Contacts of the strand formed by residues 307 - 318 (chain A) in PDB entry 2W77
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 VAL 307 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
300A PRO* 3.7 3.6 - - - +
301A LEU* 2.8 52.3 + - + -
302A THR* 3.5 30.7 + - + +
305A GLY 3.8 3.9 - - - +
306A ASN* 1.3 90.6 - - - +
308A ARG* 1.3 57.1 - - - +
336A LEU* 5.1 3.1 - - + -
337A GLU 3.2 11.2 - - - +
338A PHE* 4.1 29.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 308 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64A ARG* 4.6 7.1 - - - +
272A LYS* 5.7 1.2 - - - +
273A PRO* 4.1 8.8 + - + +
274A THR* 3.5 26.7 - - - +
275A HIS* 3.3 46.2 + - + +
299A GLY 3.3 7.6 - - - +
300A PRO* 4.1 6.7 - - + -
301A LEU* 4.1 7.1 - - - +
305A GLY 3.4 16.9 + - - +
306A ASN 4.4 3.8 + - - -
307A VAL* 1.3 72.3 - - - +
309A GLY* 1.3 58.5 + - - +
336A LEU* 3.3 4.2 - - - +
337A GLU* 2.7 72.4 + - + +
339A ASP* 2.7 44.3 + - - -
345A MET* 4.0 8.1 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 309 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
273A PRO* 3.2 8.0 - - - +
298A SER* 3.3 0.5 - - - -
299A GLY 2.8 35.5 + - - -
301A LEU* 4.0 7.1 - - - +
308A ARG* 1.3 75.3 - - - +
310A ARG* 1.3 64.0 + - - +
335A ILE 3.4 10.1 - - - -
336A LEU* 4.3 0.9 - - - -
1816A N8E 3.6 20.9 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 310 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
142A GLU* 2.9 40.2 + - - -
271A LYS* 3.3 30.5 - - + +
272A LYS 3.0 26.8 + - - +
273A PRO* 3.7 9.1 - - + +
274A THR* 4.8 4.2 - - - +
278A LYS* 4.8 4.6 - - - +
296A ASP* 2.8 39.7 + - - +
297A VAL 3.1 14.6 - - - +
298A SER* 3.1 20.1 + - - +
309A GLY* 1.3 76.2 - - - +
311A ALA* 1.3 65.4 + - - +
312A VAL* 4.8 5.6 - - + +
333A TYR* 3.8 2.6 - - + +
334A GLY* 3.5 4.7 - - - -
335A ILE* 3.1 41.6 + - + +
1816A N8E 3.7 4.2 - - - +
1822A PO4 4.7 3.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 311 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
295A LEU* 3.9 0.5 - - - +
296A ASP* 3.4 1.9 - - - -
297A VAL* 2.7 48.5 + - + +
310A ARG* 1.3 75.7 - - - +
312A VAL* 1.3 62.7 + - - +
333A TYR 3.3 7.6 - - - +
334A GLY* 5.1 0.2 - - - -
1816A N8E 3.5 30.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 312 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
241A ALA* 3.8 36.6 - - + +
242A ILE* 3.9 17.7 - - + -
271A LYS* 4.7 4.5 - - + -
294A GLU* 5.1 1.1 - - + -
295A LEU 3.1 14.1 - - - +
296A ASP* 4.0 19.5 - - + +
310A ARG* 4.8 3.4 - - + -
311A ALA* 1.3 78.3 - - - +
313A ALA* 1.3 66.3 + - - +
331A VAL* 4.8 0.9 - - + -
332A TYR* 3.2 4.2 - - - +
333A TYR* 2.8 56.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 313 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
294A GLU* 3.5 1.9 - - - +
295A LEU* 3.0 40.7 + - + +
312A VAL* 1.3 76.9 - - - +
314A ALA* 1.3 63.4 + - - +
331A VAL 3.2 7.9 - - - -
332A TYR* 4.0 22.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 314 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
239A ASP* 4.5 1.1 - - - +
241A ALA* 4.0 25.4 - - + -
292A ARG* 4.3 10.5 - - - +
293A SER 3.3 13.2 - - - +
294A GLU* 4.2 6.1 - - + +
313A ALA* 1.3 76.4 - - - +
315A TYR* 1.3 62.0 + - - +
329A THR* 4.7 0.4 - - - -
330A SER* 3.5 3.3 - - - -
331A VAL* 2.9 45.1 + - + +
332A TYR* 5.9 0.5 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 315 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
291A TYR 4.1 0.8 - - - +
292A ARG* 3.4 2.8 - - - +
293A SER* 2.8 44.4 + - - +
314A ALA* 1.3 75.1 - - - +
316A GLN* 1.3 63.9 + - - +
317A ASP* 4.1 22.0 + - + +
328A LYS* 3.2 43.8 - - + +
329A THR* 3.4 17.9 - - - -
330A SER* 3.8 16.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 316 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
183A ASN* 4.5 7.8 + - - +
239A ASP* 4.5 1.7 - - - +
290A ASN* 2.6 34.6 + - - +
291A TYR 3.3 7.9 - - - +
292A ARG* 2.8 49.0 + - + +
315A TYR* 1.3 79.4 - - - +
317A ASP* 1.3 65.3 + - - +
318A LYS* 4.8 15.6 - - + +
327A ARG 3.6 1.5 - - - +
328A LYS* 3.3 2.9 - - - +
329A THR* 2.7 53.9 + - + +
808A MET* 5.2 2.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 317 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
289A ASP 3.3 6.2 - - - +
291A TYR* 2.9 37.9 + - + +
315A TYR* 4.1 21.6 + - + +
316A GLN* 1.3 74.5 - - - +
318A LYS* 1.3 68.4 + - - +
319A HIS* 4.7 6.1 + - - -
326A GLU* 3.8 19.2 - - - +
327A ARG 3.8 3.2 - - - +
328A LYS* 4.0 23.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 318 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
184A ASN* 5.1 3.4 - - - +
289A ASP 3.3 4.5 - - - -
290A ASN* 3.7 36.6 - - - +
316A GLN* 4.8 12.8 - - + +
317A ASP* 1.3 79.7 + - - +
319A HIS* 1.3 78.3 + - - +
320A SER* 5.6 1.6 - - - -
325A TYR* 5.3 3.8 - - + -
326A GLU* 3.3 4.0 - - - +
327A ARG* 3.0 67.4 + - + +
329A THR* 6.1 1.8 - - - -
1819A PO4 3.1 30.0 + - - -
----------------------------------------------------------
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