Contacts of the helix formed by residues 708 - 725 (chain A) in PDB entry 2P8Q
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 708 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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664A TYR* 5.6 0.7 - - - -
668A LEU* 3.7 18.4 - - - +
706A HIS* 3.0 23.1 + - - +
707A ARG* 1.3 89.5 + - - +
709A VAL* 1.3 62.2 + - - +
710A LYS 3.5 0.7 - - - -
711A PRO* 3.4 18.4 - - - +
712A GLN* 3.6 14.2 - - - +
757A TYR* 4.5 2.6 - - - -
760A GLU* 4.1 16.8 + - - +
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Residues in contact with VAL 709 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
661A TYR 5.7 0.2 - - - +
664A TYR* 3.9 26.2 - - + +
667A CYS* 4.1 20.6 - - - -
668A LEU* 3.5 24.2 - - + -
671A VAL* 4.7 1.6 - - + -
699A ASN* 3.9 16.4 - - - +
705A VAL* 3.8 24.5 - - + -
706A HIS* 4.3 2.7 - - + -
707A ARG 3.2 0.8 + - - -
708A SER* 1.3 78.4 - - - +
710A LYS* 1.3 66.8 + - - +
712A GLN* 3.1 4.7 + - - +
713A ILE* 2.9 37.5 + - + +
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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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700A LEU* 3.6 34.2 + - + -
702A ASN* 4.7 17.1 + - - +
703A GLU* 5.7 2.8 + - - -
705A VAL* 5.6 0.2 - - - +
706A HIS 4.5 2.1 + - - +
707A ARG 3.5 8.5 + - - +
709A VAL* 1.3 77.1 - - - +
711A PRO* 1.3 72.8 - - + +
713A ILE* 2.9 5.6 + - - +
714A LEU* 2.8 31.5 + - + +
738A THR* 5.0 11.5 + - - +
741A GLN* 5.5 8.5 - - - +
742A ALA* 4.2 29.7 - - - +
757A TYR* 4.4 5.6 - - - +
761A LEU* 4.3 12.1 - - + +
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Residues in contact with PRO 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 ARG 3.3 13.0 - - - +
708A SER* 3.4 18.2 - - - +
710A LYS* 1.3 94.7 - - + +
712A GLN* 1.3 58.2 + - + +
714A LEU* 3.3 1.9 + - + -
715A SER* 2.9 23.9 + - - -
757A TYR* 4.1 13.5 - - + +
760A GLU* 4.0 19.7 - - + +
761A LEU* 3.8 23.3 - - + -
764A SER* 2.9 38.5 + - - +
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Residues in contact with GLN 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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668A LEU* 4.2 20.0 - - + +
671A VAL* 3.8 15.8 - - + +
672A GLY* 5.9 3.6 - - - -
708A SER 3.6 16.6 - - - +
709A VAL 3.1 7.5 + - - +
710A LYS 3.1 0.6 - - - -
711A PRO* 1.3 77.7 - - + +
713A ILE* 1.3 62.2 + - - +
715A SER* 3.3 12.4 + - - -
716A VAL* 2.9 35.2 + - - +
760A GLU* 4.8 11.6 - - - +
764A SER* 5.0 3.5 + - - -
48B LEU* 4.1 32.2 - - + +
52B LYS* 4.6 15.2 + - - +
55B ARG* 4.7 9.3 - - - +
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Residues in contact with ILE 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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667A CYS* 5.4 0.9 - - - -
671A VAL* 3.1 35.9 - - + -
696A LEU* 3.2 46.0 - - + +
699A ASN* 5.3 6.7 - - + +
700A LEU* 4.1 21.8 - - + -
709A VAL* 2.9 34.0 + - + +
710A LYS* 3.4 7.9 - - - +
712A GLN* 1.3 73.1 - - - +
714A LEU* 1.3 66.8 + - - +
716A VAL* 3.3 4.2 + - - +
717A PHE* 3.0 34.3 + - + -
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Residues in contact with LEU 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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700A LEU* 4.9 2.9 - - + -
710A LYS* 2.8 25.3 + - + +
711A PRO* 3.5 7.2 - - + +
713A ILE* 1.3 77.3 - - - +
715A SER* 1.3 65.2 + - - +
717A PHE* 3.0 33.8 + - + +
718A GLY 3.4 3.3 + - - -
738A THR* 4.1 24.5 - - + -
739A LEU* 4.0 20.9 - - + -
742A ALA* 4.1 9.4 - - + -
761A LEU* 3.8 28.9 - - + -
764A SER* 4.3 11.0 - - - +
765A CYS* 3.9 21.5 - - - -
768A ALA* 3.6 10.2 - - - +
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Residues in contact with SER 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 PRO 2.9 16.0 + - - -
712A GLN* 3.5 15.5 + - - -
714A LEU* 1.3 76.3 - - - +
716A VAL* 1.3 62.0 + - - +
718A GLY* 3.0 13.7 + - - -
719A ASP* 3.4 14.7 + - - +
764A SER* 3.7 16.9 + - - -
767A GLU* 2.8 30.3 + - - +
768A ALA* 5.0 1.2 - - - +
52B LYS* 5.3 1.2 - - - -
55B ARG* 3.6 25.3 + - - -
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Residues in contact with VAL 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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671A VAL* 3.3 33.0 - - + +
672A GLY* 4.7 2.5 - - - +
674A VAL* 3.5 32.5 - - + -
675A GLY* 4.1 11.4 - - - +
696A LEU* 4.6 9.4 - - + -
712A GLN* 2.9 22.8 + - + +
713A ILE* 3.7 5.4 - - - +
714A LEU 3.2 0.2 - - - -
715A SER* 1.3 74.5 - - - +
717A PHE* 1.3 66.5 + - - +
719A ASP* 3.0 12.6 + - - +
720A ILE* 2.8 29.0 + - + +
55B ARG* 5.1 3.1 - - - +
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Residues in contact with PHE 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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693A MET* 3.2 35.4 - - + -
696A LEU* 3.7 22.4 - - + -
697A LEU* 3.8 24.0 - - + -
700A LEU* 3.7 25.8 - - + -
713A ILE* 3.0 24.6 + - + -
714A LEU* 3.0 25.0 + - + +
716A VAL* 1.3 76.6 - - - +
718A GLY* 1.3 58.4 - - - +
720A ILE* 3.4 4.6 + - - +
721A ALA* 2.9 28.8 + - - +
728A PHE* 4.0 6.5 - + + -
735A VAL* 4.0 34.3 - - + -
738A THR* 4.9 3.8 - - + -
739A LEU* 5.7 1.1 - - + -
768A ALA* 5.1 4.0 - - + -
772A ILE* 5.7 2.2 - - + -
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Residues in contact with GLY 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 LEU 3.4 3.0 + - - -
715A SER 3.0 9.7 + - - -
717A PHE* 1.3 77.0 - - - +
719A ASP* 1.3 60.4 + - - +
721A ALA* 3.2 5.9 + - - +
722A LEU* 2.9 33.1 + - - +
767A GLU 4.2 2.9 - - - -
768A ALA* 3.9 25.7 - - - +
771A GLY* 3.5 10.9 - - - -
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Residues in contact with ASP 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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675A GLY* 3.6 18.9 - - - +
678A CYS* 4.0 19.7 - - + +
679A ARG* 3.6 7.3 + - + +
715A SER 3.4 5.2 + - - +
716A VAL* 3.0 12.3 + - - +
718A GLY* 1.3 72.3 - - - +
720A ILE* 1.3 69.6 + - - +
722A LEU* 3.0 15.6 + - - +
723A ALA* 2.9 23.7 + - - +
55B ARG* 2.7 57.3 + - - +
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Residues in contact with ILE 720 (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 VAL* 3.6 20.6 - - + -
678A CYS* 3.1 31.6 - - - -
685A ILE* 4.9 4.3 - - + -
689A CYS* 4.0 26.0 - - - -
692A VAL* 4.9 7.2 - - + -
693A MET* 3.2 36.1 - - + -
696A LEU* 5.0 2.9 - - + -
716A VAL* 2.8 24.8 + - + +
717A PHE* 3.6 7.4 - - - +
719A ASP* 1.3 75.3 - - - +
721A ALA* 1.3 64.0 + - - +
723A ALA* 3.2 2.5 + - - +
724A ILE* 3.0 26.5 + - + +
728A PHE* 4.2 8.1 - - + -
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Residues in contact with ALA 721 (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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717A PHE 2.9 14.9 + - - +
718A GLY 3.5 5.2 - - - +
719A ASP 3.1 0.2 - - - -
720A ILE* 1.3 76.7 - - - +
722A LEU* 1.3 57.6 + - - +
725A GLY* 2.9 30.5 + - - +
728A PHE* 3.9 34.3 - - + -
771A GLY 3.4 22.4 - - - +
772A ILE* 4.0 8.3 - - + -
775A GLY* 3.6 6.1 - - - -
776A LEU* 6.4 0.9 - - + -
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Residues in contact with LEU 722 (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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718A GLY 2.9 18.8 + - - +
719A ASP* 3.0 20.6 + - - +
721A ALA* 1.3 77.3 - - - +
723A ALA* 1.3 60.7 + - - +
725A GLY* 4.3 3.5 + - - -
771A GLY* 3.7 21.5 - - - +
774A GLN* 3.9 24.0 - - + +
775A GLY* 4.1 6.1 - - - +
55B ARG* 5.8 1.8 - - + -
58B TYR* 4.0 37.2 + - + -
59B VAL* 3.6 31.4 - - + -
62B ALA* 5.4 7.9 - - + -
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Residues in contact with ALA 723 (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 CYS* 3.8 32.8 - - + +
682A GLN* 4.0 14.8 - - - +
683A SER* 3.3 27.1 + - - -
685A ILE* 4.1 9.2 - - + -
719A ASP 2.9 14.9 + - - +
720A ILE 3.2 4.7 + - - +
722A LEU* 1.3 79.6 - - - +
724A ILE* 1.3 58.2 + - - +
725A GLY 3.7 0.2 - - - -
58B TYR* 4.7 6.3 - - + +
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Residues in contact with ILE 724 (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 SER* 5.8 0.2 - - - -
685A ILE* 3.9 8.3 - - + -
686A ILE* 3.6 31.3 - - + +
689A CYS* 3.5 30.1 - - + -
720A ILE* 3.0 23.3 + - + +
723A ALA* 1.3 79.6 - - - +
725A GLY* 1.3 65.9 + - - +
726A GLY 3.2 1.0 + - - -
727A GLU* 3.1 27.3 + - + +
728A PHE* 3.3 46.2 - - + +
731A TYR* 4.4 11.0 - - + -
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Residues in contact with GLY 725 (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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721A ALA 2.9 15.3 + - - -
722A LEU 4.3 2.3 + - - -
723A ALA 3.7 1.8 - - - -
724A ILE* 1.3 74.5 - - - +
726A GLY* 1.3 58.2 + - - -
728A PHE* 2.8 33.3 + - - +
775A GLY* 3.1 25.4 - - - -
776A LEU* 4.0 5.6 - - - +
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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
------------------------------------------------------------
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