +
689A PHE* 1.3 69.8 + - - +
691A GLN* 3.1 9.6 + - - +
692A VAL* 3.2 13.9 + - - +
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Residues in contact with PHE 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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575A GLY* 3.3 25.2 + - - +
579A MET* 3.5 29.2 - - + -
654A LEU* 4.0 19.3 - - + -
685A PHE* 3.1 18.3 + - + +
686A PHE* 3.3 10.3 - + - +
688A ASN* 1.3 80.0 - - - +
690A ALA* 1.3 65.8 + - - +
691A GLN 3.4 0.2 + - - -
692A VAL* 3.4 5.2 + - - +
717A ARG 4.8 0.9 - - - -
718A ILE* 4.6 7.6 - - + -
721A THR* 3.3 28.3 - - + -
722A LEU* 4.0 29.8 - - + -
2001A BIR 3.1 63.9 - + - -
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Residues in contact with ALA 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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82A PHE* 3.6 12.6 - - + +
83A PHE* 5.5 0.7 - - + -
86A ALA* 3.5 25.4 - - + -
87A CYS* 3.9 4.8 - - - -
686A PHE 2.9 17.2 + - - +
687A LEU 3.6 0.9 - - - +
689A PHE* 1.3 77.4 - - + +
691A GLN* 1.3 58.9 + - - +
693A TRP* 2.9 25.8 + - - +
694A CYS 3.7 2.6 + - - -
718A ILE* 3.8 30.6 - - + +
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Residues in contact with GLN 691 (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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67A ARG* 3.2 26.9 + - - +
68A LEU* 3.0 36.8 + - - +
71A ASN* 3.3 19.8 + - - +
72A MET* 3.8 1.4 - - - +
86A ALA* 2.9 30.7 + - + +
105A ASN* 2.9 27.2 - - - +
562A PRO* 5.5 2.2 - - - +
687A LEU* 3.1 35.6 + - + +
688A ASN 3.1 4.4 + - - +
690A ALA* 1.3 72.2 - - - +
692A VAL* 1.3 66.6 + - - +
693A TRP 2.9 2.9 + - - -
694A CYS* 3.2 16.5 + - - -
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Residues in contact with VAL 692 (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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105A ASN* 4.1 1.0 - - - +
106A PHE* 3.8 28.3 + - + +
562A PRO* 4.5 18.5 - - + +
563A PHE* 3.7 35.4 - - + +
576A GLY* 4.9 6.1 - - - -
688A ASN* 3.2 12.7 + - - +
689A PHE* 3.4 12.8 - - - +
691A GLN* 1.3 78.2 - - - +
693A TRP* 1.3 70.2 + - + +
694A CYS 3.9 0.7 + - - +
2001A BIR 3.4 38.4 - - + -
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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