Contacts of the helix formed by residues 337 - 354 (chain A) in PDB entry 6XWQ
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 337 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
335A PRO 5.1 0.9 - - - -
336A LEU* 1.3 75.8 - - - +
338A LEU* 1.3 61.9 + - - +
339A GLY* 3.7 5.4 - - - +
340A GLN* 3.1 32.9 - - + +
341A GLN* 2.6 38.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 338 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
337A THR* 1.3 81.4 + - - +
339A GLY* 1.3 63.3 + - - +
341A GLN* 3.2 10.9 + - - +
342A LEU* 2.9 49.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 339 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
128A GLN* 4.6 10.4 - - - +
337A THR* 3.3 6.5 - - - +
338A LEU* 1.3 82.8 - - - +
340A GLN* 1.3 60.3 + - - +
342A LEU* 3.2 6.3 + - - +
343A VAL* 2.9 29.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 340 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
127A ALA* 4.2 23.3 - - + +
128A GLN* 5.5 4.5 - - + +
334A HIS* 6.1 0.9 - - - +
335A PRO 3.8 5.9 + - - -
336A LEU* 3.3 38.3 - - + +
337A THR* 3.1 45.1 + - + +
339A GLY* 1.3 75.0 - - - +
341A GLN* 1.3 57.4 + - - +
343A VAL* 3.1 12.0 - - + +
344A VAL* 2.9 32.4 + - - +
373A VAL* 4.3 9.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 341 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
100A PHE* 3.7 32.0 - - + -
103A LEU* 3.6 24.8 - - + +
104A ILE* 6.5 0.2 - - - -
107A ARG* 5.0 11.3 + - - -
336A LEU* 4.7 3.1 - - + +
337A THR 2.6 22.9 + - - +
338A LEU* 3.4 8.8 - - - +
339A GLY 3.2 0.2 - - - -
340A GLN* 1.3 71.8 - - - +
342A LEU* 1.3 75.6 + - + +
344A VAL* 3.1 10.8 - - - +
345A VAL* 2.9 33.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 342 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
338A LEU* 2.9 41.2 + - + +
339A GLY* 3.2 6.7 + - - +
341A GLN* 1.3 97.2 - - + +
343A VAL* 1.3 58.2 + - - +
345A VAL* 3.5 24.3 - - + +
346A LEU* 3.8 11.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 343 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
127A ALA 5.0 0.4 - - - +
128A GLN* 4.3 27.8 - - + +
130A PRO* 3.8 35.9 - - + -
339A GLY 2.9 15.5 + - - +
340A GLN* 3.1 23.1 - - + +
342A LEU* 1.3 77.3 - - - +
344A VAL* 1.3 61.6 + - - +
345A VAL 3.3 0.4 - - - -
346A LEU* 3.2 7.9 + - + +
347A THR* 2.9 29.4 + - + +
372A SER 6.5 0.4 - - - -
373A VAL* 4.8 14.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 344 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99A VAL* 4.6 1.1 - - + -
103A LEU* 3.7 20.4 - - + -
322A GLY* 5.3 7.9 - - - -
325A VAL* 4.1 29.4 - - + -
336A LEU* 4.4 11.7 - - + -
340A GLN 2.9 17.9 + - - +
341A GLN* 3.1 22.0 - - - +
343A VAL* 1.3 77.8 - - + +
345A VAL* 1.3 59.4 + - - +
347A THR* 3.6 12.6 - - + -
348A ALA* 2.9 34.9 + - + +
369A VAL* 4.4 8.1 - - + -
373A VAL* 4.9 6.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 345 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96A ALA* 3.8 35.4 - - + +
99A VAL* 3.7 20.8 - - + +
100A PHE* 4.7 6.5 - - + +
103A LEU* 5.5 2.5 - - + -
341A GLN* 2.9 22.5 + - + +
342A LEU* 3.5 30.7 - - + +
344A VAL* 1.3 78.7 - - + +
346A LEU* 1.3 63.9 + - + +
348A ALA* 4.6 0.3 - - - +
349A VAL* 3.3 23.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 346 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
130A PRO* 4.9 18.8 - - + -
132A LEU* 3.8 33.4 - - + -
342A LEU 3.8 13.5 - - - +
343A VAL* 3.2 11.3 + - + +
344A VAL 3.1 0.4 - - - -
345A VAL* 1.3 84.4 - - + +
347A THR* 1.3 59.6 + - - +
349A VAL* 4.0 4.2 + - + +
350A LEU* 3.6 29.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 347 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
130A PRO* 5.8 6.3 - - - -
343A VAL* 2.9 23.8 + - + +
344A VAL* 3.5 13.9 - - + +
346A LEU* 1.3 77.0 - - - +
348A ALA* 1.3 61.9 + - - +
349A VAL 3.3 1.8 - - - -
350A LEU* 3.4 8.7 + - - +
351A ALA* 2.9 28.7 + - - +
368A MET 4.2 5.4 + - - -
369A VAL* 3.6 10.8 - - + +
372A SER* 3.3 37.3 - - - +
373A VAL* 5.6 0.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 348 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99A VAL* 3.9 28.3 - - + -
318A ALA* 4.6 7.1 - - - +
321A GLN* 3.8 19.1 - - + +
322A GLY 5.1 2.0 - - - +
344A VAL* 2.9 22.3 + - + +
345A VAL 4.6 0.2 - - - +
347A THR* 1.3 75.7 - - - +
349A VAL* 1.3 60.6 + - - +
351A ALA* 4.3 1.1 - - - -
352A SER* 2.9 33.8 + - - -
369A VAL* 4.4 8.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 349 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92A LEU* 4.6 13.0 - - + +
95A SER* 4.1 17.3 - - - +
96A ALA* 4.1 30.3 - - + +
99A VAL* 4.6 3.8 - - + -
345A VAL 3.3 19.7 + - - +
346A LEU* 4.1 7.0 - - + +
347A THR 3.3 0.4 - - - -
348A ALA* 1.3 77.4 - - - +
350A LEU* 1.3 65.2 + - + +
352A SER* 3.2 6.4 + - - -
353A ILE* 2.9 54.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 350 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92A LEU* 6.3 0.4 - - + -
132A LEU* 4.8 13.5 - - + +
135A THR* 3.6 38.7 + - + +
136A LEU* 6.1 7.4 - - + -
346A LEU* 3.6 28.7 - - + +
347A THR* 3.4 9.2 + - - +
348A ALA 3.4 0.2 - - - -
349A VAL* 1.3 87.8 - - + +
351A ALA* 1.3 58.5 + - - +
353A ILE* 4.3 13.1 - - + +
354A GLY* 4.0 11.6 + - - -
365A MET* 5.1 1.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 351 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
321A GLN* 3.6 18.2 - - - +
347A THR* 2.9 18.5 + - - +
348A ALA 3.9 0.2 - - - +
349A VAL 3.2 0.2 - - - -
350A LEU* 1.3 78.1 - - - +
352A SER* 1.3 58.9 + - - +
353A ILE 3.5 0.2 - - - -
354A GLY 4.3 0.4 - - - -
355A THR* 2.8 15.2 + - - -
365A MET* 3.2 40.2 - - + +
368A MET* 4.7 9.4 - - + +
369A VAL* 4.3 11.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 352 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95A SER* 5.3 2.1 - - - -
312A ILE 5.2 0.2 + - - -
314A MET* 3.2 39.9 + - - +
317A THR* 4.5 5.8 - - - -
318A ALA* 3.8 28.4 - - - +
321A GLN* 4.0 6.9 + - - +
348A ALA 2.9 19.0 + - - -
349A VAL* 3.2 6.8 + - - -
351A ALA* 1.3 74.5 - - - +
353A ILE* 1.3 71.1 + - - +
354A GLY 3.3 0.2 - - - -
355A THR* 3.0 16.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 353 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91A TYR* 6.2 1.3 - - + -
92A LEU* 3.7 22.2 - - + -
95A SER* 5.2 6.3 - - - +
153A VAL* 5.3 1.9 - - - +
154A LEU* 3.9 27.9 - - + +
311A THR 3.1 20.4 - - - +
312A ILE* 3.2 45.5 - - + +
349A VAL* 2.9 41.9 + - + +
350A LEU* 4.6 12.3 - - + +
352A SER* 1.3 80.8 + - - +
354A GLY* 1.3 57.9 + - - +
355A THR 3.1 5.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 354 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
153A VAL* 4.8 11.6 + - - +
154A LEU* 5.0 18.1 - - - +
350A LEU 4.0 12.3 + - - -
351A ALA 4.3 3.8 + - - -
352A SER 3.3 0.6 - - - -
353A ILE* 1.3 79.1 - - - +
355A THR* 1.3 59.8 + - - +
356A ALA 3.8 1.2 + - - -
365A MET* 4.6 13.2 - - - +
----------------------------------------------------------
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