Contacts of the strand formed by residues 316 - 319 (chain A) in PDB entry 5H1Y
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 316 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
239A VAL* 3.9 21.8 - - + -
240A ILE* 3.7 28.5 - - + -
243A CYS* 3.7 18.8 - - - -
258A PRO* 4.7 0.2 - - - -
260A GLY* 3.4 6.5 - - - +
262A ILE* 6.1 1.3 - - + -
277A LEU* 3.8 22.9 - - + -
281A CYS* 3.7 17.9 - - - -
292A LEU* 3.9 17.9 - - + -
293A ARG 3.1 2.0 + - - -
294A CYS* 3.1 30.9 - - - +
295A ALA 2.8 31.2 + - - -
314A VAL* 3.2 5.1 - - - +
315A HIS* 1.3 89.0 - - + +
317A MET* 1.3 55.2 + - - +
318A VAL* 5.6 0.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 317 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
258A PRO* 4.0 19.7 - - + -
260A GLY 3.0 6.7 + - - -
261A LEU* 3.5 25.0 - - + +
262A ILE* 2.9 27.5 + - - +
277A LEU* 5.7 0.2 - - - -
295A ALA* 3.2 16.6 - - + +
296A LEU 5.6 0.4 - - - +
297A CYS* 3.9 29.4 - - + -
306A GLN* 5.2 3.6 - - - +
310A ILE* 4.1 26.2 - - + -
314A VAL* 4.5 10.8 - - + -
316A MET* 1.3 76.2 - - - +
318A VAL* 1.3 68.8 + - - +
319A ALA* 4.5 0.4 - - + -
324A LEU* 4.5 13.0 - - - -
333A VAL* 4.8 16.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 318 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
262A ILE* 3.4 17.7 - - + +
264A CYS* 3.8 11.4 - - - -
270A ALA* 3.4 36.8 - - + +
273A THR* 4.5 7.2 - - + -
274A HIS* 3.9 19.7 - - + +
277A LEU* 3.7 28.7 - - + -
294A CYS* 6.1 0.2 - - + -
295A ALA 2.8 12.7 + - - +
296A LEU* 3.4 11.8 - - + +
297A CYS 2.8 25.0 + - - -
316A MET 5.6 0.4 - - - -
317A MET* 1.3 74.6 - - - +
319A ALA* 1.3 62.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 319 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
261A LEU* 4.6 2.2 - - + -
262A ILE 2.8 9.3 + - - +
263A ILE* 3.4 6.9 - - + -
264A CYS* 2.8 27.2 + - - +
270A ALA* 4.9 1.6 - - - -
297A CYS* 3.2 25.4 - - + +
298A ILE* 4.6 1.6 - - - -
317A MET* 4.1 6.5 - - + -
318A VAL* 1.3 77.1 - - - +
320A THR* 1.3 63.3 + - - +
324A LEU* 3.8 30.7 - - + -
----------------------------------------------------------
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