Contacts of the helix formed by residues 706 - 719 (chain A) in PDB entry 4ZGA
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 TYR 706 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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675A GLN* 4.1 26.9 - - + -
676A MET* 3.3 26.9 - - + -
677A SER 4.6 0.7 - - - +
705A MET* 1.3 74.8 - - - +
707A PRO* 1.3 74.0 - - + +
708A ALA 4.0 4.7 - - - +
709A PHE* 3.1 6.8 + - + +
710A LYS* 3.0 17.5 + - - +
755A GLN* 3.2 25.0 + - - -
764A VAL* 5.1 3.3 - - + +
798A HIS* 3.2 41.8 + + - +
799A ARG 3.5 25.6 - - - +
800A PRO* 3.6 38.7 - - + +
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Residues in contact with PRO 707 (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 GLN 3.4 22.4 - - - +
677A SER* 4.2 12.6 - - - -
705A MET 4.1 2.5 - - - +
706A TYR* 1.3 86.9 - - + +
708A ALA* 1.3 61.7 + - - +
709A PHE 3.2 0.3 + - - -
710A LYS* 3.3 22.3 + - + +
711A ARG* 3.4 17.0 + - - +
800A PRO 5.6 1.3 - - - +
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Residues in contact with ALA 708 (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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706A TYR* 3.1 1.8 - - - +
707A PRO* 1.3 80.2 - - - +
709A PHE* 1.3 62.6 + - - +
711A ARG* 3.9 13.0 - - - +
712A VAL* 4.1 2.9 - - - +
799A ARG 3.8 3.8 - - - +
800A PRO 3.1 32.9 + - - +
801A ASP* 3.7 9.4 - - - -
802A ASN* 2.8 40.1 + - - +
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Residues in contact with PHE 709 (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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705A MET* 3.7 22.0 - - + -
706A TYR* 3.1 13.3 + - + +
708A ALA* 1.3 75.6 - - - +
710A LYS* 1.3 54.3 + - - +
711A ARG 3.1 2.0 - - - -
712A VAL* 2.5 40.7 + - + +
713A TRP* 3.0 50.2 + + + -
768A TYR* 3.9 27.8 - + + -
796A LEU* 4.0 26.7 - - + -
797A PRO 3.9 23.8 - - - -
798A HIS* 3.9 27.1 - + + -
799A ARG 4.3 4.6 + - - +
802A ASN* 5.4 0.4 - - - -
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Residues in contact with LYS 710 (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 SER* 3.1 36.1 + - - +
678A TYR* 3.4 23.5 + - - +
679A GLY* 5.0 2.2 - - - -
705A MET* 3.6 20.6 - - + +
706A TYR 3.0 14.9 + - - +
707A PRO* 3.3 13.2 + - + +
709A PHE* 1.3 74.1 - - - +
711A ARG* 1.3 55.5 + - - +
713A TRP* 4.3 8.1 - - - -
714A ASN* 2.7 54.7 + - - +
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Residues in contact with ARG 711 (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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707A PRO 3.4 11.5 + - - +
708A ALA* 3.9 14.6 - - - +
709A PHE 2.9 0.4 + - - -
710A LYS* 1.3 76.4 - - - +
712A VAL* 1.3 66.3 + - + +
714A ASN* 4.0 4.3 - - - +
715A TYR* 3.2 23.0 + - - +
802A ASN* 4.2 11.4 - - - +
808A SER* 3.0 32.3 + - - -
809A SER 4.1 4.2 + - - -
810A GLU 3.1 18.6 + - - -
812A GLU* 2.7 38.8 + - + +
815A TRP* 3.8 16.1 - - + -
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Residues in contact with VAL 712 (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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708A ALA 4.1 7.9 - - - +
709A PHE* 2.5 27.7 + - + +
711A ARG* 1.3 71.5 - - - +
713A TRP* 1.3 65.9 + - - +
715A TYR* 3.2 4.9 + - - +
716A PHE* 3.1 20.9 + - + +
796A LEU* 4.4 22.4 - - + -
802A ASN* 4.2 5.2 - - - +
815A TRP* 3.5 36.8 - - + -
816A VAL* 4.2 21.8 - - + +
819A LEU* 4.6 17.5 - - + -
820A MET* 5.0 2.7 - - + -
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Residues in contact with TRP 713 (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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679A GLY* 5.3 0.4 - - - -
680A PHE 3.0 23.1 + - - -
681A LEU* 4.2 15.0 - - + -
705A MET* 3.4 30.0 - - + +
709A PHE* 3.0 36.0 + + + -
710A LYS* 3.8 4.9 - - - +
712A VAL* 1.3 76.8 - - - +
714A ASN* 1.3 59.9 + - - +
716A PHE* 3.1 24.2 + + - +
717A GLN* 2.9 65.1 + - + +
735A SER* 3.9 18.8 - - - -
768A TYR* 4.3 18.6 - + + -
769A TYR 4.2 3.8 - - - -
770A SER* 3.8 20.2 - - - -
794A PHE* 4.3 11.7 - + - -
796A LEU* 4.8 4.5 - - + -
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Residues in contact with ASN 714 (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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710A LYS* 2.7 50.2 + - - +
711A ARG* 4.0 4.7 - - - +
713A TRP* 1.3 75.0 - - - +
715A TYR* 1.3 57.7 + - - +
717A GLN* 4.8 9.6 - - - +
718A ARG* 2.8 77.7 + - - +
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Residues in contact with TYR 715 (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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711A ARG 3.2 16.0 + - - +
712A VAL 3.2 4.7 + - - +
714A ASN* 1.3 75.8 - - - +
716A PHE* 1.3 65.5 + - - +
719A VAL* 3.0 57.7 + - + +
720A LEU* 3.0 44.5 + - + +
811A ASP* 5.1 2.7 - - - -
812A GLU* 3.6 26.2 - - + -
813A SER* 3.2 39.1 + - - -
816A VAL* 3.7 17.3 - - + -
817A GLU* 5.0 6.0 + - + -
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Residues in contact with PHE 716 (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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634A TYR* 5.0 2.0 - - - -
712A VAL* 3.1 14.0 + - + +
713A TRP* 3.5 32.1 - + + +
715A TYR* 1.3 79.6 - - - +
717A GLN* 1.3 70.6 + - + +
720A LEU* 3.9 14.8 - - + -
721A VAL* 3.0 55.9 + - + +
724A TYR* 4.2 4.7 - + - -
733A VAL* 4.5 7.9 - - + -
735A SER* 4.3 3.8 - - - -
770A SER* 3.5 24.2 - - - -
772A ILE* 3.8 17.3 - - + -
794A PHE* 3.6 26.0 - + - -
796A LEU* 5.7 1.3 - - + -
820A MET* 3.8 26.5 - - + -
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Residues in contact with GLN 717 (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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634A TYR* 4.8 3.2 + - - +
680A PHE* 3.1 9.3 + - - +
681A LEU 2.6 31.7 + - - -
683A PRO* 3.5 34.0 - - + +
684A PRO* 5.4 1.0 - - - +
686A LEU* 3.5 27.8 - - - +
713A TRP* 2.9 52.6 + - + +
714A ASN* 4.2 8.5 - - - +
716A PHE* 1.3 93.0 - - + +
718A ARG* 1.3 61.7 + - + +
721A VAL* 3.9 10.8 - - - +
722A LYS 5.2 0.3 + - - -
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Residues in contact with ARG 718 (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 PRO* 5.6 1.1 - - + +
684A PRO* 5.7 6.7 - - - +
685A TYR* 3.3 69.1 + - + +
686A LEU* 5.6 0.4 - - - -
714A ASN* 2.8 53.1 + - - +
717A GLN* 1.3 83.9 - - + +
719A VAL* 1.3 65.5 + - + +
722A LYS* 5.3 5.3 - - - +
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Residues in contact with VAL 719 (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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715A TYR* 3.0 53.7 + - + +
718A ARG* 1.3 83.8 - - + +
720A LEU* 1.3 70.2 + - + +
721A VAL 3.3 2.5 + - - -
722A LYS* 3.5 6.9 + - - +
723A LYS* 3.3 23.3 + - + +
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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
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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