Contacts of the helix formed by residues 669 - 688 (chain A) in PDB entry 5ZRV
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 SER 669 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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667A VAL 4.0 2.0 + - - -
668A SER* 1.3 77.4 - - - +
670A ASP* 1.3 65.6 + - - +
671A GLU 3.4 2.5 - - - +
672A ASP* 3.7 7.5 - - - +
673A ILE* 3.0 18.9 + - - -
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Residues in contact with ASP 670 (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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574A LEU 5.7 0.5 - - - +
669A SER* 1.3 69.0 - - - +
671A GLU* 1.3 59.3 + - - +
673A ILE* 3.3 1.6 + - - +
674A GLN* 2.9 26.5 + - - -
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Residues in contact with GLU 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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669A SER 3.4 0.2 - - - -
670A ASP* 1.3 74.2 - - - +
672A ASP* 1.3 57.0 + - - +
674A GLN* 3.5 1.6 + - - +
675A PHE* 3.0 25.8 + - - -
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Residues in contact with ASP 672 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
668A SER* 5.1 4.3 - - - +
669A SER* 3.3 15.7 + - - +
670A ASP 3.2 0.8 - - - -
671A GLU* 1.3 77.0 - - - +
673A ILE* 1.3 56.8 + - - +
675A PHE* 3.4 1.2 + - - -
676A ARG* 2.8 24.9 + - - -
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Residues in contact with ILE 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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668A SER* 5.1 1.8 - - - +
669A SER 3.0 13.7 + - - -
670A ASP* 3.9 1.3 - - - +
672A ASP* 1.3 72.0 - - - +
674A GLN* 1.3 65.8 + - - +
676A ARG* 3.7 2.6 - - - +
677A LEU* 3.0 20.8 + - - -
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Residues in contact with GLN 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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574A LEU 6.1 0.9 - - - -
670A ASP 2.9 16.9 + - - -
671A GLU* 3.8 2.2 - - - +
672A ASP 3.3 0.2 - - - -
673A ILE* 1.3 76.1 - - - +
675A PHE* 1.3 57.1 + - - +
677A LEU* 3.4 0.7 + - - -
678A VAL* 3.0 24.8 + - - -
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Residues in contact with PHE 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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671A GLU 3.0 15.8 + - - -
672A ASP 3.7 2.7 - - - -
674A GLN* 1.3 75.0 - - - +
676A ARG* 1.3 56.3 + - - +
678A VAL* 4.4 1.8 - - - +
679A THR* 2.8 27.6 + - - +
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Residues in contact with ARG 676 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
672A ASP 2.8 16.0 + - - -
673A ILE* 3.2 4.7 + - - +
674A GLN 3.2 0.6 - - - -
675A PHE* 1.3 76.6 - - - +
677A LEU* 1.3 55.7 + - - +
679A THR 3.9 0.2 - - - -
680A ARG* 3.0 26.3 + - - -
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Residues in contact with LEU 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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553A PRO 5.8 0.2 - - - +
554A MET* 5.7 4.7 - - - +
673A ILE 3.0 15.7 + - - -
674A GLN 3.9 1.1 - - - -
676A ARG* 1.3 74.6 - - - +
678A VAL* 1.3 57.2 + - - +
680A ARG* 3.9 0.7 - - - +
681A PHE* 3.0 25.3 + - - -
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Residues in contact with VAL 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 GLN 3.0 16.0 + - - -
675A PHE* 4.0 2.0 - - - +
677A LEU* 1.3 78.1 - - - +
679A THR* 1.3 56.0 + - - +
681A PHE* 3.2 2.1 + - - +
682A VAL* 2.8 26.7 + - - -
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Residues in contact with THR 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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675A PHE* 2.8 22.6 + - - +
676A ARG* 4.0 0.4 - - - +
678A VAL* 1.3 68.6 - - - +
680A ARG* 1.3 60.6 + - - +
682A VAL* 3.5 1.9 + - - +
683A ASN* 2.9 23.9 + - - -
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Residues in contact with ARG 680 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
553A PRO 5.3 7.2 - - - -
676A ARG 3.0 17.2 + - - -
677A LEU 4.0 0.9 - - - -
679A THR* 1.3 73.5 - - - +
681A PHE* 1.3 60.1 + - - +
683A ASN* 3.1 2.4 + - - +
684A GLU* 3.0 25.5 + - - -
744A PHE* 6.4 2.0 - - - +
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Residues in contact with PHE 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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550A CYS* 5.5 7.8 - - - +
553A PRO 5.3 5.2 + - - -
554A MET* 5.9 3.8 - - - +
677A LEU 3.0 15.8 + - - -
678A VAL* 3.2 4.5 + - - +
680A ARG* 1.3 75.9 - - - +
682A VAL* 1.3 55.6 + - - +
684A GLU* 3.4 2.6 + - - +
685A ALA* 2.9 22.7 + - - -
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Residues in contact with VAL 682 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
678A VAL 2.8 15.0 + - - -
679A THR* 3.8 2.2 - - - +
681A PHE* 1.3 74.4 - - - +
683A ASN* 1.3 60.4 + - - +
685A ALA* 3.5 4.3 - - - +
686A VAL* 2.8 25.1 + - - -
717A PRO* 4.8 20.7 - - - +
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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
----------------------------------------------------------
679A THR 2.9 16.8 + - - -
680A ARG* 3.1 5.1 + - - +
682A VAL* 1.3 75.9 - - - +
684A GLU* 1.3 56.4 + - - +
686A VAL* 3.5 1.4 + - - +
687A MET* 2.9 23.0 + - - -
746A PRO* 6.2 3.1 - - - -
747A CYS* 5.6 7.6 + - - +
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Residues in contact with GLU 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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550A CYS* 6.1 7.9 - - - +
680A ARG 3.0 13.5 + - - -
681A PHE 3.8 2.9 - - - -
683A ASN* 1.3 78.2 - - - +
685A ALA* 1.3 56.5 + - - +
687A MET* 3.0 16.7 + - - +
688A CYS* 3.3 9.7 + - - -
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Residues in contact with ALA 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 PHE 2.9 16.3 + - - -
682A VAL* 3.3 5.8 + - - +
684A GLU* 1.3 75.0 - - - +
686A VAL* 1.3 55.8 + - - +
688A CYS* 4.2 9.9 + - - +
717A PRO* 5.6 7.6 - - - -
718A PHE* 5.4 6.6 + - - -
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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
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682A VAL 2.8 15.0 + - - -
683A ASN 3.7 1.8 - - - -
685A ALA* 1.3 75.6 - - - +
687A MET* 1.3 65.5 + - - +
688A CYS 3.1 10.6 - - - +
690A GLN* 4.6 3.6 + - - -
747A CYS* 6.5 1.1 - - - -
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Residues in contact with MET 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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683A ASN 2.9 16.3 + - - -
684A GLU* 3.0 7.2 + - - +
686A VAL* 1.3 77.6 - - - +
688A CYS* 1.3 61.2 + - - +
689A LEU 3.6 0.2 + - - -
690A GLN* 3.3 15.6 + - - -
691A GLU 4.1 3.5 + - - -
747A CYS* 6.2 3.6 - - - +
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Residues in contact with CYS 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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684A GLU 3.3 10.4 + - - -
685A ALA* 4.2 7.0 - - - +
686A VAL* 3.1 15.7 - - - +
687A MET* 1.3 76.0 - - - +
689A LEU* 1.3 57.0 + - - +
690A GLN 3.1 4.9 + - - -
693A ILE* 5.6 1.8 - - - +
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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