Contacts of the strand formed by residues 326 - 331 (chain K) 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 ILE 326 (chain K).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
324K ASP 5.4 0.7 - - - +
325K LEU* 1.3 74.1 - - - +
327K ALA* 1.3 61.9 + - - +
340K GLN 3.4 1.1 - - - +
341K ILE* 2.9 6.3 - - - -
342K TYR* 2.8 43.6 + - + +
343K GLN 5.5 1.8 - - - +
387K PRO* 4.5 1.1 - - - -
388K LYS* 3.4 8.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 327 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
326K ILE* 1.3 76.4 - - - +
328K GLU* 1.3 60.7 + - - +
339K TYR* 5.7 3.6 - - + -
340K GLN 3.1 6.7 - - - +
341K ILE* 4.8 5.2 - - + -
375K ILE* 5.5 11.0 - - + -
387K PRO* 3.8 20.6 - - + -
388K LYS 2.9 9.9 + - - +
389K PHE* 4.4 9.9 - - + -
390K LYS* 3.0 30.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 328 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
327K ALA* 1.3 76.7 - - - +
329K ILE* 1.3 56.2 + - - +
338K THR 3.6 0.2 - - - +
339K TYR* 2.8 33.6 - - - +
340K GLN* 2.8 18.9 + - + +
390K LYS* 4.3 12.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 329 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
327K ALA 4.5 0.2 + - - -
328K GLU* 1.3 75.9 - - - +
330K GLN* 1.3 61.1 + - - +
337K TRP* 5.5 6.5 - - + -
338K THR 2.9 8.5 - - - +
339K TYR* 4.6 6.3 - - + -
371K ALA* 5.7 8.1 - - + -
390K LYS 4.0 11.9 + - - +
391K LEU* 5.8 2.0 - - - -
392K PRO* 3.7 22.6 - - + +
419K THR* 5.0 3.6 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 330 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
328K GLU 4.4 0.2 - - - -
329K ILE* 1.3 75.5 - - - +
331K LYS* 1.3 64.4 + - - +
337K TRP* 3.2 8.9 - - - +
338K THR* 2.7 44.7 + - - +
392K PRO* 5.1 0.7 - - - -
419K THR* 4.9 14.8 - - - -
422K LEU* 5.3 6.5 - - + -
423K VAL* 4.7 21.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 331 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
405J TYR 4.4 4.2 - - - +
406J TRP* 2.5 40.2 + - - +
407J GLN* 4.1 12.8 - - - +
408J ALA* 4.3 8.3 - - + +
330K GLN* 1.3 74.9 - - - +
332K GLN* 1.3 60.1 + - - +
333K GLY 3.5 3.8 + - - +
336K GLN 4.2 3.6 - - - +
337K TRP* 4.7 2.0 - - - +
392K PRO* 5.1 4.4 - - + +
419K THR* 5.8 0.2 - - - -
423K VAL* 4.4 16.5 - - - +
----------------------------------------------------------
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