Contacts of the helix formed by residues 677 - 691 (chain A) in PDB entry 3H44
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 677 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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192A LYS* 2.9 53.5 + - - +
196A ASN* 5.5 3.2 - - - +
676A GLU* 1.3 75.5 + - - +
678A PRO* 1.4 64.5 - - + +
679A HIS* 3.3 16.8 - - - +
680A GLN* 2.8 43.5 + - - +
681A HIS* 3.3 7.3 + - - -
786A HIS* 3.1 25.3 + - - -
851A GLN* 3.1 26.9 - - - +
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Residues in contact with PRO 678 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
676A GLU 3.7 0.2 - - - -
677A GLN* 1.4 85.8 - - + +
679A HIS* 1.3 63.3 + - - +
680A GLN 2.9 0.5 + - - -
681A HIS* 3.1 8.8 + - + +
682A ALA* 2.9 22.0 + - - +
783A ASN* 4.0 12.8 - - + +
786A HIS* 3.7 26.5 - - + -
788A ASN* 3.8 22.4 - - + +
789A SER* 3.8 2.9 - - - -
790A GLY* 3.5 24.9 - - - +
851A GLN* 3.3 20.9 - - - +
958A VAL* 3.8 10.2 - - + +
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Residues in contact with HIS 679 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
677A GLN* 3.6 16.1 - - + +
678A PRO* 1.3 78.3 - - - +
680A GLN* 1.3 79.7 + - + +
682A ALA* 3.4 9.9 - - - +
683A MET* 3.0 40.3 + - - +
790A GLY* 4.1 4.4 - - - -
832A ILE* 3.5 35.8 - - + +
849A ILE* 3.9 23.4 - - + +
850A ILE 4.5 4.3 - - - +
851A GLN* 3.0 33.1 + - + +
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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
----------------------------------------------------------
673A PHE* 4.8 4.5 - - + -
676A GLU* 3.0 34.2 + - + +
677A GLN* 2.8 32.6 + - - +
679A HIS* 1.3 95.3 + - + +
681A HIS* 1.3 57.9 + - - +
682A ALA 3.1 0.9 - - - -
683A MET* 3.6 11.1 - - - +
684A TYR* 2.7 37.1 + - - +
687A ARG* 5.0 2.0 + - - +
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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
----------------------------------------------------------
673A PHE* 3.2 51.8 + + - -
674A ARG* 3.8 17.9 + - - -
676A GLU* 3.7 18.9 + - + -
677A GLN 3.3 2.5 + - - -
678A PRO 3.1 9.4 + - - +
680A GLN* 1.3 75.7 - - - +
682A ALA* 1.3 63.6 + - - +
684A TYR* 3.1 2.3 + - - +
685A TYR* 2.9 49.0 + + + -
782A ARG 4.8 2.3 + - - -
783A ASN* 3.3 36.8 + - + +
784A GLU 5.4 0.4 - - - -
958A VAL* 3.9 14.0 - - + +
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Residues in contact with ALA 682 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
678A PRO 2.9 12.9 + - - +
679A HIS* 3.4 15.7 - - - +
681A HIS* 1.3 78.1 - - - +
683A MET* 1.3 62.6 + - - +
685A TYR* 3.4 3.3 + - - +
686A LEU* 3.0 20.4 + - - +
791A ILE* 4.1 7.4 - - - +
792A GLU* 3.9 28.5 - - + +
849A ILE* 5.7 0.2 - - + -
956A VAL* 3.7 12.4 - - + +
958A VAL* 3.4 19.2 - - + +
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Residues in contact with MET 683 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
679A HIS* 3.0 29.0 + - - +
680A GLN* 3.2 12.5 + - + +
682A ALA* 1.3 75.4 - - + +
684A TYR* 1.3 64.7 + - - +
686A LEU* 3.2 3.1 + - - +
687A ARG* 3.0 49.1 + - - +
792A GLU* 3.3 19.9 - - + +
838A ARG* 5.1 1.2 + - - -
847A ARG* 3.9 16.8 - - - +
849A ILE* 3.8 29.2 - - + -
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Residues in contact with TYR 684 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
673A PHE* 3.6 33.4 - + + -
680A GLN 2.7 21.3 + - - +
681A HIS 3.5 2.2 - - - +
683A MET* 1.3 71.8 - - - +
685A TYR* 1.3 95.4 + + - +
687A ARG* 3.1 27.8 + - + +
688A LEU* 3.0 51.7 + - + +
695A TRP 5.3 1.3 - - - -
696A THR* 3.4 10.7 - - - -
697A LYS* 2.8 56.9 + - + +
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Residues in contact with TYR 685 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
673A PHE* 5.3 3.3 - + - -
681A HIS* 2.9 53.7 + + + +
682A ALA 3.7 3.1 - - - +
684A TYR* 1.3 96.4 - + - +
686A LEU* 1.3 63.8 + - - +
688A LEU* 3.3 13.6 + - + +
689A LEU* 2.9 26.6 + - - +
779A TYR* 3.9 28.0 - + + -
781A GLN* 3.6 41.0 + - + +
782A ARG 4.8 3.3 + - - -
956A VAL* 3.8 24.5 - - + -
958A VAL* 4.3 4.7 - - + -
995A MET* 4.8 1.7 - - - +
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Residues in contact with LEU 686 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
682A ALA 3.0 14.4 + - - +
683A MET 3.2 6.9 + - - +
685A TYR* 1.3 77.6 - - - +
687A ARG* 1.3 62.2 + - - +
689A LEU* 3.1 4.6 + - + +
690A MET* 3.1 42.3 + - + +
792A GLU* 3.3 35.7 - - + +
794A TYR* 4.0 18.4 - - + -
838A ARG* 3.1 27.6 - - - +
954A VAL* 4.3 26.0 - - + -
956A VAL* 3.9 18.8 - - + +
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Residues in contact with ARG 687 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
680A GLN* 5.0 1.2 + - - +
683A MET* 3.0 42.9 + - - +
684A TYR* 3.2 34.2 - - + +
686A LEU* 1.3 76.0 - - - +
688A LEU* 1.3 61.3 + - + +
690A MET* 3.5 1.0 + - - +
691A THR* 2.4 35.9 + - - +
694A ALA* 5.2 1.1 - - - -
838A ARG* 4.2 19.6 - - - +
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Residues in contact with LEU 688 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
684A TYR* 3.0 53.7 + - + +
685A TYR* 3.5 12.3 - - + +
687A ARG* 1.3 80.4 - - + +
689A LEU* 1.3 60.9 + - - +
690A MET 3.5 0.2 + - - -
691A THR 3.7 3.8 - - - +
694A ALA* 3.8 29.3 - - + +
695A TRP 3.9 18.8 - - - +
696A THR* 3.7 19.7 - - + -
995A MET* 3.3 20.6 - - + -
999A LYS* 3.0 28.2 + - - -
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Residues in contact with LEU 689 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
685A TYR 2.9 18.7 + - - +
686A LEU* 3.1 6.3 + - + +
688A LEU* 1.3 77.4 - - - +
690A MET* 1.3 78.3 + - + +
691A THR 3.5 0.2 - - - -
769A VAL* 3.8 1.6 - - - +
779A TYR* 3.7 28.7 - - + -
954A VAL* 4.7 5.4 - - + -
956A VAL* 4.3 14.6 - - + -
992A ILE* 4.0 21.8 - - + -
995A MET* 3.4 33.4 - - + -
998A PHE* 3.5 32.5 - - + -
999A LYS* 3.5 19.8 - - - +
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Residues in contact with MET 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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686A LEU* 3.1 31.4 + - + +
687A ARG 4.4 0.9 - - - +
689A LEU* 1.3 106.1 - - + +
691A THR* 1.3 60.6 + - - +
768A GLU* 3.3 27.0 - - + +
769A VAL* 3.1 34.7 + - + +
771A LEU* 4.2 15.0 - - + -
794A TYR* 4.5 11.2 - - + -
838A ARG* 4.2 11.0 - - - +
841A ASN* 4.2 1.5 + - - -
954A VAL* 4.1 31.0 - - + -
998A PHE* 3.5 28.9 - - + -
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Residues in contact with THR 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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624A ILE* 6.2 2.7 - - + -
687A ARG* 2.4 35.6 + - - +
688A LEU 3.7 0.9 + - - +
689A LEU 3.5 0.2 - - - -
690A MET* 1.3 78.8 - - - +
692A GLU* 1.3 70.7 + - - +
693A VAL* 3.3 14.8 + - - +
694A ALA* 4.5 6.2 - - - +
766A TYR* 4.3 15.0 - - + -
767A ARG 4.0 0.4 - - - +
769A VAL* 5.0 0.9 - - - -
838A ARG* 5.9 0.5 + - - -
841A ASN* 3.6 32.0 + - - +
999A LYS* 3.0 23.2 + - - +
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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
------------------------------------------------------------
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