Contacts of the helix formed by residues 705 - 718 (chain A) in PDB entry 2XRG
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 705 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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674A GLN* 3.5 29.2 - - + -
675A MET* 3.7 19.9 - - + +
704A MET* 1.3 76.1 - - - +
706A PRO* 1.4 71.7 - - + +
707A ALA 4.2 3.4 - - - +
708A PHE* 3.2 12.3 + - + +
709A LYS* 3.3 11.4 + - - +
754A GLN* 3.1 27.5 + - - -
763A VAL* 4.8 2.0 - - + +
797A HIS* 3.2 54.3 + + - +
798A ARG 3.9 8.5 - - - +
799A PRO* 3.7 47.7 - - + +
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Residues in contact with PRO 706 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
674A GLN 3.5 22.2 - - - +
675A MET 5.3 0.4 - - - -
676A SER* 4.3 13.7 - - - -
704A MET 3.9 2.2 - - - +
705A TYR* 1.4 84.0 - - + +
707A ALA* 1.4 59.1 + - + +
709A LYS* 3.4 27.1 + - + +
710A ARG* 4.1 8.7 + - - +
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Residues in contact with ALA 707 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
705A TYR 3.2 0.4 - - - -
706A PRO* 1.4 76.6 - - - +
708A PHE* 1.4 64.8 + - - +
709A LYS 3.6 0.2 + - - -
710A ARG* 3.7 16.7 + - - +
711A VAL* 4.5 0.7 + - - +
798A ARG 4.5 0.4 - - - +
799A PRO* 3.4 34.3 - - + +
800A ASP* 4.0 10.3 - - - +
801A ASN* 3.0 29.2 + - - +
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Residues in contact with PHE 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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704A MET* 3.8 29.8 - - + -
705A TYR* 3.2 9.9 + - + +
707A ALA* 1.4 75.4 - - - +
709A LYS* 1.4 64.5 + - - +
710A ARG 3.2 0.7 - - - -
711A VAL* 3.1 27.8 + - + +
712A TRP* 3.2 40.0 + + + -
767A TYR* 4.0 31.0 - + + -
795A LEU* 4.3 15.5 - - + -
796A PRO 3.3 31.4 - - - -
797A HIS* 4.1 17.5 - + + -
798A ARG* 4.0 15.9 + - + +
801A ASN* 5.2 3.8 - - - -
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Residues in contact with LYS 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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676A SER* 3.8 20.9 - - - +
677A TYR 3.3 22.7 - - - +
678A GLY* 5.2 2.2 - - - -
704A MET* 4.3 17.0 - - + +
705A TYR 3.3 10.8 + - - +
706A PRO* 3.4 22.7 - - + +
707A ALA 3.3 0.4 - - - -
708A PHE* 1.4 77.4 - - - +
710A ARG* 1.4 55.3 + - - +
712A TRP* 4.6 5.6 - - - +
713A ALA* 2.9 38.5 + - - +
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Residues in contact with ARG 710 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
706A PRO 4.5 7.0 - - - +
707A ALA* 3.7 18.6 + - - +
709A LYS* 1.4 76.7 - - - +
711A VAL* 1.4 60.1 + - - +
713A ALA* 4.5 2.3 - - - +
714A TYR* 3.6 23.2 + - - +
801A ASN* 4.4 11.1 - - - +
807A SER* 2.8 32.5 + - - -
808A SER* 4.8 3.0 + - - +
809A GLU 3.7 10.3 + - - -
810A ASP* 5.5 0.2 - - - +
811A GLU* 2.9 39.6 + - - +
814A TRP* 3.5 22.5 - - + -
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Residues in contact with VAL 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 ALA 4.9 0.9 - - - +
708A PHE* 3.1 22.3 + - + +
710A ARG* 1.4 73.6 - - - +
712A TRP* 1.4 64.8 + - - +
714A TYR* 3.5 4.5 + - - +
715A PHE* 3.3 22.1 + - + +
795A LEU* 4.5 22.9 - - + -
801A ASN* 4.1 15.7 - - - +
814A TRP* 3.7 31.2 - - + -
815A VAL* 4.2 20.4 - - + +
818A LEU* 4.2 21.1 - - + -
819A MET* 5.3 3.4 - - - -
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Residues in contact with TRP 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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678A GLY* 5.8 0.2 - - - -
679A PHE 3.5 12.6 + - - -
680A LEU* 4.6 15.0 - - + -
704A MET* 3.6 31.0 - - + +
708A PHE* 3.2 38.3 + + + +
709A LYS* 4.3 3.8 - - - +
711A VAL* 1.4 76.2 - - - +
713A ALA* 1.4 61.4 + - - +
715A PHE* 3.6 31.1 + + + +
716A GLN* 3.2 60.8 + - + +
734A SER* 4.4 24.9 - - - -
767A TYR* 4.5 18.8 - + + -
768A TYR 4.5 7.6 - - - -
769A SER* 4.8 4.7 - - - -
795A LEU* 4.5 16.8 - - + -
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Residues in contact with ALA 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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684A TYR* 4.3 18.4 - - - +
709A LYS* 2.9 22.2 + - + +
710A ARG* 4.5 3.1 - - - +
712A TRP* 1.4 75.9 - - - +
714A TYR* 1.4 58.4 + - - +
716A GLN* 3.4 5.6 + - - +
717A ARG* 2.9 35.5 + - + +
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Residues in contact with TYR 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 ARG 3.6 17.0 + - - +
711A VAL 3.5 4.6 + - - +
712A TRP 3.5 0.2 - - - -
713A ALA* 1.4 77.6 - - - +
715A PHE* 1.3 56.0 + - - +
717A ARG* 4.9 7.2 - - - +
718A VAL* 2.9 61.6 + - + +
719A LEU* 3.4 35.1 + - + +
810A ASP* 5.6 1.3 - - - -
811A GLU* 3.7 26.7 - - + -
812A SER* 3.4 36.7 - - - -
815A VAL* 3.7 24.2 - - + -
816A GLU* 5.2 4.0 - - + -
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Residues in contact with PHE 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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633A TYR* 5.2 4.9 - - - -
711A VAL* 3.3 14.4 + - + +
712A TRP* 3.8 32.3 - + + +
713A ALA 3.3 0.2 - - - -
714A TYR* 1.3 78.5 - - - +
716A GLN* 1.3 72.8 + - + +
719A LEU* 3.3 17.8 + - + +
720A VAL* 3.0 52.7 + - + +
723A TYR* 4.2 16.6 - + - -
732A VAL* 5.1 3.6 - - + -
734A SER* 6.1 0.2 - - - -
769A SER* 4.0 24.7 - - - -
771A ILE* 4.3 15.5 - - + -
793A PHE* 5.0 3.4 - + - -
795A LEU* 6.0 1.8 - - + -
815A VAL* 5.7 0.2 - - + -
819A MET* 3.7 34.5 - - + -
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Residues in contact with GLN 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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633A TYR* 4.7 3.4 + - - +
679A PHE* 3.2 25.7 + - - +
680A LEU 3.2 18.6 + - - -
682A PRO* 3.6 36.1 - - + +
683A PRO* 4.7 2.8 - - - +
684A TYR* 4.4 12.3 - - + -
685A LEU* 3.4 27.7 - - - +
712A TRP* 3.2 40.1 + - - +
713A ALA* 3.4 4.9 + - - +
715A PHE* 1.3 89.1 - - + +
717A ARG* 1.3 60.2 + - - +
720A VAL* 4.2 9.3 - - + +
721A LYS 5.4 0.5 + - - -
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Residues in contact with ARG 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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641A VAL* 3.9 29.8 - - + +
684A TYR* 4.0 42.6 - - + -
713A ALA* 2.9 18.0 + - - +
714A TYR* 5.1 7.1 - - - +
716A GLN* 1.3 77.7 - - - +
718A VAL* 1.4 82.9 + - + +
721A LYS* 5.1 2.1 - - - +
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Residues in contact with VAL 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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714A TYR* 2.9 52.3 + - + +
717A ARG* 1.4 112.0 - - + +
719A LEU* 1.3 66.4 + - + +
720A VAL 3.6 1.5 + - - -
721A LYS* 3.9 6.2 + - - +
722A LYS* 3.6 20.6 + - + +
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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