Contacts of the strand formed by residues 210 - 217 (chain B) in PDB entry 3V4P
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 PHE 210 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
136B TYR* 3.8 22.2 - + - -
138B LEU* 3.8 20.0 - - + -
176B SER 3.2 12.1 - - - -
208B PHE* 3.7 3.9 - - - +
209B SER* 1.3 83.8 - - - +
211B HIS* 1.3 77.1 + - - +
212B HIS* 3.8 11.9 - - + -
245B ALA* 3.4 33.4 - - + +
248B GLN* 3.9 26.9 - - + -
249B ALA* 4.9 7.0 - - + -
256B ILE* 5.2 3.1 - - + -
294B LEU* 3.7 31.6 - - + -
299B LEU* 3.4 9.4 - - - +
300B TYR* 3.1 35.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 211 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
175B GLY* 3.2 2.6 - - - -
176B SER* 2.6 52.5 + - - +
205B GLN* 4.4 10.5 - - - -
208B PHE* 3.5 11.2 - + + -
210B PHE* 1.3 76.7 - - - +
212B HIS* 1.3 78.2 + - - +
213B VAL* 3.4 12.1 + - + +
230B GLN* 3.7 28.8 + - - -
297B ASN* 3.7 16.2 - - + -
298B GLY 3.3 7.9 + - - -
299B LEU* 3.4 17.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 212 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
136B TYR* 2.6 38.9 + + - +
210B PHE* 3.8 17.4 - + + -
211B HIS* 1.3 81.1 + - - +
213B VAL* 1.3 62.8 + - - +
214B LEU 3.5 26.5 - - - -
215B SER* 3.1 29.2 + - - -
255B GLN* 3.4 21.1 + - + -
256B ILE* 4.0 12.7 - - + +
294B LEU* 4.4 12.8 - - + -
297B ASN 4.5 3.5 - - - +
298B GLY* 3.0 20.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 213 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
174B PHE* 2.9 43.9 + - + +
176B SER* 4.2 4.3 - - - +
211B HIS* 3.4 26.4 + - + +
212B HIS* 1.3 77.0 - - - +
214B LEU* 1.3 60.0 + - + +
215B SER 4.3 0.6 + - - -
226B GLU* 3.4 43.5 - - + +
230B GLN* 4.0 25.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 214 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
172B ILE 5.2 1.6 - - - +
173B GLY* 3.2 2.0 - - - -
174B PHE* 2.9 43.9 + - + +
212B HIS* 3.5 8.5 - - - -
213B VAL* 1.3 82.4 - - + +
215B SER* 1.3 78.3 + - - +
217B THR* 4.0 20.9 - - + -
222B ALA* 3.6 28.9 - - + +
223B PHE* 3.6 26.9 - - + +
226B GLU* 4.4 15.9 - - + -
227B VAL* 6.4 0.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 215 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
172B ILE 3.7 0.7 - - - +
212B HIS* 3.1 21.9 + - - -
214B LEU* 1.3 92.7 - - - +
216B LEU* 1.3 68.9 + - - +
217B THR* 3.0 8.4 + - - +
255B GLN 3.4 8.9 + - - -
256B ILE 3.4 15.9 - - - -
257B GLY* 5.3 1.3 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 216 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
134B ASP* 3.3 23.1 - - + +
135B LEU 3.3 29.4 - - - +
136B TYR* 4.2 5.6 - - + +
171B ARG* 2.6 60.6 + - - +
172B ILE 3.2 2.7 - - - -
173B GLY* 3.4 9.6 - - - +
214B LEU 3.8 1.2 + - - -
215B SER* 1.3 70.7 - - - +
217B THR* 1.3 58.8 + - - +
256B ILE* 3.1 17.5 + - + +
257B GLY 3.3 15.7 - - - +
258B TRP* 3.6 31.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 217 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
171B ARG* 3.4 9.1 - - - +
172B ILE* 2.8 37.0 + - + +
214B LEU* 4.0 23.1 - - + -
215B SER 3.7 11.2 - - - +
216B LEU* 1.3 73.9 - - - +
218B GLY* 1.3 67.3 + - - +
219B ASP* 3.5 30.7 + - + +
222B ALA* 5.1 2.7 - - + -
----------------------------------------------------------
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