Contacts of the strand formed by residues 325 - 331 (chain A) in PDB entry 1C2O
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 325 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
223A HIS 4.5 5.3 + - - -
224A ARG* 3.1 33.8 + - + +
225A ALA 3.4 15.2 + - - -
323A ASP 3.0 27.5 + - - -
324A LEU* 1.3 87.3 - - - +
326A VAL* 1.3 60.6 + - - +
424A ARG* 3.5 21.3 - - + +
483A PHE* 3.4 18.4 - - + -
486A THR 3.5 7.1 - - - +
487A GLY* 3.2 26.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 326 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
213A ILE* 4.4 5.2 - - + -
225A ALA 3.2 6.3 - - - +
227A LEU* 3.5 18.6 - - + -
324A LEU* 3.5 33.4 - - + +
325A GLN* 1.3 81.1 - - - +
327A LEU* 1.3 72.4 + - - +
328A VAL* 3.5 18.6 - - + -
418A LEU* 4.1 22.4 - - + -
423A ALA* 4.8 1.8 - - + -
424A ARG 3.0 10.9 + - - +
425A VAL* 3.3 7.6 - - + +
426A TYR* 3.1 23.7 + - - +
483A PHE* 3.5 5.9 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 327 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
225A ALA 2.9 5.9 + - - -
226A VAL* 3.3 10.9 - - + -
227A LEU 3.0 22.7 + - - -
326A VAL* 1.3 76.8 - - - +
328A VAL* 1.3 83.5 + - - +
426A TYR* 3.8 9.4 - - + +
428A TYR* 3.3 34.5 - - + -
479A TYR 5.3 0.4 - - - +
480A TRP* 3.7 43.3 - - + +
483A PHE* 3.6 33.2 - - + -
489A PRO* 5.2 5.8 - - + -
500A TRP* 4.1 20.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 328 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
227A LEU* 3.6 21.1 - - + +
231A THR* 5.9 1.3 - - + -
326A VAL* 3.5 19.3 - - + -
327A LEU* 1.3 82.0 - - - +
329A GLY* 1.3 63.9 + - - +
411A VAL* 3.2 37.5 - - + +
414A LEU* 4.9 13.0 - - + -
415A ALA* 5.2 7.4 - - + -
418A LEU* 5.4 1.1 - - + -
425A VAL* 4.4 11.9 - - + -
426A TYR 3.0 11.8 + - - +
427A ALA* 3.0 24.7 - - + -
428A TYR* 3.1 11.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 329 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
227A LEU 3.4 6.4 + - - +
229A SER 3.4 13.9 + - - -
328A VAL* 1.3 80.9 - - - +
330A VAL* 1.3 73.2 + - - +
411A VAL* 3.9 8.2 - - - +
427A ALA* 5.4 0.7 - - - -
428A TYR* 3.1 36.6 - - - -
524A LEU* 6.3 0.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 330 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
229A SER* 4.4 4.0 - - - -
329A GLY* 1.3 83.0 - - - +
331A VAL* 1.3 74.0 + - - +
334A GLU* 3.4 16.6 - - - +
407A VAL* 4.2 0.9 - - + -
408A VAL* 3.7 31.2 - - + -
411A VAL* 3.3 31.9 - - + -
428A TYR* 3.3 10.3 + - - -
429A ILE* 3.3 25.3 - - + -
430A PHE 2.7 30.5 + - - -
524A LEU* 5.2 1.3 - - + -
525A ARG* 6.0 1.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 331 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
229A SER* 3.8 3.8 - - - +
330A VAL* 1.3 91.8 - - - +
332A LYS* 1.3 70.0 + - - +
333A ASP 3.4 0.3 + - - -
334A GLU* 3.0 35.6 + - - +
408A VAL* 5.1 1.2 - - - +
428A TYR* 5.6 0.7 - - + -
429A ILE* 4.5 3.3 - - - +
430A PHE* 3.4 29.2 - - + -
445A VAL* 3.5 27.8 - - + +
446A PRO 3.9 13.0 - - - +
447A HIS* 4.0 3.4 - - - -
448A GLY 4.7 0.2 - - - +
450A GLU* 3.7 26.7 - - + +
525A ARG* 5.9 0.3 + - - -
----------------------------------------------------------
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