Contacts of the strand formed by residues 252 - 255 (chain D) in PDB entry 4CQM
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 252 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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225C HIS* 3.0 17.3 + - - -
226C VAL 4.9 1.0 - - - +
234C GLN* 5.1 1.4 - - - +
177D ILE* 3.6 26.7 - - - +
181D GLN* 5.0 4.0 + - - +
196D SER* 3.2 9.7 - - - -
198D LEU* 3.6 27.0 - - - +
251D THR* 1.3 79.6 - - - +
253D VAL* 1.3 61.2 + - - +
254D GLU* 3.9 3.1 - - - +
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Residues in contact with VAL 253 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
215C PHE* 4.2 10.5 - - + -
222C ILE* 4.2 19.3 - - + -
225C HIS* 3.5 12.8 - - + +
227C LEU* 3.7 20.0 - - + -
196D SER 2.9 11.5 + - - +
197D VAL* 3.7 7.0 - - - +
198D LEU 3.0 21.6 + - - -
236D VAL* 3.7 24.9 - - + -
239D PHE* 6.0 0.4 - - + -
240D LEU* 4.3 28.3 - - + -
248D ILE* 5.5 0.2 - - + -
251D THR* 4.4 9.9 - - + +
252D SER* 1.3 73.9 - - - +
254D GLU* 1.3 63.0 + - - +
255D VAL* 3.5 1.6 + - - +
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Residues in contact with GLU 254 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
160C ARG* 5.3 4.7 + - - -
222C ILE* 3.7 24.7 - - - +
223C THR 5.4 0.2 + - - -
225C HIS* 3.1 33.7 + - + +
157D ILE* 3.4 22.5 - - + +
160D LYS* 3.1 34.8 + - - +
198D LEU* 3.3 26.2 - - + +
252D SER* 4.9 4.7 - - - +
253D VAL* 1.3 71.4 - - - +
255D VAL* 1.3 59.5 + - - +
256D THR* 3.8 11.7 + - + +
260D PHE 4.0 3.1 - - - +
261D MET* 4.3 8.5 - - - +
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Residues in contact with VAL 255 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
219C SER* 5.2 0.4 - - - +
221C TYR* 3.5 38.3 - - + +
222C ILE* 3.8 17.0 - - + -
197D VAL* 4.0 21.5 - - + -
198D LEU 3.0 4.0 + - - -
199D PRO* 3.2 19.1 - - + +
200D GLY 2.7 23.4 + - - -
202D ILE* 4.5 1.2 - - - +
232D ASP* 4.2 18.4 - - + +
233D VAL* 4.4 9.4 - - + +
236D VAL* 4.2 12.6 - - + -
253D VAL 4.4 0.4 - - - +
254D GLU* 1.3 72.8 - - - +
256D THR* 1.3 53.9 + - - +
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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
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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) + - + + + + + -
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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