Contacts of the strand formed by residues 317 - 323 (chain A) in PDB entry 1J71
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 THR 317 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
186A ALA* 4.2 22.0 - - + +
187A LEU 3.1 16.6 - - - +
188A PRO* 4.5 4.0 - - + -
189A VAL* 3.8 1.8 - - - +
195A LEU* 6.0 0.2 - - - +
312A ASP* 2.9 47.8 + - - +
315A ASP* 3.5 16.0 - - + +
316A LYS* 1.3 84.1 - - - +
318A ILE* 1.3 67.8 + - - +
319A SER* 4.9 0.9 + - - -
573A EOH 4.7 3.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 318 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
185A THR 3.8 0.7 - - - +
187A LEU* 2.8 33.7 + - - +
189A VAL* 3.9 13.2 - - + -
195A LEU* 3.9 39.3 - - + +
197A VAL* 3.7 26.5 - - + -
217A LEU* 3.9 15.0 - - + -
309A ILE* 3.7 28.3 - - + -
310A VAL 3.4 4.0 - - - +
311A TYR* 4.1 18.6 - - + -
317A THR* 1.3 80.1 - - - +
319A SER* 1.3 64.1 + - - +
320A LEU* 4.0 5.6 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 319 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
184A LEU* 4.2 13.9 - - - +
185A THR 3.2 11.7 - - - -
186A ALA* 3.3 23.6 + - - +
308A TYR 3.6 0.5 - - - +
309A ILE* 3.4 6.4 - - - +
310A VAL* 2.9 47.3 + - - -
317A THR* 4.2 1.8 + - - -
318A ILE* 1.3 72.2 - - - +
320A LEU* 1.3 62.9 - - - +
573A EOH 3.6 23.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 320 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
183A THR 3.9 2.4 - - - +
184A LEU* 3.8 2.2 - - - -
185A THR* 3.2 27.9 + - - +
187A LEU* 4.1 17.5 - - + -
197A VAL* 5.1 1.8 - - + -
217A LEU* 4.0 15.5 - - + -
264A PHE* 3.9 40.6 - - + -
268A VAL* 4.1 17.8 - - + +
270A ILE* 4.5 9.4 - - + -
303A PHE* 5.0 2.2 - - + -
307A ALA* 4.4 7.0 - - + -
308A TYR 3.6 2.5 - - - +
309A ILE* 3.4 39.3 - - + -
318A ILE* 4.3 5.4 - - + -
319A SER* 1.3 79.6 - - - +
321A ALA* 1.3 65.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 321 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
180A TYR* 3.8 26.7 - - + -
181A THR 4.0 6.1 - - - +
183A THR 4.3 4.3 - - - +
184A LEU* 3.5 24.9 - - + -
270A ILE* 3.6 12.1 - - - +
308A TYR 2.9 26.0 + - - +
320A LEU* 1.3 78.9 - - - +
322A GLN* 1.3 67.0 + - - +
323A VAL 3.3 0.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 322 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
180A TYR* 3.3 4.3 - - - +
181A THR* 3.0 47.1 + - - +
269A LYS 4.1 5.8 + - - +
270A ILE* 3.5 14.0 - - + +
271A THR* 2.8 53.9 + - - +
306A ARG* 3.4 28.9 + - - +
321A ALA* 1.3 70.8 - - - +
323A VAL* 1.3 70.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 323 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
159A TYR* 3.5 31.6 - - + -
179A LYS 3.5 13.5 - - - +
180A TYR* 4.3 0.4 - - - +
181A THR* 4.8 2.4 + - - +
305A ARG 3.7 7.9 - - - +
306A ARG* 3.1 47.6 + - - +
307A ALA 4.0 12.3 - - - +
308A TYR* 4.3 2.9 - - + +
321A ALA 3.3 3.5 + - - -
322A GLN* 1.3 84.2 + - - +
324A LYS* 1.3 64.8 + - - +
325A TYR* 3.7 24.3 - - + -
----------------------------------------------------------
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