Contacts of the strand formed by residues 328 - 331 (chain A) in PDB entry 6CP3
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 VAL 328 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
169A ILE* 3.4 23.8 - - + +
177A LYS* 3.7 42.6 - - + +
181A ALA* 5.3 2.0 - - + -
269A VAL* 5.0 3.4 - - + -
270A TYR 3.6 17.0 + - - +
271A ASP* 3.5 26.2 - - + +
272A ASP* 3.3 13.5 - - + +
273A LEU 2.8 27.5 + - - +
326A LEU 4.6 1.3 - - - +
327A PRO* 1.3 81.6 - - - +
329A ILE* 1.3 67.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 329 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
168A LEU* 3.7 21.1 - - + +
169A ILE 3.5 6.3 + - - -
170A ILE* 4.0 10.1 - - + +
171A GLY 2.9 27.6 + - - +
177A LYS* 4.1 0.5 - - - +
273A LEU* 3.8 29.2 - - + -
274A SER* 3.9 8.5 - - - +
328A VAL* 1.3 85.0 - - - +
330A GLU* 1.3 61.6 + - - +
331A THR* 3.2 10.1 + - + +
340A ILE* 4.5 7.2 - - + -
341A PRO* 3.7 34.5 - - + -
344A VAL* 4.0 27.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 330 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
171A GLY 3.5 6.1 - - - -
173A ARG* 3.5 35.7 - - + +
177A LYS* 4.2 11.8 - - - +
272A ASP* 3.5 21.6 + - + +
274A SER* 3.2 25.7 + - - +
275A LYS* 4.1 16.1 + - - -
328A VAL* 4.0 2.8 + - - +
329A ILE* 1.3 69.6 - - - +
331A THR* 1.3 69.3 + - - +
332A GLN* 3.7 13.9 - - - +
341A PRO* 5.7 0.3 - - - +
600A ATP 4.7 7.3 + - - -
323D ALA* 4.3 11.6 - - - +
326D PHE* 4.9 3.1 - - - +
327D ALA* 5.3 6.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 331 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
170A ILE* 3.7 30.7 - - + -
171A GLY* 3.2 8.9 + - - +
172A ASP* 2.4 31.2 + - - -
173A ARG* 4.2 12.6 + - - +
329A ILE* 3.2 4.2 + - + +
330A GLU* 1.3 80.2 - - - +
332A GLN* 1.3 73.2 + - - +
333A GLY 4.1 0.9 + - - -
335A ASP* 3.3 26.5 + - - +
336A VAL* 5.3 0.2 - - + -
341A PRO* 3.8 21.3 - - + -
353A PHE* 6.1 1.5 - - + -
----------------------------------------------------------
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