Contacts of the strand formed by residues 1334 - 1337 (chain D) in PDB entry 6PUO
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 ARG1334 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1273D PRO* 3.8 23.1 - - + +
1274D PRO 3.2 8.2 + - - +
1275D PHE* 3.8 17.0 - - + -
1276D TYR* 2.7 33.5 + - - +
1333D LEU* 1.3 76.5 - - - +
1335D GLY* 1.3 56.7 + - - +
1435D THR* 4.7 1.6 - - - +
1436D ASP* 4.2 6.5 - - + +
1437D ASN* 4.3 8.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY1335 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1275D PHE* 4.7 4.9 - - - +
1276D TYR 3.3 11.4 - - - -
1277D THR* 4.8 0.7 - - - -
1290D GLY 5.6 3.8 - - - -
1334D ARG* 1.3 75.9 - - - +
1336D ARG* 1.3 60.8 + - - -
1337D GLY 3.4 2.0 - - - -
1342D PHE* 4.3 3.6 - - - -
1435D THR* 3.0 22.0 + - - -
1437D ASN* 3.1 26.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG1336 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1276D TYR 3.6 2.4 + - - -
1277D THR* 3.9 19.0 - - - -
1281D LYS* 4.5 8.3 - - + -
1287D ASP 5.7 2.9 - - - +
1289D MET 5.0 0.2 - - - -
1290D GLY* 4.4 13.3 - - - +
1335D GLY* 1.3 73.1 - - - -
1337D GLY* 1.3 65.5 + - - +
1339D LEU* 3.6 17.6 + - - +
1340D SER 5.6 3.6 - - - +
1341D CYS 6.3 0.4 - - - -
1342D PHE* 3.6 26.5 - - + -
1435D THR* 4.1 3.2 - - - +
1438D ALA* 3.8 17.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY1337 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1247D TYR* 3.4 15.7 - - - -
1276D TYR 3.4 15.2 + - - -
1277D THR* 3.7 3.3 - - - +
1278D ALA* 2.9 25.1 + - - +
1281D LYS* 4.1 6.1 - - - +
1335D GLY 3.4 1.4 - - - -
1336D ARG* 1.3 81.4 - - - +
1338D SER* 1.3 59.3 + - - -
1339D LEU 3.7 0.3 + - - +
1433D ARG 5.8 0.2 - - - -
1435D THR* 3.9 13.9 - - - +
----------------------------------------------------------
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