Contacts of the helix formed by residues 318 - 325 (chain A) in PDB entry 2CRX
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 318 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
306A ILE* 3.9 24.3 - - + +
307A PRO* 5.4 3.4 - - + -
310A MET* 3.1 40.7 - - + +
316A THR 3.2 2.3 + - - -
317A ASN* 1.3 71.5 - - - +
319A ASN* 1.3 59.6 + - + +
321A VAL* 3.8 8.4 + - - +
322A MET* 3.4 17.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 319 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
317A ASN* 2.2 20.1 + - + +
318A VAL* 1.3 68.9 - - + +
320A ILE* 1.3 54.1 + - - +
321A VAL 3.2 1.8 - - - -
322A MET* 2.7 25.4 + - - +
323A ASN* 2.6 52.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 320 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
315A TRP* 3.4 30.1 - - + +
316A THR 4.3 3.1 - - - +
317A ASN* 2.5 40.1 + - + +
319A ASN* 1.3 71.7 - - - +
321A VAL* 1.3 57.5 + - - +
323A ASN* 3.0 38.9 + - + +
324A TYR* 3.3 29.8 + - + +
15D G 3.2 45.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 321 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
296A ALA* 4.8 3.1 - - + -
306A ILE* 3.5 25.6 - - + -
309A ILE* 3.5 27.8 - - + +
310A MET* 4.6 8.7 - - - -
315A TRP* 3.5 47.3 - - + -
316A THR 4.9 2.0 - - - +
317A ASN 3.8 0.4 + - - +
318A VAL 3.8 9.2 + - - +
319A ASN 3.2 0.6 - - - -
320A ILE* 1.3 76.2 - - - +
322A MET* 1.3 57.0 + - - +
324A TYR* 3.4 10.7 + - - +
325A ILE* 3.1 34.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 322 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
306A ILE* 4.7 10.5 - - - -
318A VAL 3.4 7.2 + - - +
319A ASN* 2.7 37.6 + - - +
321A VAL* 1.3 77.0 - - - +
323A ASN* 1.3 51.2 + - - +
324A TYR 2.7 8.5 + - - -
325A ILE* 3.4 33.4 - - + +
326A ARG* 2.6 41.8 + - + +
331A GLU* 3.2 38.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 323 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
133A GLN* 5.8 2.1 + - - -
319A ASN* 2.6 39.5 + - - +
320A ILE* 3.3 26.0 - - + +
322A MET* 1.3 73.3 - - - +
324A TYR* 1.3 65.0 + - + +
326A ARG* 3.8 41.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 324 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
134A ALA* 5.4 3.8 - - + -
289A HIS* 4.1 9.3 - + - -
293A VAL* 3.8 46.9 - - + +
296A ALA* 5.0 4.5 - - + -
297A ARG* 3.8 26.0 + - - +
315A TRP* 3.2 39.1 - + - -
320A ILE* 3.5 24.5 - - + +
321A VAL* 3.4 14.6 - - - +
322A MET 2.7 1.6 + - - -
323A ASN* 1.3 87.3 - - + +
325A ILE* 1.3 63.5 + - + +
326A ARG* 3.2 8.3 + - - +
327A ASN* 4.1 4.7 - - - +
15D G 2.3 45.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 325 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
296A ALA* 4.1 26.7 - - + +
297A ARG* 4.1 11.2 - - + +
300A ALA* 4.0 28.0 - - + -
306A ILE* 4.5 8.5 - - + -
309A ILE* 4.6 4.9 - - + -
321A VAL* 3.3 26.7 - - + +
322A MET* 3.1 36.3 + - + -
324A TYR* 1.3 74.6 - - - +
326A ARG* 1.3 62.9 + - - +
327A ASN* 3.6 1.6 - - - -
328A LEU* 3.0 20.9 - - + +
331A GLU* 3.1 22.5 - - - +
----------------------------------------------------------
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