Contacts of the strand formed by residues 288 - 295 (chain A) in PDB entry 3HA3
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 288 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
178A SER* 3.5 2.1 - - - -
179A VAL* 2.9 45.2 + - + +
181A TYR* 3.5 22.2 + - + +
217A THR* 4.5 2.1 + - - -
236A SER* 2.6 33.2 + - - -
238A ARG* 3.4 16.6 + - - +
282A PHE* 3.4 15.3 - - - -
287A LEU* 1.3 74.2 - - - +
289A CYS* 1.3 75.1 + - - +
290A SER* 4.1 8.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 289 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44A CYS* 4.1 0.9 - - - -
146A GLU* 3.8 22.9 - - - -
176A GLN* 4.0 4.5 - - - -
177A SER 3.4 20.6 - - - +
178A SER* 4.2 1.3 - - - -
235A LEU 3.6 0.2 - - - +
236A SER* 3.4 5.0 - - - -
237A LEU* 2.8 57.4 + - + +
238A ARG 4.6 1.9 - - - +
241A TYR* 3.8 27.8 - - + -
282A PHE* 3.9 3.9 - - + -
288A ASP* 1.3 81.6 + - - +
290A SER* 1.3 61.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 290 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
175A VAL 3.5 2.8 - - - +
176A GLN* 3.3 4.9 - - - -
177A SER 2.9 31.3 + - - +
179A VAL* 4.2 2.1 - - - +
217A THR* 2.7 31.2 + - - +
220A MET* 4.3 9.1 - - - +
234A PRO* 4.2 8.6 - - - +
235A LEU 3.3 6.1 - - - -
236A SER* 5.2 1.6 - - - -
237A LEU* 5.2 0.2 - - - -
288A ASP* 4.1 8.3 + - - -
289A CYS* 1.3 76.6 + - - +
291A LEU* 1.3 61.5 + - - +
292A VAL* 3.7 19.1 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 291 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64A LEU* 3.5 36.6 - - + -
65A ASN* 3.5 36.3 - - - +
68A LYS* 3.8 29.3 + - + -
174A THR* 3.8 15.5 - - + -
175A VAL 3.7 2.9 - - - +
176A GLN* 4.1 11.9 - - + +
234A PRO* 3.7 1.0 - - - +
235A LEU* 2.8 42.4 + - + +
237A LEU* 4.4 10.3 - - + +
289A CYS 4.3 0.2 + - - -
290A SER* 1.3 71.6 - - - +
292A VAL* 1.3 61.3 + - - +
293A THR* 4.2 3.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 292 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
174A THR* 3.2 5.7 - - - -
175A VAL 2.9 32.7 + - - +
217A THR* 5.1 0.7 - - + -
220A MET* 3.5 35.0 - - + -
221A VAL* 4.5 4.3 - - + -
231A VAL* 3.5 26.0 - - + -
234A PRO* 3.9 25.4 - - + -
290A SER* 4.0 6.5 - - - -
291A LEU* 1.3 75.2 - - - +
293A THR* 1.3 64.0 + - - +
294A TYR* 3.4 32.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 293 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68A LYS* 3.7 41.3 + - + +
69A LEU* 5.9 0.2 - - + -
172A ARG* 5.4 1.6 - - + -
173A MET 3.5 8.3 - - - +
174A THR* 3.9 8.4 - - + +
231A VAL* 3.6 14.4 - - - +
232A PRO* 3.4 32.8 + - + +
234A PRO* 5.6 0.6 - - - +
291A LEU* 4.2 2.5 + - - +
292A VAL* 1.3 76.5 - - - +
294A TYR* 1.3 63.3 + - - +
295A LEU* 3.8 28.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 294 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
160A PHE* 3.3 23.9 - + - -
172A ARG* 3.3 6.2 - - - +
173A MET* 2.8 53.0 + - + +
175A VAL* 3.5 23.1 - - + -
220A MET* 2.8 42.8 + - - +
224A GLY* 3.6 16.2 - - - -
229A PHE* 3.4 27.6 - + + -
230A THR 3.6 3.4 - - - -
231A VAL* 3.7 20.6 - - + -
292A VAL* 3.4 30.4 - - + +
293A THR* 1.3 73.6 - - - +
295A LEU* 1.3 62.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 295 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
171A GLY 4.1 2.7 - - - -
172A ARG* 3.6 43.3 - - + +
229A PHE* 3.4 5.1 - - - -
230A THR* 2.7 55.2 + - + +
232A PRO* 3.9 26.9 - - + -
293A THR* 3.8 20.9 - - + -
294A TYR* 1.3 73.5 - - - +
296A LYS* 1.3 64.4 + - - +
299A ALA* 3.9 12.3 - - + -
300A ALA 5.6 1.3 - - - +
----------------------------------------------------------
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