Contacts of the strand formed by residues 247 - 250 (chain D) in PDB entry 3EI4
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 HIS 247 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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163D LYS* 5.2 8.2 + - - -
206D SER* 3.6 3.4 - - - -
207D LEU 5.5 0.4 - - - -
245D VAL 3.4 0.8 - - - -
246D THR* 1.3 83.2 + - - +
248D VAL* 1.3 83.5 + - - +
249D ALA* 3.6 24.0 - - + -
259D ALA 4.0 0.5 - - - +
260D THR* 3.6 2.1 - - - +
261D ALA* 2.8 33.7 + - + +
292D ASN 4.0 0.9 - - - +
293D ALA* 3.2 41.9 - - + +
294D ALA 3.5 21.0 + - - +
295D CYS* 3.8 18.0 - - + +
341D LYS* 3.3 19.2 - - + +
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Residues in contact with VAL 248 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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163D LYS* 4.5 0.3 + - - -
206D SER* 3.6 24.2 - - - +
207D LEU 3.0 24.3 + - - +
208D ASP* 3.3 5.0 - - + +
217D VAL* 3.6 40.8 - - + +
218D THR 4.5 1.1 - - - -
219D GLY* 4.0 13.2 - - - +
225D VAL* 4.9 4.3 - - + -
245D VAL* 3.7 15.0 - - + -
247D HIS* 1.3 85.2 + - - +
249D ALA* 1.3 65.9 + - - +
258D LEU* 3.7 12.1 - - + -
259D ALA 3.6 3.4 - - - -
260D THR* 3.8 9.9 - - + -
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Residues in contact with ALA 249 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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163D LYS* 5.5 1.1 - - - +
208D ASP* 3.4 10.5 - - - +
247D HIS* 3.6 19.5 - - + -
248D VAL* 1.3 78.2 - - - +
250D LEU* 1.3 60.5 + - - +
258D LEU* 3.8 2.7 - - - -
259D ALA* 2.8 35.1 + - + +
294D ALA 3.8 11.4 - - - +
295D CYS* 4.4 9.6 - - + -
296D PHE* 3.4 15.2 - - + +
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Residues in contact with LEU 250 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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208D ASP* 3.0 44.8 + - + +
209D VAL 4.1 9.6 - - - +
210D SER* 4.0 20.4 - - - -
213D SER* 4.4 0.2 - - - +
215D MET* 4.1 20.6 - - + -
217D VAL* 3.7 22.9 - - + -
227D LEU* 5.3 0.9 - - + -
249D ALA* 1.3 74.5 - - - +
251D ASN* 1.3 65.1 + - - +
252D PRO* 3.5 4.9 - - - +
255D ASP 3.9 19.7 - - - +
257D PHE 3.7 9.9 - - - +
258D LEU* 4.2 14.6 - - + +
272D LEU* 4.9 10.1 - - + -
296D PHE* 3.9 2.7 - - - -
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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
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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