Contacts of the strand formed by residues 325 - 331 (chain D) 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 D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
223D HIS 4.5 5.1 + - - -
224D ARG* 3.1 33.9 + - + +
225D ALA 3.4 15.4 + - - -
323D ASP 3.0 26.9 + - - -
324D LEU* 1.3 88.2 - - - +
326D VAL* 1.3 60.0 + - - +
424D ARG* 3.5 21.5 - - + +
483D PHE* 3.4 17.9 - - + -
486D THR 3.5 6.9 - - - +
487D GLY* 3.2 26.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 326 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
213D ILE* 4.4 5.4 - - + -
225D ALA 3.2 5.4 - - - +
227D LEU* 3.5 18.2 - - + -
324D LEU* 3.5 32.8 - - + +
325D GLN* 1.3 82.7 - - - +
327D LEU* 1.3 74.0 + - - +
328D VAL* 3.5 18.4 - - + -
418D LEU* 4.1 22.9 - - + -
423D ALA* 4.8 1.3 - - + -
424D ARG 3.0 9.9 + - - +
425D VAL* 3.3 7.3 - - + +
426D TYR* 3.1 23.9 + - - +
483D PHE* 3.5 5.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 327 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
225D ALA 2.9 6.5 + - - -
226D VAL* 3.3 11.6 - - + -
227D LEU 3.0 22.6 + - - -
326D VAL* 1.3 77.5 - - - +
328D VAL* 1.3 85.0 + - - +
426D TYR* 3.8 8.3 - - + +
428D TYR* 3.3 33.9 - - + -
480D TRP* 3.7 43.3 - - + +
483D PHE* 3.6 34.1 - - + -
489D PRO* 5.2 6.1 - - + -
500D TRP* 4.1 20.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 328 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
227D LEU* 3.6 20.6 - - + +
230D GLY 6.1 0.2 - - - +
231D THR* 5.8 1.3 - - + -
326D VAL* 3.5 19.5 - - + -
327D LEU* 1.3 81.7 - - - +
329D GLY* 1.3 64.1 + - - +
411D VAL* 3.2 37.5 - - + +
414D LEU* 4.9 12.8 - - + -
415D ALA* 5.2 7.4 - - + -
418D LEU* 5.4 1.1 - - + -
425D VAL* 4.4 11.9 - - + -
426D TYR 3.0 11.0 + - - +
427D ALA* 3.0 25.6 - - + -
428D TYR* 3.1 12.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 329 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
227D LEU 3.4 6.5 + - - +
229D SER 3.4 13.2 + - - -
328D VAL* 1.3 82.2 - - - +
330D VAL* 1.3 72.9 + - - +
411D VAL* 3.9 8.2 - - - +
427D ALA* 5.4 0.4 - - - -
428D TYR* 3.1 36.8 - - - -
524D LEU* 6.3 0.9 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 330 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
229D SER* 4.4 4.5 - - - +
329D GLY* 1.3 82.7 - - - +
331D VAL* 1.3 71.8 + - - +
334D GLU* 3.4 15.7 - - - +
407D VAL* 4.2 1.1 - - + -
408D VAL* 3.7 32.1 - - + -
411D VAL* 3.3 31.9 - - + -
428D TYR* 3.3 10.5 + - - +
429D ILE* 3.3 26.2 - - + -
430D PHE 2.7 31.5 + - - -
524D LEU* 5.2 1.1 - - + -
525D ARG* 6.0 1.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 331 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
229D SER* 3.8 4.5 - - - +
330D VAL* 1.3 91.0 - - - +
332D LYS* 1.3 70.1 + - - +
333D ASP 3.4 0.2 + - - -
334D GLU* 3.0 35.3 + - - +
408D VAL* 5.1 0.7 - - - +
428D TYR* 5.6 0.2 - - + -
429D ILE* 4.5 3.3 - - - +
430D PHE* 3.4 29.4 - - + -
445D VAL* 3.5 26.9 - - + +
446D PRO 3.9 12.8 - - - +
447D HIS* 4.0 2.7 - - - -
448D GLY 4.7 0.2 - - - +
450D GLU* 3.7 27.1 - - + +
525D 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