Contacts of the strand formed by residues 388 - 396 (chain A) in PDB entry 1WL4
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 MET 388 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90A MET* 3.9 34.3 - - + -
91A ILE* 5.9 2.2 - - + -
286A VAL* 3.2 15.7 - - - +
287A GLY* 4.3 4.7 - - - -
293A MET 3.9 1.9 - - - +
296A GLY* 3.8 11.1 - - - -
383A CYS* 3.7 3.3 - - - -
384A ILE* 2.9 57.6 + - + +
385A GLY 4.6 7.0 - - - +
386A GLY* 5.1 3.1 - - - +
387A GLY* 1.3 83.1 - - - +
389A GLY* 1.3 58.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 389 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90A MET* 5.3 0.2 - - - +
285A GLN* 3.3 4.9 - - - +
286A VAL* 2.9 34.2 + - - +
296A GLY 3.8 20.9 - - - -
300A ALA* 3.8 6.2 - - - +
382A LEU 3.4 11.0 - - - -
384A ILE* 4.1 4.3 - - - +
388A MET* 1.3 75.4 - - - +
390A ILE* 1.3 62.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 390 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90A MET* 4.4 7.4 - - - -
93A GLY* 3.9 15.9 - - - +
96A LEU* 4.1 9.0 - - + -
97A LYS* 3.6 47.1 - - + +
100A CYS* 4.1 15.9 - - - -
283A TRP* 4.9 0.9 - - + -
284A SER 3.3 13.2 - - - +
285A GLN* 4.7 7.2 - - + -
300A ALA* 3.8 4.2 - - - +
381A ALA* 3.1 4.5 - - - +
382A LEU* 2.9 47.4 + - + +
384A ILE* 3.9 18.8 - - + -
389A GLY* 1.3 75.0 - - - +
391A ALA* 1.3 63.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 391 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96A LEU* 4.3 4.3 - - - -
100A CYS* 5.0 0.2 - - - -
283A TRP* 3.1 6.6 - - - +
284A SER* 2.9 33.7 + - - +
300A ALA* 3.7 30.5 - - + +
301A ILE* 3.9 7.4 - - + +
304A ALA* 4.2 5.2 - - + -
379A VAL* 4.7 3.1 - - + -
380A ALA 3.1 11.0 - - - +
381A ALA* 3.8 10.5 - - + -
390A ILE* 1.3 78.7 - - - +
392A MET* 1.3 60.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 392 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96A LEU* 4.1 24.7 - - + -
99A VAL* 3.8 24.5 - - + -
100A CYS* 3.7 30.1 - - - +
103A VAL* 4.6 2.0 - - + -
280A ILE* 4.0 29.4 - - + -
282A SER 3.4 11.9 - - - +
283A TRP* 4.1 4.3 - - + +
304A ALA* 4.9 0.2 - - - -
363A LEU* 4.4 8.3 - - - -
378A GLY 3.9 0.5 - - - +
379A VAL* 3.2 6.2 - - - +
380A ALA* 2.8 35.7 + - + +
391A ALA* 1.3 75.1 - - - +
393A CYS* 1.3 71.9 + - - +
394A VAL* 4.0 17.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 393 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
280A ILE* 3.8 1.2 - - - -
281A VAL* 2.8 31.4 + - + -
282A SER* 2.8 34.9 + - - +
304A ALA* 3.6 26.0 - - - -
305A VAL* 3.8 16.4 - - - -
308A ALA* 4.3 1.3 - - + -
310A TRP* 3.7 28.9 - - + -
378A GLY 3.4 4.0 - - - -
379A VAL* 3.9 7.6 - - - -
392A MET* 1.3 71.9 - - - +
394A VAL* 1.3 60.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 394 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10A ILE* 4.7 4.9 - - + -
278A ALA* 4.2 7.2 - - + -
279A ARG 3.2 11.4 - - - +
280A ILE* 4.4 7.9 - - + -
281A VAL* 4.1 1.1 - - - -
310A TRP* 3.4 8.8 - - - -
363A LEU* 4.1 13.0 - - + -
366A LEU* 4.0 15.0 - - + -
367A LEU* 4.2 9.6 - - + -
370A LEU* 3.9 23.1 - - + -
378A GLY 2.9 39.0 + - - +
392A MET* 4.0 25.6 - - + +
393A CYS* 1.3 79.8 - - - +
395A GLN* 1.3 61.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 395 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
278A ALA* 3.8 3.6 - - - -
279A ARG* 2.8 71.5 + - + +
281A VAL* 3.8 14.2 - - + +
310A TRP* 3.5 14.0 + - + -
376A SER* 3.2 20.6 + - - +
377A ARG* 3.5 38.8 + - + +
394A VAL* 1.3 76.0 - - - +
396A ARG* 1.3 72.8 + - - +
397A GLU* 3.3 0.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 396 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
277A LEU 3.4 18.8 - - - +
278A ALA* 4.0 2.4 - - + +
279A ARG* 5.9 0.2 + - - -
367A LEU 5.3 0.2 - - - -
370A LEU* 4.0 9.7 - - + +
371A GLU* 3.8 36.2 + - - +
374A GLY* 3.5 28.2 + - - -
375A ARG 3.0 37.6 + - - +
376A SER* 2.7 16.2 + - - +
395A GLN* 1.3 80.2 + - - +
397A GLU* 1.3 74.8 + - - +
----------------------------------------------------------
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