Contacts of the strand formed by residues 636 - 642 (chain A) in PDB entry 3L2P
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 TRP 636 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
606A VAL* 4.7 12.1 - - + -
608A LEU* 4.5 28.9 - - + -
628A CYS 3.9 3.6 - - - -
629A TYR* 3.3 49.4 - + + -
635A LYS* 1.3 83.5 - - - +
637A CYS* 1.3 60.2 + - - +
692A ALA* 5.1 13.2 - - + -
709A THR* 5.0 0.9 + - - -
729A TRP* 3.4 41.1 - + + -
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 637 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
608A LEU* 4.6 3.5 - - - +
627A GLY* 3.0 4.5 - - - -
628A CYS* 2.7 56.9 + - - +
630A ASP* 4.5 17.0 - - + -
636A TRP* 1.3 77.8 - - - +
638A THR* 1.3 59.7 + - - +
709A THR* 3.4 24.0 - - - -
710A ALA* 3.5 28.0 - - - -
735A LEU* 4.9 8.3 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 638 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
625A LEU* 3.4 33.7 - - - +
626A MET 4.1 0.2 + - - -
627A GLY* 4.2 4.0 - - - -
637A CYS* 1.3 69.0 - - - +
639A VAL* 1.3 62.8 + - - +
707A ALA 4.8 1.8 - - - +
708A HIS* 3.2 27.8 + - + +
709A THR* 2.5 48.9 + - + +
710A ALA* 3.2 20.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 639 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
605A LEU* 4.0 21.8 - - + -
626A MET 3.1 7.6 + - - +
627A GLY* 3.8 17.3 - - - -
628A CYS* 4.1 7.9 - - - +
638A THR* 1.3 77.8 - - - +
640A THR* 1.3 60.7 + - - +
708A HIS* 2.9 14.3 - - - -
710A ALA* 4.3 10.8 - - + -
713A ILE* 3.4 18.1 - - + +
714A SER* 2.8 23.0 + - - -
715A ILE* 3.9 20.2 - - + -
738A LEU* 3.8 25.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 640 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
605A LEU* 4.7 1.3 - - + -
625A LEU* 4.5 1.8 - - - -
626A MET* 2.9 39.5 + - + +
639A VAL* 1.3 82.7 - - - +
641A LYS* 1.3 71.5 + - - +
642A CYS* 5.1 1.1 - - + -
697A ILE* 4.5 8.3 - - + -
708A HIS* 3.3 11.8 - - - -
714A SER* 4.0 3.1 - - - -
715A ILE* 4.1 21.6 + - + -
718A PRO* 3.8 18.8 - - + +
34D G 3.6 0.2 + - - -
35D A 3.1 28.3 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 641 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
611A PHE* 3.5 37.2 - - + -
623A ILE* 3.8 11.8 - - + +
624A PHE 3.1 9.6 - - - +
625A LEU* 4.1 15.3 - - + -
626A MET 4.5 0.2 - - - +
640A THR* 1.3 88.3 + - - +
642A CYS* 1.3 65.9 + - - +
708A HIS* 4.6 4.9 - - + +
718A PRO* 3.7 7.3 - - - +
34D G 2.5 42.6 + - - +
35D A 2.8 31.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 642 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
623A ILE* 4.0 2.8 - - - +
624A PHE* 2.7 48.1 + - + +
626A MET* 3.9 21.1 - - + -
640A THR* 5.1 0.9 - - + -
641A LYS* 1.3 78.3 - - - +
643A ALA* 1.3 63.7 + - - +
644A GLY 3.8 16.6 - - - -
646A HIS* 5.5 2.5 - - - -
695A TRP* 5.6 2.9 - - + -
697A ILE* 4.4 8.3 - - + -
718A PRO* 4.4 9.6 - - + -
719A ARG* 4.0 10.3 - - - -
720A CYS* 3.9 25.4 - - - -
34D G 4.6 3.8 - - - -
----------------------------------------------------------
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