Contacts of the helix formed by residues 249 - 257 (chain A) in PDB entry 2CMH
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 PRO 249 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
175A LEU* 5.3 8.3 - - + -
247A ALA 4.5 2.5 - - - +
248A LEU* 1.3 92.2 - - + +
250A LYS* 1.3 66.0 + - - +
251A ASN* 3.3 21.1 - - - +
252A LEU* 3.4 23.9 + - + -
253A GLN* 3.1 18.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 250 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
249A PRO* 1.3 71.8 - - - +
251A ASN* 1.3 63.3 + - - +
253A GLN* 3.2 17.4 + - - +
254A GLU* 3.2 22.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 251 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
249A PRO* 3.3 29.3 - - - +
250A LYS* 1.3 75.8 - - - +
252A LEU* 1.3 80.8 + - - +
254A GLU* 3.3 13.1 + - - +
255A VAL* 2.9 23.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 252 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
174A PRO* 4.1 30.7 - - + +
175A LEU* 4.6 12.3 - - + +
178A HIS* 4.0 26.9 - - + +
248A LEU* 4.3 9.0 - - + -
249A PRO* 3.4 32.5 + - + +
250A LYS 3.3 0.2 - - - -
251A ASN* 1.3 91.9 - - - +
253A GLN* 1.3 65.6 + - - +
254A GLU 3.3 0.2 + - - -
255A VAL* 3.4 11.1 + - + +
256A PHE* 3.1 48.0 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 253 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
248A LEU* 3.8 34.8 + - + +
249A PRO 3.1 11.2 + - - +
250A LYS* 3.2 19.7 + - - +
252A LEU* 1.3 78.5 - - - +
254A GLU* 1.3 57.0 + - - +
256A PHE 3.7 0.3 - - - -
257A LYS* 2.8 31.2 + - - +
260A ILE* 4.5 13.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 254 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
250A LYS* 3.2 11.9 + - + +
251A ASN* 3.6 10.8 - - - +
252A LEU 3.2 0.4 - - - -
253A GLN* 1.3 78.9 - - - +
255A VAL* 1.3 58.9 + - + +
257A LYS* 3.1 51.9 + - - +
38B ASP 5.7 1.0 - - - +
53B ASN* 5.7 0.7 - - - +
54B PHE* 6.1 1.0 - - - -
178C HIS* 3.4 13.3 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 255 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
178A HIS* 4.3 18.8 - - + +
182A GLN* 2.7 40.1 + - + +
251A ASN* 2.9 23.3 - - + +
252A LEU* 3.4 12.5 + - + +
254A GLU* 1.3 75.4 - - + +
256A PHE* 1.3 81.4 + - + +
178C HIS* 4.1 10.5 - - + +
179C VAL* 3.6 10.2 - - - +
182C GLN* 5.3 0.9 - - - +
255C VAL* 4.7 23.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 256 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
174A PRO* 4.0 8.3 - - + -
178A HIS* 3.4 31.9 - - + -
181A MET* 3.4 31.4 - - + -
182A GLN* 3.5 28.5 - - + +
185A LEU* 4.2 11.9 - - + -
197A PRO* 4.7 7.0 - - + -
248A LEU* 4.8 9.4 - - + -
252A LEU* 3.1 33.1 + - + +
255A VAL* 1.3 97.2 - - + +
257A LYS* 1.3 70.0 + - - +
258A ASP 3.6 0.9 - - - -
259A ASN* 3.0 12.1 + - - -
260A ILE* 2.9 37.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 257 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
253A GLN 2.8 14.7 + - - +
254A GLU* 3.1 40.9 + - - +
256A PHE* 1.3 80.8 - - - +
258A ASP* 1.3 91.5 + - - +
260A ILE* 2.7 31.6 + - - +
178C HIS* 3.3 22.8 + - - -
179C VAL* 4.2 4.6 - - + +
----------------------------------------------------------
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