Contacts of the strand formed by residues 322 - 327 (chain D) in PDB entry 2CEA
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 PHE 322 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
196D GLY* 3.5 22.2 - - - -
197D ILE 3.8 10.3 - - - -
198D LEU* 4.4 17.2 - - + +
259D ILE* 5.3 0.7 - - + -
262D ILE* 3.9 18.2 - - + -
287D LEU* 5.1 4.5 - - + -
291D MET* 3.9 27.1 - - + -
302D VAL* 3.9 27.4 - - + -
304D ALA* 3.8 20.9 - - + -
316D LEU* 3.1 48.8 + - + +
317D LEU* 3.5 27.9 - - + +
321D ARG* 1.3 80.3 - - + +
323D ASP* 1.3 60.5 + - - +
324D LYS 3.4 4.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 323 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
194D PRO* 3.6 26.8 - - - +
196D GLY 3.7 0.2 + - - -
317D LEU 4.3 7.2 - - - +
318D ARG 4.3 1.1 - - - +
319D PRO* 3.6 17.9 - - + +
320D GLY* 2.9 27.9 + - - -
321D ARG 3.8 5.6 - - - +
322D PHE* 1.3 71.7 - - - +
324D LYS* 1.3 62.5 + - - +
325D LYS* 4.1 1.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 324 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
172D GLU* 3.0 49.6 + - - +
173D LEU* 5.9 0.2 - - - +
175D GLU* 3.4 25.1 + - - +
176D VAL* 4.4 8.3 - - - +
194D PRO* 4.3 21.8 - - + +
196D GLY 4.0 7.2 + - - +
197D ILE* 3.5 17.3 - - + +
198D LEU* 2.8 26.5 + - - +
322D PHE 4.9 0.7 - - - -
323D ASP* 1.3 87.0 + - - +
325D LYS* 1.3 67.1 + - - +
326D ILE* 4.9 5.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 325 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
172D GLU* 4.5 5.9 - - - +
198D LEU* 3.2 17.7 - - + +
200D VAL* 4.6 12.6 - - + -
323D ASP 4.1 2.0 + - - +
324D LYS* 1.3 78.8 - - - +
326D ILE* 1.3 65.9 + - - +
327D VAL* 4.1 24.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 326 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
169D ALA* 3.8 30.7 - - + -
172D GLU* 4.3 25.6 - - + +
173D LEU* 3.5 37.9 - - + -
197D ILE* 3.8 16.8 - - + -
198D LEU 2.8 9.7 + - - -
199D LEU* 3.6 18.3 - - + -
200D VAL* 2.8 31.4 + - - +
324D LYS* 4.9 7.4 - - + -
325D LYS* 1.3 80.8 - - - +
327D VAL* 1.3 68.9 + - - +
328D VAL* 3.6 3.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 327 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
168D GLU* 6.0 1.9 - - - +
169D ALA* 4.8 5.0 + - - +
200D VAL* 3.5 17.0 - - + +
201D GLY* 5.8 1.1 - - - -
325D LYS* 4.1 26.0 - - + -
326D ILE* 1.3 81.1 - - - +
328D VAL* 1.3 64.0 + - - +
329D ASP* 3.5 31.0 + - - +
----------------------------------------------------------
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