Contacts of the strand formed by residues 699 - 705 (chain A) in PDB entry 1N1M
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 GLU 699 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
640A LEU* 4.5 0.7 - - - +
648A LYS* 3.2 35.7 + - - +
649A CYS* 3.1 16.6 - - + +
650A GLY 2.9 26.2 + - - -
698A VAL* 1.3 73.2 - - - +
700A TYR* 1.3 59.1 + - - +
729A ASP 6.1 0.2 - - - -
731A GLN* 6.1 0.8 - - + +
758A PHE* 3.5 13.7 - - + -
761A GLN* 3.0 30.8 + - - +
762A CYS* 4.6 1.2 - - - -
----------------------------------------------------------
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
----------------------------------------------------------
636A THR* 5.3 0.2 - - + -
637A SER* 2.7 27.2 + - - -
640A LEU* 3.6 24.2 - - + -
650A GLY 3.5 3.4 - - - -
652A ALA* 3.7 24.8 - - + +
695A PHE* 3.6 37.9 - + + -
698A VAL* 3.6 5.9 + - + +
699A GLU* 1.3 73.9 - - - +
701A LEU* 1.3 67.6 + - - +
702A LEU* 3.7 33.3 - - + +
719A ILE* 4.0 13.5 - - + +
723A LEU* 4.0 23.1 - - + -
729A ASP 5.7 0.2 - - - +
730A PHE* 3.6 15.4 - - + +
731A GLN* 2.9 31.4 + - - +
758A PHE* 4.1 1.6 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 701 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
650A GLY 3.0 7.5 + - - +
651A ILE* 3.4 27.7 - - + +
652A ALA 2.9 28.6 + - - +
700A TYR* 1.3 78.0 - - - +
702A LEU* 1.3 65.7 + - - +
703A ILE* 3.6 27.6 - - + -
731A GLN* 3.6 18.2 - - + +
732A ALA* 4.4 4.0 - - - +
754A HIS* 4.4 20.4 - - + +
755A MET* 4.5 4.0 - - - -
758A PHE* 3.7 46.4 - - + -
----------------------------------------------------------
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
----------------------------------------------------------
652A ALA 3.8 8.1 - - - +
655A PRO* 4.2 7.4 - - + -
700A TYR* 3.7 31.8 - - + +
701A LEU* 1.3 71.2 - - - +
703A ILE* 1.3 67.4 + - - +
716A SER* 3.0 49.6 - - - +
719A ILE* 4.0 8.5 - - + -
720A SER* 4.0 15.9 - - - +
730A PHE* 4.6 7.6 - - + -
731A GLN 3.0 13.3 + - - +
732A ALA* 3.4 2.6 - - - +
733A MET 3.1 24.8 + - - +
734B TRP* 4.0 19.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 703 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
651A ILE* 4.1 7.0 - - + -
652A ALA 2.9 13.8 + - - +
653A VAL* 4.2 4.9 - - + -
654A ALA* 2.8 24.1 + - - -
655A PRO* 3.9 2.8 - - - +
701A LEU* 3.6 33.7 - - + -
702A LEU* 1.3 81.8 - - - +
704A HIS* 1.3 69.8 + - - +
733A MET* 3.3 20.0 - - + +
735A TYR* 3.7 24.9 - - + -
742A ILE* 4.4 2.7 - - + -
751A ILE* 3.7 23.3 - - + -
754A HIS* 4.8 5.6 - - + -
755A MET* 4.0 20.9 - - + -
734B TRP* 5.4 0.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 704 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
654A ALA* 3.4 27.4 - - - +
655A PRO* 4.0 2.0 + - + -
703A ILE* 1.3 80.1 - - - +
705A GLY* 1.3 85.4 + - - +
708A ASP* 3.4 20.6 + - + -
711A VAL* 2.7 38.1 + - - +
712A HIS 3.4 7.7 + - - -
713A PHE* 3.5 31.4 - + + -
716A SER* 3.0 39.7 - - - +
733A MET 3.4 4.4 + - - -
734A TRP* 3.5 1.9 - - - -
735A TYR 3.4 16.6 + - - -
742A ILE* 4.6 4.5 - - - -
734B TRP* 5.0 2.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 705 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
654A ALA* 5.2 0.8 - - - +
704A HIS* 1.3 91.0 + - - +
706A THR* 1.3 64.8 + - - -
707A ALA 3.2 3.0 + - - -
708A ASP* 3.5 10.6 + - - +
713A PHE* 3.4 4.4 - - - +
735A TYR* 3.5 13.9 - - - -
738A GLU* 3.5 20.2 - - - -
739A ASP 4.7 2.9 + - - -
742A ILE* 4.1 11.8 - - - +
----------------------------------------------------------
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