Contacts of the strand formed by residues 695 - 705 (chain A) in PDB entry 4QUM
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 695 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
664A PHE* 4.4 2.7 - - + -
665A ALA* 3.2 35.0 - - + +
670A ASN* 3.4 47.1 - - + +
673A LYS* 3.9 36.2 - - + +
674A ASN* 2.8 28.6 + - - -
681A PRO* 3.3 18.0 - - + +
686A ARG* 3.5 26.7 - - - +
687A VAL 5.4 0.4 - - - -
689A LEU* 3.5 10.2 - - - +
694A ASP* 1.3 79.4 - - - +
696A ILE* 1.3 77.2 + - - +
697A ASN* 3.8 10.5 - - - -
727A GLN* 4.1 8.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 696 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
673A LYS* 5.8 1.3 - - - -
681A PRO* 4.3 2.3 - - - +
686A ARG* 4.8 1.9 - - - +
687A VAL* 3.7 27.2 + - + +
689A LEU* 3.8 18.4 - - + -
695A TYR* 1.3 94.2 - - - +
697A ASN* 1.3 71.1 + - + +
698A ALA* 2.9 25.6 + - + +
717A THR* 4.4 9.6 - - - +
718A GLN* 6.0 2.2 - - + +
724A THR* 5.1 7.4 - - + +
727A GLN* 3.9 26.9 - - + +
728A PHE* 4.0 20.6 - - + +
731A VAL* 4.0 10.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 697 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
673A LYS 4.2 2.7 + - - +
674A ASN* 2.8 30.1 + - - +
679A VAL* 2.9 25.3 + - - +
681A PRO* 3.8 11.1 - - - +
695A TYR* 3.8 9.1 - - - -
696A ILE* 1.3 74.0 - - - +
698A ALA* 1.3 50.9 + - - +
717A THR* 2.4 25.8 + - - -
718A GLN* 3.3 42.5 + - - +
844A ALA 5.7 0.2 - - - -
881A ARG* 3.0 30.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 698 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
681A PRO* 3.9 2.8 - - - +
686A ARG* 3.3 9.9 - - - +
687A VAL* 3.0 41.9 + - + -
696A ILE* 2.9 18.7 + - + +
697A ASN* 1.3 77.5 + - - +
699A SER* 1.3 63.6 + - - +
715A ILE* 4.2 6.1 - - + -
716A ALA 3.3 8.3 - - - +
717A THR* 3.3 17.7 - - - +
731A VAL* 5.6 1.3 - - + -
881A ARG* 4.1 2.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 699 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
681A PRO* 3.7 12.8 - - - +
685A THR* 3.3 9.4 + - - -
687A VAL* 4.0 5.4 - - - -
698A ALA* 1.3 75.2 + - - +
700A TYR* 1.3 63.9 + - - +
701A VAL* 3.6 1.4 + - - +
715A ILE* 3.4 4.5 - - - -
716A ALA 2.8 33.4 + - - -
880A GLN 3.5 21.5 + - - -
881A ARG* 2.9 40.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 700 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
684A THR 5.7 0.7 - - - -
685A THR* 2.7 38.1 + - + +
686A ARG 3.6 16.8 - - - -
687A VAL* 3.7 17.7 - - + +
688A LEU* 4.1 10.6 + - + +
699A SER* 1.3 72.9 - - - +
701A VAL* 1.3 65.1 + - - +
702A ASN* 4.2 15.7 - - - +
714A TYR 3.8 4.5 - - - -
715A ILE* 4.0 21.5 - - + -
735A GLN* 3.1 33.0 + - - -
837A PRO* 5.8 2.2 - - + -
880A GLN* 3.5 20.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 701 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
699A SER 3.9 9.0 - - - +
700A TYR* 1.3 81.2 - - - +
702A ASN* 1.3 61.6 + - - +
703A MET* 4.4 14.6 - - + -
714A TYR* 2.8 57.1 + - + +
716A ALA* 3.9 17.9 - - + -
853A VAL* 4.7 1.6 - - + -
877A MET* 4.5 7.4 - - + +
880A GLN* 3.5 18.4 - - + +
881A ARG* 4.0 22.0 - - + +
884A MET* 4.3 18.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 702 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
700A TYR* 4.6 16.2 - - - +
701A VAL* 1.3 78.4 + - - +
703A MET* 1.3 61.2 + - - +
704A GLU* 3.9 10.6 - - - +
711A VAL* 3.9 14.1 - - + -
712A ASN 3.7 2.2 - - - -
713A LYS* 3.3 34.9 - - - +
714A TYR 4.0 2.1 + - - +
876A LYS* 3.5 9.2 - - - -
880A GLN* 2.6 35.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 703 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
701A VAL* 4.4 2.9 - - + -
702A ASN* 1.3 78.9 - - - +
704A GLU* 1.3 64.2 + - - +
705A ILE* 3.8 5.7 + - + +
710A LEU 3.9 0.2 - - - +
711A VAL* 3.4 2.5 - - - -
712A ASN* 2.9 42.0 + - + +
714A TYR* 4.0 11.7 - - + -
853A VAL* 3.6 20.4 - - + -
857A THR* 3.9 22.9 - - + +
873A ILE* 3.6 44.2 - - + +
876A LYS* 3.9 20.4 - - + +
877A MET* 3.6 21.8 - - + -
880A GLN* 4.2 7.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 704 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
702A ASN* 4.4 11.7 - - - +
703A MET* 1.3 74.9 - - - +
705A ILE* 1.3 64.5 + - - +
706A PRO* 3.3 20.4 - - + +
710A LEU 3.4 7.4 - - - +
711A VAL* 4.2 20.4 - - + +
857A THR* 5.9 0.9 - - - +
876A LYS* 3.3 35.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 705 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
703A MET* 4.4 5.4 - - + +
704A GLU* 1.3 75.2 - - - +
706A PRO* 1.3 68.8 - - + +
707A ALA* 4.6 1.3 - - + +
708A ALA* 2.9 19.0 + - + +
710A LEU* 2.7 44.1 + - + +
712A ASN* 4.5 7.0 - - - +
857A THR* 4.2 24.2 - - + +
860A CYS* 3.5 33.4 - - + -
861A LEU* 3.6 28.9 - - + -
864A ARG* 5.2 1.6 - - - -
866A LEU* 3.9 18.8 - - + -
----------------------------------------------------------
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