Contacts of the strand formed by residues 310 - 319 (chain A) in PDB entry 3L81
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 ARG 310 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
303A GLN 3.9 1.6 - - - +
304A TRP* 3.2 4.3 - - - -
305A ASP* 2.9 36.3 + - + +
308A SER* 3.4 22.6 + - - +
309A GLY* 1.3 76.5 - - - +
311A LEU* 1.3 60.3 + - - +
312A GLN* 4.2 0.6 - - - +
343A LEU* 3.5 35.4 - - - +
379A GLN* 3.0 38.5 + - - +
380A MET 3.7 5.0 + - - -
381A ASP* 5.2 3.8 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 311 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
302A VAL* 3.7 30.1 - - + -
303A GLN 3.6 7.2 - - - +
304A TRP* 3.9 20.0 - - + -
309A GLY 3.4 0.8 + - - -
310A ARG* 1.3 75.6 - - - +
312A GLN* 1.3 58.5 + - - +
313A VAL* 4.0 6.7 - - + -
336A LEU* 4.7 3.4 - - + -
337A PRO* 4.4 19.5 - - + -
340A VAL* 5.2 0.7 - - + -
378A PHE 3.6 1.2 - - - +
379A GLN* 3.6 3.3 - - - +
380A MET* 2.8 68.2 + - + +
382A VAL* 3.8 28.0 - - + -
402A LEU* 4.8 7.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 312 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
301A SER* 3.6 3.0 + - - +
302A VAL* 3.3 5.7 - - - +
303A GLN* 2.8 74.6 + - + +
310A ARG 4.2 0.4 - - - -
311A LEU* 1.3 73.9 - - - +
313A VAL* 1.3 65.5 + - - +
314A TYR* 4.1 4.4 - - - +
377A LEU* 3.6 27.4 - - + +
378A PHE 3.4 2.9 - - - +
379A GLN* 3.1 33.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 313 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
301A SER 3.6 2.2 - - - -
302A VAL* 4.4 18.6 - - + -
311A LEU* 4.0 13.2 - - + -
312A GLN* 1.3 76.3 - - - +
314A TYR* 1.3 61.0 + - - +
315A LEU* 3.8 30.5 - - + -
334A LEU* 4.2 14.1 - - + -
336A LEU* 5.0 1.1 - - + -
361A LEU* 5.9 0.4 - - + -
377A LEU* 3.6 2.2 - - - -
378A PHE* 2.8 48.2 + - + +
380A MET* 3.2 29.8 - - + -
402A LEU* 4.5 11.0 - - + -
453A ILE* 6.3 0.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 314 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
299A PHE* 4.5 4.0 - - + -
300A PRO* 3.3 4.0 - - - +
301A SER* 2.7 60.3 + - - +
312A GLN* 4.1 4.2 - - - +
313A VAL* 1.3 74.7 - - - +
315A LEU* 1.3 62.0 + - - +
316A LYS* 4.0 28.2 - - + +
375A SER* 3.4 35.7 + - - -
376A GLY 3.5 12.1 - - - -
377A LEU* 3.8 26.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 315 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
298A LEU* 4.3 15.5 - - + -
299A PHE 3.9 1.3 - - - -
300A PRO* 3.8 20.6 - - + -
313A VAL* 3.8 21.5 - - + -
314A TYR* 1.3 84.7 - - - +
316A LYS* 1.3 59.8 + - - +
317A LEU 4.2 0.2 - - - -
332A LEU* 3.9 20.0 - - + -
334A LEU* 4.5 8.3 - - + -
361A LEU* 4.3 9.0 - - + -
363A TRP* 3.6 36.1 - - + -
375A SER* 3.0 6.5 - - - -
376A GLY 2.8 38.1 + - - +
378A PHE* 4.1 14.4 - - + -
453A ILE* 4.9 3.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 316 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
298A LEU* 3.5 6.4 - - - +
299A PHE* 2.9 69.6 + - + +
314A TYR* 4.0 24.2 - - + +
315A LEU* 1.3 74.3 - - - +
317A LEU* 1.3 65.6 + - - +
318A ARG* 5.1 1.6 - - - -
373A GLN* 3.1 40.5 - - + +
374A LEU 3.4 11.0 - - - +
375A SER* 4.2 3.1 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 317 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
296A PHE* 3.9 33.7 - - + -
297A ARG 3.5 15.9 - - - +
298A LEU* 4.2 16.6 - - + -
315A LEU 4.2 0.4 - - - -
316A LYS* 1.3 75.9 - - - +
318A ARG* 1.3 59.3 + - - +
319A CYS 4.2 0.2 - - - -
330A VAL* 4.3 20.9 - - + -
332A LEU* 5.3 0.4 - - + -
363A TRP* 4.6 12.3 - - + -
365A LEU* 4.4 18.4 - - + -
368A VAL* 5.7 0.7 - - + -
373A GLN* 3.4 3.5 - - - -
374A LEU* 2.8 45.4 + - + +
407A LEU* 4.0 25.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 318 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
296A PHE* 3.4 8.1 - - - -
297A ARG* 2.8 52.6 + - + +
299A PHE* 3.5 35.1 - - + -
316A LYS* 4.1 1.7 + - - -
317A LEU* 1.3 73.3 - - - +
319A CYS* 1.3 65.4 + - - +
320A ASP* 2.6 38.8 + - - +
371A GLY* 5.0 2.7 - - - +
372A SER 3.4 10.1 - - - +
373A GLN* 3.8 28.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 319 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
295A PRO 3.4 8.5 - - - -
296A PHE* 3.9 9.4 - - + -
317A LEU* 4.2 0.8 + - - +
318A ARG* 1.3 72.1 - - - +
320A ASP* 1.3 63.6 + - - +
321A LEU* 3.4 40.8 - - - -
368A VAL* 3.8 24.0 - - + -
369A GLN 3.3 28.5 - - - +
371A GLY* 2.9 28.1 + - - -
372A SER* 3.0 10.4 + - - +
374A LEU* 5.3 0.6 - - + +
----------------------------------------------------------
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