Contacts of the helix formed by residues 686 - 705 (chain A) in PDB entry 6DBU
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 ASP 686 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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682A VAL* 3.8 10.5 - - - +
683A ASP* 2.8 30.0 - - + +
684A GLU 4.9 0.4 - - - -
685A SER* 1.3 73.4 - - - +
687A HIS* 1.3 65.9 + - - +
688A GLU* 3.1 5.3 + - + +
689A THR* 3.0 30.0 + - - -
690A LEU* 3.6 15.2 + - - +
34B LYS* 4.6 25.1 - - + +
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Residues in contact with HIS 687 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
685A SER 3.0 8.1 + - - +
686A ASP* 1.3 71.9 - - - +
688A GLU* 1.3 62.4 + - - +
690A LEU* 3.8 8.2 - - + +
691A THR* 2.9 44.3 + - - -
736A GLU* 3.6 43.0 + - + +
737A MET* 4.5 4.2 - - - -
804A LYS 5.2 1.3 - - - -
806A PHE* 3.6 15.0 - + - -
34B LYS* 5.9 0.6 - - - +
35B GLY* 4.7 16.2 - - - -
36B TRP* 3.0 37.7 + + + +
98B PRO* 4.4 3.7 + - + +
99B ASN* 3.0 31.1 + - - -
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Residues in contact with GLU 688 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
560A TRP* 5.0 5.3 - - - -
567A VAL* 5.0 9.4 - - - +
686A ASP* 3.1 7.4 - - + +
687A HIS* 1.3 79.8 - - - +
689A THR* 1.3 71.8 + - - +
691A THR* 3.8 2.3 - - - -
692A ALA* 2.9 28.6 + - - +
16B GLN* 4.9 4.5 - - - +
34B LYS* 5.3 12.3 - - + +
35B GLY 5.7 3.0 - - - +
73B ARG* 2.3 56.5 + - - +
96B ARG* 5.4 0.7 - - - -
98B PRO* 3.8 15.5 - - + +
100B ASN* 2.9 19.6 + - - +
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Residues in contact with THR 689 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
560A TRP* 5.0 8.2 - - + -
571A THR* 3.2 41.0 + - + +
682A VAL* 3.6 14.9 - - + +
686A ASP* 3.0 21.2 + - - -
688A GLU* 1.3 86.6 + - - +
690A LEU* 1.3 63.5 + - - +
692A ALA* 3.5 5.1 - - + +
693A ILE* 2.9 35.7 + - + +
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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
----------------------------------------------------------
619A CYS* 5.3 0.9 - - - -
640A VAL* 4.2 17.5 - - + -
680A MET* 3.6 30.7 - - + -
682A VAL* 4.7 5.4 - - + +
683A ASP 5.0 5.2 - - - +
684A GLU* 4.0 14.8 - - - +
686A ASP 3.6 16.3 + - - +
687A HIS* 3.8 7.4 - - + +
688A GLU 3.2 0.4 - - - -
689A THR* 1.3 78.7 - - - +
691A THR* 1.3 57.9 + - - +
693A ILE* 4.0 0.3 - - - +
694A LEU* 2.9 45.0 + - + +
733A MET* 4.0 18.6 - - + -
736A GLU* 4.8 4.7 - - - +
737A MET* 3.7 30.1 - - + -
806A PHE* 6.0 0.7 - - + -
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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
----------------------------------------------------------
687A HIS* 2.9 40.7 + - - -
688A GLU 3.8 2.2 - - - -
690A LEU* 1.3 75.7 - - - +
692A ALA* 1.3 66.0 + - - +
694A LEU* 4.5 0.7 - - - +
695A GLY* 2.9 26.0 + - - +
806A PHE* 3.7 32.4 - - + -
98B PRO 4.3 6.5 - - - -
99B ASN* 3.7 32.2 + - + -
100B ASN* 4.1 6.4 - - - +
172B TRP* 5.3 0.9 - - - -
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Residues in contact with ALA 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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560A TRP* 4.6 16.2 - - + -
688A GLU* 2.9 23.5 + - - +
689A THR* 3.2 10.7 + - - +
691A THR* 1.3 78.9 - - - +
693A ILE* 1.3 63.3 + - + +
695A GLY* 4.7 0.3 - - - -
696A PRO* 4.1 5.5 - - - +
100B ASN* 3.2 32.5 + - - +
172B TRP* 5.1 2.1 - - - -
173B ASN* 3.3 26.7 + - - +
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Residues in contact with ILE 693 (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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556A GLY* 4.0 12.3 - - - +
557A LEU* 4.3 19.3 - - + +
560A TRP* 4.7 14.1 - - + -
571A THR* 4.0 24.5 - - + -
573A SER* 3.5 23.3 - - - +
575A ARG* 5.0 7.1 + - - +
678A CYS* 5.1 3.8 - - - -
680A MET* 3.4 30.1 - - + -
682A VAL* 5.0 1.1 - - + -
689A THR* 2.9 26.4 + - + +
690A LEU 4.3 0.2 - - - +
692A ALA* 1.3 78.1 - - + +
694A LEU* 1.3 65.5 + - - +
695A GLY 3.2 0.4 - - - -
696A PRO* 3.3 15.0 - - - +
697A VAL* 5.0 1.9 + - - +
173B ASN* 6.0 0.9 - - - +
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Residues in contact with LEU 694 (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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619A CYS* 4.8 5.8 - - - -
640A VAL* 5.4 1.1 - - + -
642A PHE* 4.5 27.8 - - + -
678A CYS* 4.7 9.0 - - - -
680A MET* 3.2 40.6 - - + -
690A LEU* 2.9 32.5 + - + +
691A THR* 4.3 3.4 - - - +
693A ILE* 1.3 76.0 - - - +
695A GLY* 1.3 65.5 + - - +
697A VAL* 2.9 26.5 + - + +
698A VAL* 3.2 14.1 + - + +
737A MET* 4.6 15.3 - - + -
806A PHE* 5.0 8.7 - - + -
807A MET* 4.6 13.7 - - + -
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Residues in contact with GLY 695 (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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691A THR* 2.9 17.6 + - - +
694A LEU* 1.3 74.3 - - - +
696A PRO* 1.3 69.8 - - - +
698A VAL* 3.0 11.0 + - - +
699A ALA* 2.9 22.7 + - - +
806A PHE* 5.3 5.6 - - - -
172B TRP* 3.5 24.4 - - - -
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Residues in contact with PRO 696 (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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558A SER* 4.2 7.6 - - - +
575A ARG* 3.5 26.5 - - - +
692A ALA 4.1 5.4 - - - +
693A ILE* 3.3 16.8 - - - +
695A GLY* 1.3 87.4 - - - +
697A VAL* 1.3 55.6 + - - +
699A ALA* 3.3 4.5 + - + +
700A GLU* 2.9 35.3 + - - +
169B THR* 4.0 17.2 - - - +
172B TRP* 3.5 34.7 - - + -
173B ASN* 3.9 8.3 - - - +
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Residues in contact with VAL 697 (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 ARG* 4.0 35.0 - - - +
578A TYR* 3.6 32.2 - - + -
642A PHE* 4.1 21.5 - - + -
677A LEU* 4.2 10.8 - - + -
678A CYS* 4.8 7.2 - - + -
693A ILE 5.1 1.3 - - - +
694A LEU* 2.9 20.5 + - + +
696A PRO* 1.3 76.3 - - - +
698A VAL* 1.3 63.9 + - + +
700A GLU* 3.2 9.3 + - - +
701A ARG* 3.0 23.4 + - + +
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Residues in contact with VAL 698 (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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694A LEU* 3.2 14.5 + - + +
695A GLY* 3.0 12.4 + - - +
697A VAL* 1.3 78.7 - - + +
699A ALA* 1.3 59.2 + - - +
701A ARG* 3.3 13.0 + - - +
702A LYS* 2.9 45.5 + - - +
806A PHE* 3.8 37.9 - - + +
807A MET* 4.1 31.4 - - + -
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Residues in contact with ALA 699 (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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543A LYS 5.3 0.3 - - - +
544A ASN* 4.7 15.0 + - - +
695A GLY 2.9 12.2 + - - +
696A PRO* 3.7 10.1 - - + +
698A VAL* 1.3 79.5 - - + +
700A GLU* 1.3 63.4 + - - +
702A LYS* 3.4 7.4 + - - +
703A ALA* 2.9 25.5 + - - +
169B THR* 5.0 3.6 - - + -
172B TRP* 4.5 23.8 - - + +
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Residues in contact with GLU 700 (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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542A LEU* 4.6 2.1 - - - +
545A VAL* 3.2 36.9 - - - +
575A ARG* 5.7 3.8 - - - +
577A ARG* 4.7 6.3 + - - +
578A TYR* 4.0 27.8 - - + +
579A ASP* 4.7 5.3 - - - -
696A PRO 2.9 19.8 + - - +
697A VAL* 3.2 10.7 + - - +
699A ALA* 1.3 75.9 - - - +
701A ARG* 1.3 63.0 + - - +
703A ALA* 3.1 7.3 + - - +
704A MET* 2.9 38.2 + - + +
169B THR* 2.7 33.0 + - + +
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Residues in contact with ARG 701 (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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578A TYR* 4.8 14.1 - - + -
617A GLU* 2.3 48.8 + - - +
642A PHE* 5.2 1.6 - - - -
697A VAL* 3.0 16.0 + - + +
698A VAL* 3.8 11.6 + - - +
700A GLU* 1.3 76.9 - - - +
702A LYS* 1.3 65.9 + - - +
704A MET* 3.0 20.8 + - - +
705A MET* 3.4 32.3 + - - +
724A PHE* 3.6 41.8 + - + +
807A MET* 3.8 30.9 - - - +
808A GLU* 4.1 18.2 + - - +
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Residues in contact with LYS 702 (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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698A VAL* 2.9 34.7 + - - +
699A ALA* 3.9 6.7 - - - +
701A ARG* 1.3 87.0 - - - +
703A ALA* 1.3 59.3 + - - +
705A MET* 4.4 19.1 + - + +
706A GLU* 4.2 12.6 - - - +
772A HIS* 5.0 10.9 + - - -
806A PHE 4.7 8.2 + - - -
808A GLU* 5.1 15.2 + - - +
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Residues in contact with ALA 703 (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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542A LEU* 3.2 19.5 - - + +
543A LYS* 3.6 41.2 + - + +
544A ASN* 5.1 0.9 - - - +
545A VAL* 4.9 1.3 - - + -
699A ALA 2.9 18.0 + - - +
700A GLU* 3.6 5.8 - - - +
702A LYS* 1.3 78.4 - - - +
704A MET* 1.3 60.0 + - - +
705A MET 3.5 0.4 - - - -
706A GLU* 3.7 17.7 + - - +
707A SER* 4.2 1.9 + - - -
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Residues in contact with MET 704 (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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538A TRP* 3.6 38.3 + - + +
542A LEU* 4.0 15.3 - - + -
578A TYR* 4.4 9.6 - - + -
579A ASP* 3.6 29.6 - - + +
582A LEU* 4.1 25.1 - - - -
700A GLU* 2.9 20.8 + - - +
701A ARG* 3.0 9.3 + - - +
703A ALA* 1.3 74.9 - - - +
705A MET* 1.3 62.9 + - - +
706A GLU 3.0 6.5 + - - -
707A SER* 3.6 15.9 + - - +
722A PHE* 4.8 13.9 - - + +
724A PHE* 4.3 16.6 - - + -
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Residues in contact with MET 705 (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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701A ARG* 3.4 26.4 + - - +
702A LYS* 4.4 23.5 + - + +
703A ALA 3.5 0.6 - - - -
704A MET* 1.3 75.5 - - - +
706A GLU* 1.3 68.5 + - - +
707A SER 4.4 2.3 - - - +
721A ARG* 4.4 14.0 + - - -
722A PHE* 4.6 15.4 - - - +
723A PHE* 6.0 0.4 - - - -
724A PHE* 3.9 27.8 - - + +
808A GLU* 4.3 23.1 - - - +
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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