Contacts of the helix formed by residues 700 - 714 (chain A) in PDB entry 1QU2
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 ASP 700 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
433A LYS* 2.7 24.8 + - - -
627A TYR* 5.5 0.4 - - - -
695A ASN* 2.9 41.9 + - - +
698A ASN* 3.0 29.0 + - - +
699A PHE* 1.3 74.5 - - - +
701A TYR* 1.3 63.2 + - - +
702A LEU* 3.3 3.6 - - - +
703A ASN* 3.5 24.5 + - - +
704A ILE* 3.6 1.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 701 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73A LEU* 3.9 18.2 - - + -
76A PHE* 3.8 33.9 - + + -
77A ILE* 3.1 33.1 + - + +
583A LEU* 6.2 0.4 - - + -
623A SER* 3.1 30.1 - - - +
627A TYR* 3.7 20.9 - + + -
696A TYR* 3.8 35.1 + + - -
699A PHE* 3.4 39.1 + - + -
700A ASP* 1.3 69.9 - - - +
702A LEU* 1.3 67.1 + - - +
703A ASN 3.2 0.7 - - - -
704A ILE* 3.0 13.3 + - + +
705A TYR* 3.0 19.2 + - - +
759A ILE* 5.0 3.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 702 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
623A SER 3.1 10.7 + - - +
624A SER* 3.2 24.0 - - - +
625A THR 3.6 6.0 + - - +
626A ASP* 3.6 32.5 - - + +
627A TYR* 5.9 1.2 - - - -
700A ASP* 3.3 1.9 - - - +
701A TYR* 1.3 77.8 - - - +
703A ASN* 1.3 63.8 + - - +
705A TYR* 3.2 3.6 + - + -
706A GLN* 3.0 41.1 + - + +
12T U 4.0 3.4 - - - +
13T C 3.3 45.1 - - - +
14T A 4.8 1.6 - - - +
1208T MG 4.5 7.0 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 703 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
695A ASN* 3.4 33.4 + - - +
700A ASP* 3.5 20.2 + - - +
701A TYR 3.2 0.6 - - - -
702A LEU* 1.3 78.1 - - - +
704A ILE* 1.3 57.5 + - - +
706A GLN* 3.5 6.8 + - - +
707A GLU* 3.0 37.9 + - - +
13T C 5.6 0.2 + - - -
1208T MG 2.3 32.0 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 704 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
688A PHE* 5.4 0.2 - - + -
692A THR* 3.8 22.4 - - + +
695A ASN* 3.6 29.2 - - + +
696A TYR* 3.8 44.6 - - + +
700A ASP 3.6 7.2 - - - +
701A TYR* 3.0 15.3 + - + +
703A ASN* 1.3 75.9 - - - +
705A TYR* 1.3 58.8 + - - +
707A GLU* 4.5 4.0 - - - -
708A VAL* 2.7 55.7 + - + +
755A LEU 5.6 1.1 - - - +
756A LEU* 5.3 3.1 - - + -
759A ILE* 4.6 14.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 705 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
620A LEU* 3.8 37.7 - - + -
623A SER* 3.8 16.6 - - - +
624A SER* 3.5 34.5 + - - -
640A GLN* 4.5 11.1 + - - +
641A THR* 4.7 8.9 + - + -
644A ASP* 2.8 27.8 + - + -
648A ILE* 6.2 1.1 - - + -
701A TYR 3.0 11.4 + - - +
702A LEU* 3.5 8.7 - - + +
704A ILE* 1.3 77.0 - - - +
706A GLN* 1.3 78.6 + - - +
708A VAL* 4.0 4.8 - - - +
709A GLN* 3.0 55.1 + - + +
759A ILE* 6.1 0.4 - - - +
12T U 4.1 14.4 - - - -
24T G 5.7 2.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 706 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
702A LEU* 3.0 28.1 + - + +
703A ASN* 3.8 6.1 - - - +
705A TYR* 1.3 85.8 - - - +
707A GLU* 1.3 64.2 + - + +
709A GLN* 3.6 11.4 + - - +
710A ASN* 2.8 37.8 + - - +
12T U 3.1 21.2 + - - +
13T C 3.6 30.8 + - - +
23T A 4.0 22.2 + - - -
24T G 4.8 5.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 707 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
688A PHE* 4.0 16.7 - - + -
691A SER* 2.4 38.9 + - - -
692A THR* 4.3 5.8 + - - +
695A ASN* 3.3 20.6 + - - +
703A ASN* 3.0 22.0 + - - +
704A ILE* 4.0 3.4 - - - +
706A GLN* 1.3 75.2 - - + +
708A VAL* 1.3 66.8 + - - +
710A ASN* 3.2 6.0 + - - +
711A PHE* 2.8 26.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 708 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
648A ILE* 3.9 20.6 - - + -
688A PHE* 3.6 28.2 - - + -
704A ILE* 2.7 42.7 + - + +
705A TYR* 4.0 5.6 - - - +
707A GLU* 1.3 71.9 - - - +
709A GLN* 1.3 59.0 + - - +
711A PHE* 3.3 0.9 + - - +
712A ILE* 2.8 52.6 + - + +
752A MET* 5.9 1.3 - - + -
756A LEU* 3.7 24.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 709 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
644A ASP* 2.5 32.0 + - + +
648A ILE* 5.6 6.3 - - + -
705A TYR* 3.0 56.4 + - + +
706A GLN* 3.7 11.6 - - - +
707A GLU 3.2 0.4 - - - -
708A VAL* 1.3 83.5 - - + +
710A ASN* 1.3 58.8 + - - +
712A ILE* 3.2 3.1 + - - -
713A ASN* 2.5 44.9 + - - +
24T G 2.8 38.2 + - + +
25T C 3.8 5.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 710 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
684A ARG* 5.9 0.4 - - - -
706A GLN* 2.8 29.0 + - - +
707A GLU* 3.2 10.1 + - - +
709A GLN* 1.3 79.4 - - - +
711A PHE* 1.3 57.5 + - - +
714A VAL* 3.0 37.6 + - + +
715A GLU* 3.8 1.8 + - - +
23T A 2.5 32.0 + - - +
24T G 3.0 33.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 711 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
681A LEU* 5.1 4.5 - - + -
684A ARG* 3.8 36.3 - - + +
685A LEU* 4.2 20.9 - - + -
688A PHE* 4.0 20.6 - + + -
707A GLU 2.8 17.8 + - - +
708A VAL 3.7 3.4 - - - +
710A ASN* 1.3 78.6 - - - +
712A ILE* 1.3 57.9 + - - +
715A GLU* 3.3 36.1 + - + +
716A LEU* 3.2 32.8 + - + +
748A ILE* 3.7 24.9 - - + -
752A MET* 3.2 39.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 712 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
647A LYS* 4.1 18.4 - - + +
648A ILE* 3.7 31.0 - - + +
651A THR* 3.1 32.5 + - + +
652A LEU* 5.9 2.2 - - + -
708A VAL* 2.8 40.3 + - + +
709A GLN* 3.9 3.4 - - - +
711A PHE* 1.3 76.8 - - - +
713A ASN* 1.3 60.2 + - - +
716A LEU* 3.4 11.3 - - + +
717A SER* 3.0 29.1 + - - -
752A MET* 4.3 23.3 - - + -
756A LEU* 5.2 2.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 713 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
647A LYS* 3.6 27.2 - - - +
709A GLN* 2.5 45.2 + - - +
710A ASN 4.4 0.4 - - - +
712A ILE* 1.3 74.6 - - - +
714A VAL* 1.3 62.4 + - + +
717A SER* 3.7 4.4 - - - -
718A ASN* 2.9 39.5 + - - +
24T G 3.4 34.1 + - - +
25T C 3.4 22.0 + - - +
1205T MG 3.6 7.1 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 714 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
710A ASN* 3.0 19.7 + - + +
713A ASN* 1.3 77.2 - - + +
715A GLU* 1.3 80.3 + - + +
718A ASN* 3.5 16.8 - - + +
719A PHE* 3.4 22.3 + - - +
24T G 3.9 35.7 - - - +
----------------------------------------------------------
Back to top of page
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) + - + + + + + -
------------------------------------------------------------
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