Contacts of the helix formed by residues 670 - 684 (chain A) in PDB entry 1OH7
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 PHE 670 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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671A MET* 1.3 79.2 + - + +
672A VAL* 3.3 27.3 + - + -
673A GLU* 3.1 40.9 + - + +
674A MET* 3.7 19.6 - - - +
697A ARG* 5.8 1.4 - - - +
617B MET* 4.1 27.6 - - + -
775B VAL* 4.9 4.7 - - - -
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Residues in contact with MET 671 (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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670A PHE* 1.3 84.5 - - + +
672A VAL* 1.3 69.0 + - + +
674A MET* 3.2 5.2 + - - +
675A THR* 3.0 28.8 + - - +
617B MET* 5.2 2.7 - - + +
775B VAL* 4.4 23.2 - - + +
778B LEU* 3.5 28.5 - - + +
779B ALA* 4.0 18.4 - - - -
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Residues in contact with VAL 672 (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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656A ARG* 4.8 3.1 - - - +
670A PHE* 3.3 26.9 - - + +
671A MET* 1.3 79.9 - - + +
673A GLU* 1.3 58.3 + - + +
675A THR* 3.7 5.9 - - - -
676A GLU* 2.9 53.6 + - + +
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Residues in contact with GLU 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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656A ARG* 3.1 36.3 + - - +
658A GLY* 4.0 13.9 - - - -
670A PHE* 3.1 34.0 + - + +
671A MET 3.3 0.2 - - - -
672A VAL* 1.3 76.6 - - + +
674A MET* 1.3 60.5 + - + +
676A GLU* 3.7 2.8 + - - +
677A THR* 2.5 34.3 + - - -
695A ILE* 5.6 3.3 - - + +
696A GLY 5.5 3.1 + - - -
697A ARG* 3.6 39.8 + - + +
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Residues in contact with MET 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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670A PHE 3.7 16.4 - - - +
671A MET 3.2 7.3 + - - +
673A GLU* 1.3 78.5 - - + +
675A THR* 1.3 60.7 + - - +
677A THR* 3.4 5.9 + - - -
678A ALA* 3.0 21.0 + - - +
696A GLY* 5.5 0.9 - - - -
697A ARG* 3.2 35.2 - - + +
707A LEU* 3.4 35.2 - - + -
772B GLY* 4.2 8.7 - - - +
775B VAL* 4.2 18.2 - - + -
776B ALA* 3.9 14.8 - - - -
779B ALA* 3.6 16.8 - - + -
781B VAL* 3.5 15.5 - - + +
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Residues in contact with THR 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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164A GLU* 4.4 15.3 - - - +
671A MET* 3.0 28.0 + - - +
672A VAL* 3.7 7.0 - - - -
674A MET* 1.3 71.8 - - - +
676A GLU* 1.3 68.8 + - + +
677A THR 3.1 1.1 - - - -
678A ALA* 3.1 13.3 + - + +
679A ASN* 3.2 12.8 + - - +
779B ALA* 3.6 28.1 + - - +
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Residues in contact with GLU 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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164A GLU* 4.8 6.1 - - - +
272A ALA* 4.2 13.0 - - - +
275A ARG* 5.0 8.2 + - - -
655A THR 4.1 10.4 - - - +
656A ARG* 3.1 47.2 + - + +
672A VAL* 2.9 34.0 + - + +
673A GLU 3.7 4.5 - - - +
675A THR* 1.3 77.9 - - + +
677A THR* 1.3 59.7 + - - +
679A ASN* 3.3 11.9 + - - +
680A ILE* 3.3 25.0 + - - +
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Residues in contact with THR 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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656A ARG* 3.7 15.1 - - - +
673A GLU* 2.5 24.0 + - - +
674A MET* 3.5 9.7 - - - -
675A THR 3.1 0.8 - - - -
676A GLU* 1.3 72.6 - - - +
678A ALA* 1.3 65.2 + - - +
679A ASN 3.2 1.6 - - - -
680A ILE* 3.3 8.1 + - - +
681A LEU* 3.0 26.6 + - + +
692A MET* 3.8 21.8 - - + -
695A ILE* 4.3 10.5 - - + +
707A LEU* 5.8 0.9 - - + -
711A CYS* 3.9 26.7 - - - -
781B VAL* 5.1 3.4 - - + -
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Residues in contact with ALA 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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674A MET 3.0 13.8 + - - +
675A THR* 3.3 10.5 - - + +
677A THR* 1.3 75.4 - - - +
679A ASN* 1.3 58.1 + - - +
681A LEU* 3.1 7.9 + - - +
682A HIS* 3.0 40.9 + - + +
779B ALA 3.8 17.5 - - - +
780B GLY* 3.8 20.9 - - - +
781B VAL* 3.9 8.9 - - - +
782B PRO* 5.1 0.2 - - - -
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Residues in contact with ASN 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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162A ASP* 4.9 1.7 - - - +
164A GLU* 3.3 44.4 + - + +
270A ASP* 5.1 7.1 + - - +
652A ARG* 4.4 7.0 + - - +
654A PHE* 4.2 18.0 - - - -
675A THR 3.2 8.3 + - - +
676A GLU* 3.5 11.8 + - - +
677A THR 3.2 0.2 - - - -
678A ALA* 1.3 76.5 - - - +
680A ILE* 1.3 67.4 + - - +
682A HIS* 4.5 3.6 - - - -
683A ASN* 2.5 61.9 + - - +
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Residues in contact with ILE 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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270A ASP* 4.9 1.6 - - - +
654A PHE* 3.8 37.2 - - + -
655A THR 4.1 17.3 - - - +
656A ARG* 4.1 7.4 - - + -
676A GLU 3.5 12.1 - - - +
677A THR* 3.3 9.6 + - - +
679A ASN* 1.3 79.5 - - - +
681A LEU* 1.3 58.7 + - + +
684A ALA* 3.0 35.3 + - - +
690A VAL* 4.0 24.5 - - + -
692A MET* 3.5 38.8 - - + -
715A LEU* 4.4 9.0 - - + -
719A ILE* 4.5 0.2 - - - +
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Residues in contact with LEU 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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677A THR* 3.0 21.1 + - + +
678A ALA 3.1 7.8 + - - +
680A ILE* 1.3 79.5 - - + +
682A HIS* 1.3 61.9 + - - +
684A ALA 5.0 0.3 - - - +
692A MET* 5.9 0.2 - - + -
711A CYS* 3.8 45.5 - - + +
714A ASN* 3.6 23.7 - - + +
715A LEU* 4.1 14.4 - - + -
719A ILE* 3.3 26.9 - - + +
781B VAL* 4.2 7.6 - - + -
782B PRO* 4.0 28.8 - - + +
785B VAL* 4.3 8.7 - - + -
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Residues in contact with HIS 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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678A ALA* 3.0 26.6 + - + +
679A ASN* 4.4 1.4 + - - -
680A ILE 3.3 0.4 - - - -
681A LEU* 1.3 80.3 - - - +
683A ASN* 1.3 74.0 + - - +
684A ALA 3.9 2.4 - - - +
780B GLY* 3.1 32.2 + - - -
782B PRO* 3.8 23.6 - - + +
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Residues in contact with ASN 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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162A ASP* 3.8 19.0 + - - +
651A ASP* 5.2 1.4 - - - +
652A ARG* 3.9 23.3 + - - +
654A PHE* 3.9 8.4 - - + -
679A ASN* 2.5 43.1 + - - +
682A HIS* 1.3 93.2 - - - +
684A ALA* 1.3 65.6 + - - +
685A THR* 3.6 11.9 + - - +
688A SER* 4.7 0.7 + - - -
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Residues in contact with ALA 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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654A PHE* 3.7 22.7 - - + -
680A ILE 3.0 21.6 + - - +
681A LEU 5.0 0.2 - - - +
682A HIS 4.8 2.6 - - - +
683A ASN* 1.3 81.7 + - - +
685A THR* 1.3 59.7 + - - +
688A SER* 4.2 2.7 - - - +
690A VAL* 4.1 19.1 - - + -
715A LEU* 4.6 3.6 - - + -
719A ILE* 3.3 29.6 - - + +
721A ALA* 4.7 0.2 - - + -
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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