Contacts of the helix formed by residues 671 - 689 (chain A) in PDB entry 5A7R
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 ARG 671 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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669A SER* 3.0 10.8 + - - +
670A SER* 1.3 116.8 + - - +
672A LYS* 1.3 64.3 + - - +
673A PRO 3.3 1.1 - - - -
674A GLU* 3.0 11.9 + - - +
675A LYS* 3.0 25.6 + - + +
752A LEU* 3.6 23.1 - - + -
796A ALA 3.7 11.4 - - - +
797A GLU* 3.3 32.2 + - - +
798A THR* 3.7 8.7 - - - +
799A TYR 2.8 35.9 + - - -
800A ARG* 3.8 13.5 - - - +
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Residues in contact with LYS 672 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
572A ALA* 4.0 24.7 - - + -
663A ARG 3.5 21.7 + - - -
664A LEU* 3.4 22.2 - - + +
666A GLU* 3.8 15.4 + - - +
669A SER* 3.2 28.2 + - - +
671A ARG* 1.3 76.2 - - - +
673A PRO* 1.3 69.5 - - + +
674A GLU 3.2 0.2 + - - -
675A LYS* 3.2 14.2 + - + +
676A LEU* 2.9 30.3 + - + +
749A SER 3.5 29.4 + - - +
750A ALA* 4.3 10.3 - - - +
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Residues in contact with PRO 673 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
572A ALA 6.1 0.7 - - - +
575A ASP* 6.5 0.2 - - + -
576A PHE* 3.6 28.3 - - + +
580A VAL* 3.9 31.2 - - + -
669A SER 3.6 7.2 - - - +
670A SER* 3.4 20.4 - - - +
672A LYS* 1.3 95.0 - - + +
674A GLU* 1.3 62.5 + - - +
676A LEU* 4.4 0.7 - - + -
677A LYS* 3.0 36.0 + - - +
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Residues in contact with GLU 674 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
670A SER 4.3 9.5 - - - +
671A ARG* 3.0 19.6 + - - +
673A PRO* 1.3 81.0 - - - +
675A LYS* 1.3 63.0 + - - +
677A LYS* 3.5 15.5 + - - +
678A THR* 2.8 29.4 + - - -
799A TYR* 3.4 38.8 - - + +
800A ARG* 3.5 32.1 + - - +
801A TRP* 3.0 28.1 + - - +
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Residues in contact with LYS 675 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
664A LEU* 4.0 16.8 - - + -
671A ARG* 3.0 17.8 + - + +
672A LYS* 3.2 15.2 + - + +
674A GLU* 1.3 76.8 - - - +
676A LEU* 1.3 57.1 + - + +
678A THR* 3.2 8.8 + - - -
679A LEU* 3.0 34.2 + - + +
746A GLY 3.3 4.2 + - - -
747A VAL* 2.8 24.1 + - - +
749A SER 2.8 30.5 + - - +
750A ALA 4.5 2.7 - - - -
751A GLY 2.9 30.6 + - - +
752A LEU* 4.0 20.9 - - + -
760A LEU* 3.9 23.5 - - + +
799A TYR* 4.6 0.6 - - + -
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Residues in contact with LEU 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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572A ALA 4.2 11.7 - - - +
573A LEU* 4.9 7.0 - - + -
576A PHE* 3.8 42.2 - - + -
638A PHE* 5.1 3.4 - - + -
664A LEU* 4.6 29.6 - - + +
665A PHE* 4.5 20.6 - - + -
672A LYS* 2.9 25.0 + - + +
673A PRO 3.9 3.1 - - - +
675A LYS* 1.3 73.6 - - + +
677A LYS* 1.3 60.0 + - - +
679A LEU* 3.3 7.4 + - + +
680A PHE* 2.8 52.9 + - + -
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Residues in contact with LYS 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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576A PHE* 3.8 20.2 - - + -
580A VAL* 4.3 15.8 + - - +
581A LEU* 4.4 13.8 - - - +
585A GLU* 5.2 9.1 + - - -
673A PRO* 3.0 23.5 + - - +
674A GLU* 3.8 22.9 + - - +
676A LEU* 1.3 76.0 - - - +
678A THR* 1.3 57.2 + - - +
680A PHE* 3.9 0.9 - - - +
681A CYS* 3.0 29.3 + - - +
800A ARG* 5.2 8.1 - - - +
801A TRP* 4.1 29.8 + - + -
1982A GOL 3.9 18.1 + - - +
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Residues in contact with THR 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 GLU 2.8 19.3 + - - -
675A LYS* 3.5 9.0 - - - -
676A LEU 3.2 0.2 - - - -
677A LYS* 1.3 76.6 - - - +
679A LEU* 1.3 61.1 + - - +
681A CYS* 3.4 12.3 + - - +
682A TYR* 3.4 11.6 + - - +
760A LEU* 3.4 38.1 - - + +
761A ILE* 4.3 0.9 - - + +
790A SER* 3.6 21.5 + - - +
799A TYR* 2.8 27.8 + - - +
801A TRP* 3.5 17.8 - - - +
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Residues in contact with LEU 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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638A PHE* 6.2 2.2 - - + -
661A PHE* 4.2 15.5 - - + -
664A LEU* 3.5 32.1 - - + -
675A LYS 3.0 21.0 + - - +
676A LEU* 4.0 8.3 - - + +
678A THR* 1.3 77.5 - - - +
680A PHE* 1.3 58.4 + - + +
682A TYR* 3.2 8.2 + - + +
683A PHE* 2.9 45.4 + - + -
760A LEU* 4.1 22.2 - - + +
763A PRO* 4.2 18.8 - - + -
766A ILE* 4.0 26.2 - - + -
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Residues in contact with PHE 680 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
573A LEU* 5.4 5.8 - - + -
576A PHE* 3.8 28.7 - + - -
589A LEU* 3.7 31.0 - - + -
593A ILE* 4.2 15.5 - - + +
594A LEU* 4.4 3.8 - - + -
597A MET* 3.9 18.4 - - + -
638A PHE* 3.7 35.9 - + - -
676A LEU* 2.8 46.7 + - + +
677A LYS 4.2 0.2 - - - +
679A LEU* 1.3 70.8 - - + +
681A CYS* 1.3 60.7 + - - +
683A PHE* 4.3 5.8 - + - +
684A ARG* 2.8 33.1 + - - +
1982A GOL 3.8 22.7 - - - +
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Residues in contact with CYS 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 LYS 3.0 14.3 + - - +
678A THR 3.4 10.5 - - - +
679A LEU 3.2 0.2 - - - -
680A PHE* 1.3 76.1 - - - +
682A TYR* 1.3 62.8 + - - +
684A ARG* 3.8 3.2 - - - +
685A ARG* 3.2 31.8 + - - +
789A TYR 3.5 17.7 - - - -
790A SER* 3.5 18.8 - - - +
801A TRP* 3.7 16.2 - - + +
804A SER* 3.8 27.6 - - - -
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Residues in contact with TYR 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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627A GLN 4.6 0.3 + - - -
630A ILE 4.2 0.7 - - - -
631A ALA* 3.3 28.9 + - - +
634A LEU* 3.6 25.2 - - + +
678A THR 3.4 5.1 + - - +
679A LEU* 3.2 10.9 + - + +
681A CYS* 1.3 80.1 - - - +
683A PHE* 1.3 105.2 + + - +
685A ARG* 3.1 4.0 + - - +
686A VAL* 3.0 46.0 + - + +
763A PRO* 3.5 29.8 - - + -
764A GLU* 4.2 15.5 + - + +
789A TYR* 3.7 46.8 - + + +
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Residues in contact with PHE 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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593A ILE* 4.8 2.2 - - + -
597A MET* 3.6 46.7 - - + -
600A ILE* 6.1 0.2 - - + -
631A ALA* 4.5 3.4 - - + -
634A LEU* 3.6 24.5 - - + -
635A ALA* 3.7 26.0 - - + -
638A PHE* 4.1 15.5 - + + -
661A PHE* 4.3 13.0 - + - -
679A LEU* 2.9 38.2 + - + +
680A PHE* 4.1 9.9 - + + +
681A CYS 3.4 0.4 - - - -
682A TYR* 1.3 97.8 - + - +
684A ARG* 1.3 55.8 + - - +
686A VAL* 4.1 6.1 - - + -
687A THR* 2.8 40.6 + - + +
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Residues in contact with ARG 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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588A HIS* 3.8 20.2 + - - +
592A SER* 2.2 41.2 + - - -
593A ILE* 3.9 28.9 - - + +
596A ASP* 3.2 21.8 + - - +
680A PHE 2.8 20.2 + - - +
681A CYS* 3.8 5.4 - - - +
683A PHE* 1.3 76.4 - - - +
685A ARG* 1.3 60.6 + - + +
687A THR* 2.9 30.1 + - - -
688A ALA* 3.0 40.4 + - - +
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Residues in contact with ARG 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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681A CYS* 3.2 21.7 + - - +
682A TYR 3.1 4.3 + - - +
684A ARG* 1.3 81.0 - - + +
686A VAL* 1.3 59.0 + - - +
688A ALA* 3.9 3.6 - - - +
689A ALA* 3.2 29.1 + - - +
787A GLU* 4.2 11.7 + - - -
788A GLN 5.2 0.2 + - - -
789A TYR* 3.2 34.5 + - + +
804A SER* 3.0 27.0 + - - -
805A HIS 2.8 30.0 + - - -
806A GLU* 3.7 23.0 + - - +
807A ASP 5.0 0.2 - - - +
1979A GOL 3.5 32.3 + - - -
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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
----------------------------------------------------------
600A ILE* 4.7 8.5 - - + +
631A ALA* 3.7 22.9 - - + -
682A TYR* 3.0 53.8 + - + +
683A PHE* 3.9 9.2 - - + +
685A ARG* 1.3 76.0 - - - +
687A THR* 1.3 67.3 - - + +
689A ALA 3.5 17.6 - - - +
690A ALA* 3.9 7.3 + - - -
691A PRO* 4.0 21.7 - - + +
764A GLU* 5.1 0.2 - - - +
789A TYR* 3.6 24.7 - - + +
1979A GOL 4.6 1.8 - - - +
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Residues in contact with THR 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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593A ILE* 5.0 1.6 + - - +
596A ASP* 3.8 41.1 - - - +
597A MET* 4.2 11.4 - - + +
600A ILE* 4.1 21.3 - - + -
683A PHE* 2.8 24.5 + - + +
684A ARG* 2.9 25.9 + - - -
686A VAL* 1.3 81.8 - - + +
688A ALA* 1.3 63.9 + - - +
689A ALA 3.4 0.4 - - - -
690A ALA 5.4 0.2 + - - -
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Residues in contact with ALA 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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596A ASP* 5.5 0.9 - - - -
684A ARG* 3.0 37.9 + - - +
685A ARG* 3.9 4.5 - - - +
687A THR* 1.3 79.8 + - - +
689A ALA* 1.3 61.4 + - + +
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Residues in contact with ALA 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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685A ARG 3.2 10.0 + - - +
686A VAL 3.5 6.1 - - - +
687A THR 3.4 0.2 - - - -
688A ALA* 1.3 84.0 - - + +
690A ALA* 1.3 61.8 + - - +
691A PRO* 3.4 1.0 - - - +
1979A GOL 2.7 37.3 + - - +
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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
------------------------------------------------------------
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