Contacts of the strand formed by residues 332 - 336 (chain B) in PDB entry 3C3C
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 332 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
198B LYS 4.4 2.1 - - - +
199B ALA* 3.1 44.5 + - + +
203B PRO* 3.7 10.4 - - - +
204B GLU* 3.0 46.5 + - + +
206B PRO 3.1 3.2 + - - -
207B PHE* 3.2 24.5 - - + -
208B LEU* 2.7 32.2 + - - -
330B ALA* 3.6 1.1 - - - +
331B LYS* 1.3 79.9 - - - +
333B ILE* 1.3 64.5 + - - +
334B VAL* 5.1 1.1 - - + -
366B CYS* 4.2 0.4 - - - -
367B ILE* 3.5 20.6 - - + +
369B ILE* 5.4 1.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 333 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
208B LEU* 3.2 14.4 - - + +
210B ILE* 4.2 21.8 - - + -
327B VAL* 3.5 32.3 - - + -
330B ALA* 3.9 14.4 - - + -
332B GLN* 1.3 76.4 - - - +
334B VAL* 1.3 76.4 + - - +
335B TRP* 4.5 4.5 - - + +
358B VAL* 4.1 13.9 - - + -
361B ALA* 4.2 1.1 - - + -
366B CYS* 3.8 20.2 - - - -
367B ILE 3.0 9.2 + - - +
368B THR* 4.1 18.8 - - + -
369B ILE* 2.8 28.7 + - - +
370B ILE* 5.9 0.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 334 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
196B PHE* 4.8 4.5 - - + -
199B ALA* 4.5 8.3 - - + -
200B LEU* 6.0 0.9 - - + -
207B PHE* 3.5 29.6 - - + -
208B LEU 2.8 10.3 + - - +
209B ALA* 3.3 3.1 - - - +
210B ILE 2.7 32.9 + - - +
211B LEU* 5.0 2.9 - - + +
226B MET* 4.5 10.5 - - + -
332B GLN* 4.9 1.1 - - + +
333B ILE* 1.3 78.2 - - - +
335B TRP* 1.3 59.3 + - - +
336B ASN* 5.4 1.1 - - + +
369B ILE* 3.6 32.5 - - + +
402B LEU* 4.1 31.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 335 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
210B ILE* 3.2 41.3 - - + +
212B GLY 5.1 0.2 - - - +
333B ILE* 4.5 4.0 - - + -
334B VAL* 1.3 77.1 - - - +
336B ASN* 1.3 83.3 + - - +
337B GLY 2.6 25.9 + - - -
338B PRO* 4.5 1.8 - - + +
339B VAL* 4.5 9.2 - - + +
351B THR* 3.9 30.7 - - + -
354B LEU* 3.8 32.3 - - + -
355B MET* 4.0 37.5 - - + -
358B VAL* 4.2 16.6 - - + -
369B ILE 2.8 15.8 + - - +
370B ILE* 3.5 17.6 - - + -
371B GLY 3.1 25.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 336 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
210B ILE 3.0 10.6 + - - +
211B LEU* 3.6 15.7 - - + +
212B GLY 3.1 22.0 + - - +
222B LEU* 5.6 2.7 - - + +
334B VAL* 4.3 1.5 - - + +
335B TRP* 1.3 77.0 + - - +
337B GLY* 1.3 65.2 + - - +
371B GLY* 4.4 11.8 - - - +
395B GLY* 3.8 29.0 + - - +
398B SER* 4.1 12.7 - - - -
399B LEU* 3.2 30.4 - - + +
402B LEU* 5.1 11.9 - - + +
----------------------------------------------------------
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