Contacts of the strand formed by residues 674 - 678 (chain A) in PDB entry 1S0Q
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 GLN 674 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
671A VAL* 3.0 27.4 + - + +
672A PRO 4.5 3.6 - - - +
673A TYR* 1.3 83.3 - - + +
675A VAL* 1.3 79.0 + - - +
685A GLY* 3.8 11.3 - - - -
686A GLY 3.7 5.7 + - - -
708A ARG 4.6 2.4 - - - +
709A LEU* 4.9 0.2 - - - -
710A GLY 4.7 9.5 + - - -
711A GLU 5.1 3.3 + - - +
778A SER* 2.7 38.1 + - - +
779A GLY* 4.4 2.0 - - - -
780A TRP* 3.6 32.0 - - + -
794A LEU* 3.8 17.7 - - + -
838A GLY* 4.5 0.2 - - - -
839A PRO* 3.2 21.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 675 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
673A TYR 3.6 11.7 - - - +
674A GLN* 1.3 96.1 + - - +
676A SER* 1.3 58.6 + - - +
677A LEU* 4.0 14.6 - - + -
685A GLY* 3.4 2.4 - - - -
686A GLY* 2.9 41.6 + - - +
688A LEU* 3.9 14.1 - - + +
694A VAL* 3.8 18.2 - - + -
707A VAL* 4.1 5.4 - - + -
708A ARG 3.5 9.9 - - - +
709A LEU* 3.2 29.4 - - + -
780A TRP* 3.6 5.1 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 676 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
675A VAL* 1.3 73.7 - - - +
677A LEU* 1.3 66.1 + - - +
678A ASN* 4.8 2.8 + - - +
682A HIS* 2.9 33.0 + - - +
684A CYS 3.7 4.0 - - - -
706A GLN 3.8 0.2 - - - +
707A VAL* 3.8 1.2 - - - -
708A ARG* 2.8 50.1 + - - +
711A GLU* 4.7 1.1 - - - -
714A ILE* 4.3 11.2 - - - +
780A TRP* 3.7 18.5 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 677 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
675A VAL* 4.0 20.2 - - + -
676A SER* 1.3 73.0 - - - +
678A ASN* 1.3 59.4 + - - +
682A HIS* 3.5 4.2 - - - -
683A PHE* 2.9 51.4 + - + -
684A CYS* 2.8 26.8 + - + +
685A GLY 3.7 8.7 - - - +
694A VAL* 4.6 2.2 - - + -
696A SER* 3.6 24.7 - - - +
700A CYS* 4.5 4.0 - - + -
705A ILE* 4.1 7.4 - - + -
706A GLN 3.8 2.0 - - - -
707A VAL* 4.0 18.6 - - + -
745A MET* 4.8 0.4 - - + -
747A ILE* 3.8 30.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 678 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
676A SER* 4.8 2.6 + - - +
677A LEU* 1.3 73.7 - - - +
679A SER* 1.3 60.7 + - - +
680A GLY* 2.8 26.8 + - - -
681A TYR* 3.2 28.9 + - - +
682A HIS* 3.6 4.2 - - - +
683A PHE* 3.8 2.6 - - - -
704A GLY 3.8 0.9 - - - +
705A ILE* 3.8 1.0 - - - -
706A GLN* 2.8 51.5 + - - +
708A ARG* 3.6 47.9 + - - +
714A ILE 5.9 0.4 + - - -
----------------------------------------------------------
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