Contacts of the helix formed by residues 337 - 354 (chain B) 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 B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
128B GLN* 6.0 1.8 - - - +
335B PRO 5.2 0.4 - - - -
336B LEU* 1.3 75.0 - - - +
338B LEU* 1.3 66.8 + - - +
339B GLY* 3.9 4.7 + - - +
340B GLN* 3.2 32.1 - - + +
341B GLN* 2.6 40.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 338 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
337B THR* 1.3 82.8 + - - +
339B GLY* 1.3 61.8 + - - +
341B GLN* 3.3 9.9 + - - +
342B LEU* 2.9 51.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 339 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
128B GLN* 5.2 11.5 - - - -
337B THR* 3.3 6.0 + - - +
338B LEU* 1.3 84.7 - - - +
340B GLN* 1.3 60.8 + - - +
342B LEU* 3.2 6.0 + - - +
343B VAL* 2.9 29.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 340 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
127B ALA* 4.3 8.4 - - + +
128B GLN* 4.7 15.7 - - + +
334B HIS* 3.7 21.9 + - - -
335B PRO 3.4 8.7 + - - -
336B LEU* 3.3 37.4 - - + +
337B THR* 3.2 44.3 + - + +
339B GLY* 1.3 76.1 - - - +
341B GLN* 1.3 56.9 + - - +
343B VAL* 3.1 11.3 - - + +
344B VAL* 2.9 32.4 + - - +
373B VAL* 4.3 12.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 341 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
100B PHE* 3.7 31.0 - - + -
103B LEU* 3.5 24.9 - - + +
104B ILE* 6.2 0.4 - - - +
107B ARG* 4.8 13.9 + - - -
336B LEU* 4.6 4.9 - - + +
337B THR 2.6 22.0 + - - +
338B LEU* 3.5 8.6 - - - +
340B GLN* 1.3 72.6 - - - +
342B LEU* 1.3 76.0 + - + +
344B VAL* 3.1 10.5 - - - +
345B VAL* 3.0 32.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 342 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
338B LEU* 2.9 41.0 + - + +
339B GLY* 3.2 6.2 + - - +
341B GLN* 1.3 98.3 - - + +
343B VAL* 1.3 57.9 + - - +
345B VAL* 3.5 25.2 - - + +
346B LEU* 3.9 11.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 343 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
127B ALA 5.1 1.1 - - - +
128B GLN* 4.6 23.3 - - + +
129B PRO 5.7 0.2 - - - -
130B PRO* 3.8 37.5 - - + -
339B GLY 2.9 16.4 + - - +
340B GLN* 3.1 23.1 - - + +
342B LEU* 1.3 77.2 - - - +
344B VAL* 1.3 62.2 + - - +
345B VAL 3.3 0.4 - - - -
346B LEU* 3.2 8.1 + - + +
347B THR* 2.9 30.6 + - + +
372B SER* 6.4 2.0 - - - -
373B VAL* 4.9 13.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 344 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99B VAL* 4.6 1.3 - - + -
103B LEU* 3.8 17.7 - - + -
322B GLY* 5.2 8.5 - - - +
325B VAL* 4.1 28.3 - - + -
336B LEU* 4.2 12.6 - - + -
340B GLN 2.9 23.0 + - - +
341B GLN* 3.1 18.4 - - - +
343B VAL* 1.3 77.2 - - + +
345B VAL* 1.3 59.2 + - - +
347B THR* 3.6 7.2 - - + -
348B ALA* 2.9 34.7 + - + +
369B VAL* 4.3 16.4 - - + -
373B VAL* 4.9 6.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 345 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96B ALA* 3.9 30.5 - - + +
99B VAL* 3.6 27.2 - - + +
100B PHE* 4.8 6.1 - - + +
103B LEU* 5.4 2.5 - - + -
341B GLN* 3.0 21.6 + - + +
342B LEU* 3.5 31.0 - - + +
344B VAL* 1.3 77.5 - - - +
346B LEU* 1.3 65.3 + - + +
349B VAL* 3.5 22.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 346 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
130B PRO* 4.9 18.6 - - + -
132B LEU* 3.8 34.5 - - + -
342B LEU 3.9 13.5 - - - +
343B VAL* 3.2 10.7 + - + +
344B VAL 3.1 0.2 - - - -
345B VAL* 1.3 85.9 - - + +
347B THR* 1.3 61.0 + - - +
349B VAL* 3.9 4.9 + - + +
350B LEU* 3.6 28.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 347 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
130B PRO* 5.8 5.4 - - - -
343B VAL* 2.9 25.7 + - + +
344B VAL* 3.5 11.9 - - + +
346B LEU* 1.3 75.7 - - - +
348B ALA* 1.3 62.7 + - - +
349B VAL 3.3 1.8 - - - -
350B LEU* 3.4 8.6 + - - +
351B ALA* 2.9 28.0 + - - +
368B MET 4.2 6.6 + - - -
369B VAL* 3.6 12.2 - - + +
372B SER* 3.4 35.9 + - - +
373B VAL* 5.5 2.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 348 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99B VAL* 3.9 26.7 - - + -
318B ALA* 4.6 7.5 - - - +
321B GLN* 3.7 20.1 - - + +
322B GLY 5.0 2.0 - - - +
344B VAL* 2.9 22.0 + - + +
347B THR* 1.3 74.8 - - - +
349B VAL* 1.3 60.8 + - - +
351B ALA* 3.7 1.1 - - - -
352B SER* 2.9 33.1 + - - -
369B VAL* 4.3 9.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 349 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92B LEU* 4.6 12.3 - - + +
95B SER* 3.8 29.4 - - - +
96B ALA* 3.9 17.7 - - + +
99B VAL* 4.7 3.4 - - + -
345B VAL 3.5 18.9 + - - +
346B LEU* 4.0 6.7 - - + +
347B THR 3.3 0.2 - - - -
348B ALA* 1.3 78.8 - - - +
350B LEU* 1.3 68.9 + - + +
352B SER* 3.0 8.1 + - - -
353B ILE* 2.9 53.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 350 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92B LEU* 6.3 0.4 - - + -
132B LEU* 4.9 12.1 - - + +
135B THR* 3.6 36.7 + - + +
136B LEU* 6.1 7.6 - - + -
346B LEU* 3.6 29.2 - - + +
347B THR* 3.4 8.8 + - - +
348B ALA 3.3 0.4 - - - -
349B VAL* 1.3 89.1 - - + +
351B ALA* 1.3 57.4 + - - +
352B SER 3.5 0.2 - - - -
353B ILE* 4.2 11.8 - - + +
354B GLY* 3.8 13.2 + - - -
365B MET* 4.9 1.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 351 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
321B GLN* 3.4 23.6 - - - +
347B THR* 2.9 17.0 + - - +
348B ALA* 3.3 1.5 + - - +
349B VAL 3.2 0.2 - - - -
350B LEU* 1.3 78.1 - - - +
352B SER* 1.3 51.6 + - - +
354B GLY 4.3 0.9 - - - -
355B THR* 2.6 24.8 + - - -
365B MET* 3.2 35.9 - - + +
368B MET* 4.6 9.2 - - + +
369B VAL* 4.2 9.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 352 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95B SER* 5.2 2.6 - - - -
312B ILE 4.7 1.4 + - - -
314B MET* 3.2 42.3 + - - +
317B THR* 4.4 10.5 - - - -
318B ALA* 3.8 20.6 - - - +
321B GLN* 4.6 3.1 - - - -
348B ALA 2.9 14.4 + - - -
349B VAL* 3.0 15.8 + - - -
351B ALA* 1.3 77.5 - - - +
353B ILE* 1.3 67.6 + - - +
354B GLY 3.3 0.4 - - - -
355B THR* 3.2 16.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 353 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91B TYR* 6.3 0.9 - - + -
92B LEU* 3.7 22.9 - - + -
95B SER* 5.2 6.3 - - - +
153B VAL* 5.5 2.8 - - - +
154B LEU* 3.9 29.6 - - + +
311B THR 3.5 16.1 - - - +
312B ILE* 3.5 44.1 - - + +
349B VAL* 2.9 41.2 + - + +
350B LEU* 4.6 12.6 - - + -
352B SER* 1.3 81.1 + - - +
354B GLY* 1.3 56.9 + - - +
355B THR 3.1 4.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 354 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
153B VAL* 5.0 10.5 + - - +
154B LEU* 5.0 16.5 + - - +
350B LEU 3.8 13.8 + - - -
351B ALA 4.2 3.5 + - - -
352B SER 3.3 0.8 - - - -
353B ILE* 1.3 78.8 - - - +
355B THR* 1.3 59.2 + - - +
356B ALA 3.7 2.1 + - - -
365B MET* 4.4 13.6 - - - +
----------------------------------------------------------
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