Contacts of the strand formed by residues 327 - 331 (chain C) 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 ILE 327 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
334A PHE* 4.7 6.3 - - + -
240C PHE* 4.4 9.9 - - - +
262C VAL* 3.3 42.4 - - + +
266C ASN* 4.9 9.0 - - + -
278C LYS* 3.6 34.8 - - + -
280C PHE* 4.5 4.3 - - + -
324C PRO* 3.4 28.9 - - + +
325C SER 3.9 0.9 - - - +
326C ASP* 1.3 77.0 - - - +
328C PHE* 1.3 67.1 + - - +
329C VAL* 4.2 13.7 - - + -
390C PHE 4.5 1.6 - - - +
393C PHE* 2.9 39.8 + - + -
394C LEU* 3.8 0.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 328 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
278C LYS 3.2 5.7 + - - -
279C LEU* 3.4 23.1 - - + -
280C PHE* 2.7 34.6 + - - -
281C PHE* 5.2 1.8 - + - -
327C ILE* 1.3 77.6 - - - +
329C VAL* 1.3 57.7 + - - +
330C SER* 4.0 15.7 - - - -
366C LEU* 3.7 25.4 - - + -
367C GLN* 4.6 8.7 - - + -
370C LEU* 3.4 34.8 - - + -
389C CYS* 3.7 22.7 - - + -
390C PHE 3.7 3.4 - - - -
392C ASN* 3.8 32.3 - - - -
394C LEU* 3.6 23.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 329 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
240C PHE* 4.6 12.1 - - + +
258C VAL* 4.0 3.4 - - + -
262C VAL* 3.7 28.9 - - + -
280C PHE* 3.5 7.9 - - + +
282C ILE* 3.5 32.3 - - + -
327C ILE* 4.2 11.0 - - + -
328C PHE* 1.3 77.4 - - - +
330C SER* 1.3 60.7 + - - +
331C TYR* 3.6 29.5 + - + -
389C CYS* 3.4 2.3 - - - -
390C PHE* 2.9 39.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 330 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
280C PHE 2.7 14.9 + - - -
281C PHE* 3.9 11.9 - - - -
282C ILE* 3.0 25.8 + - - +
328C PHE* 4.0 18.4 + - - -
329C VAL* 1.3 70.1 - - - +
331C TYR* 1.3 63.1 + - - +
349C TYR* 2.6 29.0 + - - -
370C LEU* 3.3 18.3 - - - +
388C GLY 3.7 3.1 + - - -
389C CYS* 4.1 7.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 331 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
390A PHE* 3.9 33.2 - + - -
393A PHE* 5.2 2.9 - - + -
240C PRO* 2.8 58.9 + - + +
241C GLY* 4.9 3.8 - - - -
258C VAL* 3.8 8.5 - - + +
282C ILE* 4.2 18.6 - - + -
329C VAL* 3.6 33.3 - - + +
330C SER* 1.3 74.3 + - - +
332C SER* 1.3 61.4 + - - +
333C THR 3.7 18.4 - - - +
335C PRO* 5.5 4.9 - - + -
349C TYR* 3.9 5.8 - - - -
387C PRO* 3.6 5.9 - - - +
388C GLY 2.7 37.5 + - - +
390C PHE* 4.3 5.6 - + + -
----------------------------------------------------------
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