Contacts of the strand formed by residues 336 - 342 (chain G) in PDB entry 1HVU
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 GLN 336 (chain G).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
331G LYS* 4.2 1.2 - - - -
332G GLN* 3.7 10.3 + - + +
333G GLY* 3.3 26.6 + - - +
334G GLN 2.9 8.3 + - - +
335G GLY* 1.3 79.8 - - - +
337G TRP* 1.3 62.0 + - - +
353G LYS* 6.3 1.6 - - + -
354G TYR 3.7 4.3 - - - +
355G ALA* 3.9 13.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 337 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
329G ILE* 5.7 2.9 - - + -
330G GLN 3.6 14.6 - - - +
331G LYS* 4.9 3.1 - - - -
332G GLN* 4.3 3.1 - - - +
336G GLN* 1.3 76.7 - - - +
338G THR* 1.3 64.7 + - - +
353G LYS* 3.2 6.9 - - - +
354G TYR* 2.8 42.4 + - + +
371G ALA* 4.9 13.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 338 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
329G ILE* 2.9 5.7 - - - +
330G GLN* 2.7 39.8 + - - -
332G GLN* 4.7 11.9 - - - -
337G TRP* 1.3 76.7 - - - +
339G TYR* 1.3 62.8 + - - +
352G GLY 3.2 11.4 - - - -
353G LYS* 4.7 3.4 - - - -
354G TYR* 4.7 0.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 339 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
327G ALA* 5.8 2.9 - - + -
328G GLU 2.7 15.7 - - - +
329G ILE* 4.0 9.0 - - + -
338G THR* 1.3 79.1 - - - +
340G GLN* 1.3 64.0 + - - +
351G THR* 3.4 2.5 - - - -
352G GLY* 2.7 35.0 + - - +
354G TYR* 6.3 2.7 - - + -
371G ALA* 6.6 0.2 - - + -
375G ILE* 5.7 9.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 340 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
326G ILE 3.4 1.7 - - - +
327G ALA* 3.0 3.6 - - - +
328G GLU* 2.7 37.7 + - + +
339G TYR* 1.3 77.9 - - - +
341G ILE* 1.3 61.4 + - - +
342G TYR* 3.9 2.7 - - + -
348G ASN* 4.7 12.8 - - + -
350G LYS 3.4 10.3 - - - +
351G THR* 4.3 8.5 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 341 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
325G LEU* 6.1 3.1 - - + -
326G ILE 3.1 10.8 - - - +
327G ALA* 4.7 8.7 - - + -
340G GLN* 1.3 73.9 - - - +
342G TYR* 1.3 52.0 + - - +
348G ASN* 3.5 2.4 - - - +
349G LEU* 2.8 34.5 + - + +
350G LYS* 2.8 23.8 + - + +
379G SER* 6.4 1.8 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 342 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
325G LEU* 3.7 4.0 - - - -
326G ILE* 2.8 38.0 + - + +
340G GLN* 3.9 2.6 - - + -
341G ILE* 1.3 71.6 - - - +
343G GLN* 1.3 62.4 + - - +
344G GLU 4.2 8.1 - - - +
345G PRO* 4.8 7.0 - - + +
347G LYS 3.8 4.0 - - - +
348G ASN* 3.3 33.0 - - + +
349G LEU* 4.1 3.4 - - - +
----------------------------------------------------------
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