Contacts of the helix formed by residues 258 - 264 (chain O) in PDB entry 3V3K
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 VAL 258 (chain O).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
240O PRO* 3.8 13.5 - - + +
241O GLY* 3.2 27.7 + - - +
242O ALA* 4.3 4.7 - - - +
243O VAL* 4.6 6.1 - - + -
256O VAL 3.7 0.8 + - - +
257O SER* 1.3 69.4 - - - +
259O GLU* 1.3 64.9 + - - +
261O ILE* 3.3 11.0 + - + +
262O VAL* 3.1 32.9 + - + +
280O PHE* 6.4 0.2 - - + -
282O ILE* 3.3 44.6 - - + -
329O VAL* 3.9 8.7 - - + -
331O TYR* 3.8 17.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 259 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
240O PHE* 3.4 108.1 + - + +
257O SER* 4.2 9.7 + - - +
258O VAL* 1.3 77.8 - - - +
260O LYS* 1.3 61.7 + - - +
262O VAL* 4.1 1.6 - - - +
263O ASN* 3.0 43.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 260 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
212O VAL* 4.4 32.2 - - + +
256O VAL* 5.0 8.5 - - + -
257O SER* 3.1 26.2 + - - +
259O GLU* 1.3 77.7 - - - +
261O ILE* 1.3 64.7 + - - +
263O ASN* 3.5 5.3 + - - +
264O ILE* 3.5 29.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 261 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
211O MET* 5.0 0.9 - - + -
215O LEU* 3.6 30.1 - - + -
232O VAL* 4.8 0.2 - - + -
234O ILE* 3.4 31.2 - - + -
243O VAL* 3.7 20.2 - - + -
256O VAL* 3.7 17.3 - - + +
257O SER 3.1 14.8 + - - +
258O VAL* 3.3 15.4 + - + +
260O LYS* 1.3 78.3 - - + +
262O VAL* 1.3 61.9 + - + +
264O ILE* 3.7 12.7 - - + +
265O PHE* 3.3 20.1 - - - -
280O PHE* 3.9 21.3 - - + -
282O ILE* 5.9 2.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 262 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
334M PHE* 5.4 1.1 - - + -
240O PHE* 4.6 17.9 - - - -
258O VAL* 3.1 24.0 + - + +
259O GLU 4.1 2.7 - - - +
261O ILE* 1.3 76.9 - - + +
263O ASN* 1.3 62.1 + - - +
264O ILE 3.2 0.2 - - - -
265O PHE* 2.9 26.3 + - - +
266O ASN* 3.7 4.0 + - + -
280O PHE* 3.8 20.9 - - + -
327O ILE* 3.3 40.2 - - + +
329O VAL* 3.6 26.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 263 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
334M PHE* 5.0 5.2 - - - -
240O GLN* 3.1 40.2 - - - +
259O GLU* 3.0 27.0 + - - +
260O LYS* 4.1 5.8 - - - +
261O ILE 3.5 0.4 - - - -
262O VAL* 1.3 77.2 - - - +
264O ILE* 1.3 58.7 + - - +
265O PHE 3.3 0.4 - - - -
266O ASN* 3.0 40.2 + - - +
269O SER* 3.6 6.2 + - - -
324O PRO* 5.5 2.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 264 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
212O VAL* 4.4 13.5 - - + +
215O LEU* 3.9 32.5 - - + +
216O LEU* 3.9 33.0 - - + -
219O ALA* 3.6 24.3 - - + +
260O LYS* 3.5 25.0 + - + +
261O ILE* 3.7 14.4 - - - +
262O VAL 3.1 0.6 + - - -
263O ASN* 1.3 78.0 - - - +
265O PHE* 1.3 62.4 + - + +
269O SER* 3.2 24.3 - - - -
270O CYS* 3.9 6.4 - - - +
----------------------------------------------------------
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