Contacts of the helix formed by residues 235 - 245 (chain D) in PDB entry 2GPV
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 ASN 235 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
234D TYR* 1.3 78.3 - - - +
236D LYS* 1.3 86.7 + - - +
237D ILE* 3.2 16.4 - - - +
238D VAL* 3.2 31.9 - - + +
239D SER* 3.3 25.2 + - - -
398D ALA* 3.4 25.3 - - - +
401D ASP* 5.1 10.4 + - + +
402D TYR* 4.5 12.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 236 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
234D TYR* 4.0 28.8 + - + +
235D ASN* 1.3 80.5 - - - +
237D ILE* 1.3 65.5 + - + +
239D SER* 3.5 3.1 + - - -
240D HIS* 3.2 21.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 237 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
235D ASN* 3.2 7.1 - - - +
236D LYS* 1.3 81.7 - - + +
238D VAL* 1.3 66.4 + - + +
240D HIS* 3.6 6.6 + - - +
241D LEU* 3.2 34.8 + - + +
287D PRO* 4.1 25.7 - - + +
394D VAL* 3.3 37.9 - - + +
395D LEU* 4.4 11.2 - - + -
397D GLU* 5.7 2.7 - - - +
398D ALA* 3.8 23.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 238 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
235D ASN* 3.2 31.6 + - + +
236D LYS 3.4 0.2 - - - -
237D ILE* 1.3 74.8 - - + +
239D SER* 1.3 62.7 + - - +
241D LEU* 3.1 6.6 + - - +
242D LEU* 2.8 34.1 + - + +
364D GLU* 3.8 42.8 - - + +
367D VAL* 4.5 2.2 - - + -
368D THR* 3.4 19.5 - - - +
398D ALA* 4.5 8.5 - - + +
402D TYR* 4.6 16.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 239 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
234D TYR* 3.3 34.3 - - - -
235D ASN 3.3 14.8 + - - -
236D LYS 3.8 3.1 - - - -
238D VAL* 1.3 78.0 - - - +
240D HIS* 1.3 62.5 + - - +
242D LEU* 3.5 15.3 + - - +
243D VAL* 3.2 28.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 240 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
236D LYS* 3.2 14.6 + - + +
237D ILE* 3.9 7.2 - - - +
238D VAL 3.2 0.4 - - - -
239D SER* 1.3 78.2 - - - +
241D LEU* 1.3 60.3 + - - +
243D VAL* 3.2 18.8 - - + +
244D ALA* 2.8 24.9 + - + +
285D HIS* 3.0 44.7 + - + +
287D PRO* 4.4 14.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 241 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
237D ILE* 3.2 29.5 + - + +
238D VAL* 3.1 7.5 + - - +
240D HIS* 1.3 74.7 - - - +
242D LEU* 1.3 61.5 + - - +
244D ALA* 3.1 8.7 + - + +
245D GLU* 2.9 29.5 + - - +
282D TRP* 4.6 13.7 + - - +
285D HIS 5.2 0.4 - - - +
286D ILE* 4.0 34.1 - - + -
287D PRO* 4.6 5.4 - - + -
367D VAL* 3.8 22.6 - - + +
368D THR* 3.9 34.3 - - + +
371D ALA* 4.2 14.8 - - + -
395D LEU* 4.3 3.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 242 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
238D VAL* 2.8 22.6 + - + +
239D SER* 3.5 19.3 - - - +
241D LEU* 1.3 76.5 - - - +
243D VAL* 1.3 61.5 + - + +
245D GLU* 3.3 20.2 - - - +
363D LYS* 4.3 30.6 - - + -
364D GLU* 4.1 36.8 - - + +
367D VAL* 4.4 10.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 243 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
239D SER 3.2 14.1 + - - +
240D HIS* 3.2 29.4 - - + +
242D LEU* 1.3 75.5 - - + +
244D ALA* 1.3 63.5 + - - +
245D GLU 3.2 5.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 244 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
240D HIS* 2.8 21.2 + - + +
241D LEU* 3.1 14.1 + - + +
243D VAL* 1.3 77.3 - - - +
245D GLU* 1.3 64.5 + - - +
246D PRO* 3.2 5.0 - - - +
282D TRP* 3.5 25.3 - - + +
285D HIS* 3.8 36.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 245 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
241D LEU 2.9 10.2 + - - +
242D LEU* 3.3 18.0 - - - +
243D VAL 3.2 6.8 - - - +
244D ALA* 1.3 75.9 - - - +
246D PRO* 1.4 85.5 - - - +
247D GLU* 5.4 1.6 - - - +
282D TRP* 4.5 4.2 + - - -
363D LYS* 4.2 23.1 - - - +
366D PHE* 3.6 14.0 - - - -
367D VAL* 3.4 21.3 - - + +
370D LYS* 3.0 32.6 + - - -
----------------------------------------------------------
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