Contacts of the helix formed by residues 268 - 275 (chain A) in PDB entry 3CMM
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 SER 268 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
141A ASN* 3.5 9.4 - - - -
142A GLU* 4.5 12.8 + - - -
145A HIS* 4.0 18.6 - - - -
164A PHE* 4.0 0.9 - - - -
166A ASP* 3.5 11.0 + - - -
267A LYS* 1.3 78.6 - - - +
269A LEU* 1.3 59.4 + - - +
270A LYS* 3.7 7.7 + - - +
271A GLN* 3.2 32.6 + - - +
272A GLN* 2.8 27.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 269 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
134A LEU* 4.3 7.9 - - + -
137A LYS* 3.9 41.3 - - + +
138A VAL* 4.2 15.7 - - + +
141A ASN* 2.8 26.7 + - + +
151A PHE* 4.4 11.4 - - + -
153A SER* 5.1 2.7 - - - +
164A PHE* 3.6 24.6 - - + -
268A SER* 1.3 69.9 - - - +
270A LYS* 1.3 54.0 + - - +
272A GLN 3.0 1.2 + - - -
273A LEU* 2.8 54.1 + - + +
388A PHE* 3.8 23.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 270 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
138A VAL* 4.2 27.9 - - + +
141A ASN* 4.2 1.2 + - - +
142A GLU* 5.6 8.5 - - - +
268A SER* 3.2 8.6 + - - +
269A LEU* 1.3 78.5 - - - +
271A GLN* 1.3 63.3 + - - +
273A LEU* 3.5 21.2 + - + +
274A SER* 4.0 6.9 + - - -
721C ASP* 5.2 9.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 271 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
145A HIS* 5.7 0.7 + - - -
267A LYS* 3.8 27.9 - - + +
268A SER* 3.2 33.6 + - - +
269A LEU 3.2 0.4 - - - -
270A LYS* 1.3 77.5 - - - +
272A GLN* 1.3 65.1 + - - +
273A LEU 3.2 0.5 + - - -
274A SER* 3.3 7.2 + - - -
275A ASN* 3.1 24.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 272 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
164A PHE* 3.5 24.9 - - + -
267A LYS* 3.6 16.5 - - + +
268A SER 2.8 19.7 + - - +
269A LEU 3.7 2.0 - - - +
271A GLN* 1.3 77.8 - - - +
273A LEU* 1.3 61.0 + - - +
275A ASN 3.3 15.9 - - - +
276A PRO* 3.0 32.5 - - - +
277A GLU* 2.9 33.2 + - - +
293A HIS* 3.7 0.9 - - - -
387A GLN* 3.2 43.7 - - - +
388A PHE* 3.7 10.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 273 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
134A LEU* 4.1 24.0 - - + -
138A VAL* 3.9 27.1 - - + -
269A LEU* 2.8 39.3 + - + +
270A LYS* 3.7 10.1 - - + +
271A GLN 3.2 0.4 - - - -
272A GLN* 1.3 73.5 - - - +
274A SER* 1.3 58.7 + - - +
293A HIS* 2.8 25.8 + - + -
297A GLN* 3.6 40.8 + - + +
333A GLN* 4.7 3.3 - - - +
336A VAL* 5.1 0.3 - - - +
388A PHE* 4.1 12.6 - - + -
390A TYR* 5.7 0.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 274 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
270A LYS 4.0 5.5 + - - -
271A GLN* 3.3 8.5 + - - -
273A LEU* 1.3 79.8 - - - +
275A ASN* 1.3 81.8 + - - +
276A PRO* 3.7 6.3 - - - +
333A GLN* 4.1 18.3 - - - +
335A GLU* 5.1 3.8 - - - +
336A VAL* 4.0 12.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 275 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
271A GLN 3.1 10.3 + - - +
272A GLN* 3.3 20.8 - - - +
274A SER* 1.3 99.5 + - - +
276A PRO* 1.3 67.9 - - - +
277A GLU* 5.3 0.2 - - - +
335A GLU* 4.9 15.0 + - - +
----------------------------------------------------------
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