Contacts of the strand formed by residues 329 - 334 (chain T) in PDB entry 1VYH
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 MET 329 (chain T).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
323T TRP* 3.5 17.0 - - - -
324T ASP* 3.7 18.8 + - - +
327T THR* 3.5 26.9 + - - +
328T GLY* 1.3 86.7 - - - +
330T CYS* 1.3 69.4 + - - +
331T LEU* 4.7 1.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 330 (chain T).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
274T GLU* 5.6 5.2 - - + -
295T GLU* 4.1 6.4 - - - +
321T LYS* 3.7 27.4 - - - +
322T MET 3.6 13.0 - - - -
323T TRP* 4.5 12.0 - - + -
329T MET* 1.3 79.6 - - - +
331T LEU* 1.3 71.4 + - - +
332T MET 3.8 9.0 - - - -
333T THR* 3.6 23.6 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 331 (chain T).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
291T SER* 5.5 3.8 - - - +
292T SER* 6.4 1.8 - - - -
295T GLU* 4.0 34.3 - - + +
310T PHE* 3.7 16.8 - - + -
322T MET* 3.0 49.8 + - + +
324T ASP* 3.3 40.4 - - + +
329T MET* 4.3 2.2 - - + +
330T CYS* 1.3 83.9 - - - +
332T MET* 1.3 67.6 + - + +
333T THR 4.1 0.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 332 (chain T).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
294T SER* 4.9 12.1 - - - -
295T GLU* 6.3 2.9 - - + -
320T ILE 5.0 0.2 - - - -
321T LYS* 3.4 2.5 - - - -
322T MET* 2.9 40.0 + - + +
330T CYS* 3.8 2.8 - - - -
331T LEU* 1.3 87.1 - - + +
333T THR* 1.3 62.6 + - - +
334T LEU* 3.7 20.2 - - + +
367T TYR* 2.8 63.7 - - + +
369T ASN* 5.5 0.2 - - - -
370T LYS* 3.4 40.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 333 (chain T).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
319T THR* 3.6 34.5 - - + +
321T LYS* 3.6 38.2 + - + +
330T CYS* 3.6 8.7 - - - -
331T LEU 4.1 1.2 + - - -
332T MET* 1.3 71.7 + - - +
334T LEU* 1.3 66.5 + - - +
335T VAL* 3.0 11.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 334 (chain T).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
319T THR* 3.8 5.0 - - - -
320T ILE* 3.3 51.9 + - + +
322T MET* 5.8 1.8 - - + -
332T MET* 3.8 39.6 - - + +
333T THR* 1.3 71.1 - - - +
335T VAL* 1.3 62.4 + - - +
336T GLY 3.6 2.4 + - - -
353T ILE* 4.0 22.0 - - + -
365T TRP* 2.8 47.5 - - + -
366T ASP 6.0 0.2 - - - -
367T TYR* 4.3 10.5 - - + -
370T LYS* 5.3 12.8 - - + +
----------------------------------------------------------
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