Contacts of the strand formed by residues 279 - 285 (chain C) in PDB entry 3H90
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 ASP 279 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
235A ARG* 2.4 38.8 + - - -
246A GLN* 4.7 2.9 - - - +
242C THR* 5.7 2.5 - - - -
243C ARG 2.9 7.7 + - - +
244C PHE* 3.3 31.0 - - + -
245C ILE 3.0 23.9 + - - +
272C LEU* 4.7 1.1 - - - -
277C GLY 5.0 1.8 - - - +
278C SER* 1.3 75.5 - - - +
280C VAL* 1.3 66.3 + - - +
281C ILE* 5.5 2.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 280 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
245C ILE* 3.1 25.8 - - + +
268C GLU* 3.5 55.0 + - + +
271C ILE* 3.6 27.8 - - + -
272C LEU* 3.5 20.5 - - + +
278C SER* 4.7 0.7 - - - -
279C ASP* 1.3 85.3 - - - +
281C ILE* 1.3 66.0 + - - +
282C ILE* 4.5 8.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 281 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
246A GLN* 3.8 45.1 - - + +
247A ILE 4.7 0.4 - - - +
248A HIS* 4.5 15.5 - - + +
281A ILE* 4.3 17.7 - - + +
283A HIS* 4.1 24.5 - - + +
245C ILE 2.9 6.5 + - - +
246C GLN* 3.3 45.4 - - + +
247C ILE 3.3 4.9 + - - +
268C GLU* 4.6 2.2 - - - -
279C ASP* 5.5 3.8 - - - +
280C VAL* 1.3 77.3 - - - +
282C ILE* 1.3 66.6 + - - +
283C HIS 3.9 0.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 282 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
283A HIS* 3.0 33.4 + - + +
247C ILE* 3.4 26.9 - - + +
249C LEU* 3.7 33.9 - - + -
264C ALA* 4.0 28.0 - - + +
267C VAL* 4.6 6.3 - - + -
268C GLU* 4.0 31.9 + - + +
271C ILE* 4.7 4.0 - - + -
280C VAL* 4.5 7.6 - - + -
281C ILE* 1.3 80.1 - - - +
283C HIS* 1.3 72.4 + - - +
284C GLN* 3.7 3.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 283 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
261A HIS* 3.3 20.2 - + - -
264A ALA* 5.4 2.5 - - + -
265A ASP* 6.4 0.2 - - - -
268A GLU* 5.4 7.5 + - - -
281A ILE* 4.0 14.4 - - + +
282A ILE* 3.0 35.4 + - + +
284A GLN* 3.6 7.9 + - - -
1C ZN 2.2 31.6 - - - -
247C ILE 3.0 6.2 + - - +
248C HIS* 3.1 53.5 - + + +
249C LEU 2.8 24.1 + - - -
281C ILE 3.9 1.4 + - - -
282C ILE* 1.3 73.5 - - - +
284C GLN* 1.3 61.6 + - - +
285C ASP* 2.7 9.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 284 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
257A LEU* 3.9 19.2 - - + +
261A HIS* 3.7 12.0 - - - -
283A HIS* 3.6 17.5 + - - -
284A GLN* 3.3 47.3 + - + +
249C LEU* 3.5 3.8 - - + -
251C MET* 3.7 23.8 - - + -
257C LEU* 5.0 2.7 - - + +
260C ALA* 3.6 5.3 - - + +
261C HIS* 3.4 36.8 - - - +
264C ALA* 3.4 16.5 - - + +
282C ILE 3.7 2.2 - - - +
283C HIS* 1.3 75.8 + - - +
285C ASP* 1.3 62.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 285 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
257A LEU* 3.9 6.3 - - - +
261A HIS* 2.8 10.5 + - - -
1C ZN 2.1 30.3 - - - -
3C ZN 1.9 37.5 - - - -
232C HIS* 2.7 14.8 - - + -
248C HIS* 3.1 2.9 + - - -
249C LEU 2.8 11.9 + - - +
250C GLU* 3.4 3.8 - - + -
251C MET* 3.1 24.3 + - - +
283C HIS* 2.7 10.2 + - - -
284C GLN* 1.3 72.6 - - - +
286C PRO* 1.4 68.9 - - + +
288C SER* 5.2 3.8 - - - +
289C VAL* 5.5 6.1 - - + -
----------------------------------------------------------
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