Contacts of the strand formed by residues 622 - 628 (chain A) in PDB entry 6Q6Q
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 ALA 622 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
619A ARG* 3.8 15.7 - - + -
621A HIS* 1.3 77.2 + - - +
623A LYS* 1.3 60.1 + - - +
667A LYS* 3.4 6.2 - - - +
668A VAL* 3.0 35.0 + - + +
697A TYR* 3.9 16.4 - - + -
698A GLN 3.3 16.8 - - - +
699A ASP* 3.4 17.0 - - - +
700A LEU* 3.8 8.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 623 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
622A ALA* 1.3 75.2 - - - +
624A ILE* 1.3 73.8 + - - +
625A VAL* 3.2 13.1 + - + +
666A ASP* 3.5 38.7 + - - +
667A LYS* 4.3 13.9 - - + +
697A TYR* 3.4 5.2 - - - -
698A GLN* 2.8 43.3 + - + +
700A LEU* 3.8 19.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 624 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
623A LYS* 1.3 76.3 + - - +
625A VAL* 1.3 61.7 + - - +
626A SER* 4.2 7.0 - - - +
627A ILE* 3.6 32.5 - - + -
664A ALA* 4.0 18.4 - - + +
665A THR 3.7 22.9 - - - +
666A ASP* 2.7 26.7 + - - +
668A VAL* 3.8 32.3 - - + -
675A VAL* 4.4 13.2 - - + -
695A ILE* 4.3 7.0 - - + -
696A VAL 4.0 3.6 - - - -
697A TYR* 4.6 8.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 625 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
623A LYS* 3.2 22.6 + - + +
624A ILE* 1.3 75.7 - - - +
626A SER* 1.3 65.6 + - - +
696A VAL* 3.3 41.0 + - + +
697A TYR 4.1 2.7 - - - +
698A GLN* 4.0 26.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 626 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
624A ILE* 3.6 1.8 - - - +
625A VAL* 1.3 86.0 - - - +
627A ILE* 1.3 69.6 + - - +
628A ASP* 4.2 0.9 - - - -
694A LYS 4.7 0.4 + - - -
695A ILE* 3.6 2.6 - - - +
696A VAL* 3.2 47.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 627 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
624A ILE* 3.6 25.8 - - + -
626A SER* 1.3 79.6 - - - +
628A ASP* 1.3 60.1 + - - +
629A LEU* 3.7 33.2 + - + +
643A THR* 4.2 19.1 - - + +
664A ALA 5.8 1.3 - - - +
665A THR 5.6 2.2 - - - +
675A VAL* 4.0 23.1 - - + -
676A CYS* 4.0 11.4 - - - -
693A VAL* 4.3 0.7 - - + -
694A LYS 3.7 2.9 - - - -
695A ILE* 4.2 15.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 628 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
626A SER* 4.2 1.0 - - - -
627A ILE* 1.3 69.6 - - - +
629A LEU* 1.3 62.5 + - - +
630A SER* 2.7 36.0 + - - -
631A GLU* 5.0 3.3 + - - +
692A ARG 4.5 2.1 - - - +
693A VAL* 3.8 7.1 - - - +
694A LYS* 2.8 50.2 + - + +
----------------------------------------------------------
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