Contacts of the helix formed by residues 337 - 354 (chain C) 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 C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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128C GLN* 6.3 0.2 - - - +
335C PRO 5.1 0.9 - - - -
336C LEU* 1.3 77.0 - - - +
338C LEU* 1.3 66.2 + - - +
339C GLY* 3.9 4.6 + - - +
340C GLN* 3.2 32.4 - - + +
341C GLN* 2.6 39.6 + - - +
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Residues in contact with LEU 338 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
337C THR* 1.3 83.3 + - - +
339C GLY* 1.3 61.9 + - - +
341C GLN* 3.3 10.5 + - - +
342C LEU* 2.9 51.5 + - + +
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Residues in contact with GLY 339 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
128C GLN* 5.3 9.4 - - - -
337C THR* 3.3 6.3 + - - +
338C LEU* 1.3 82.7 - - - +
340C GLN* 1.3 61.0 + - - +
342C LEU* 3.2 6.1 + - - +
343C VAL* 2.9 29.8 + - - +
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Residues in contact with GLN 340 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
127C ALA* 4.2 16.7 - - + +
128C GLN* 4.7 13.0 - - - +
334C HIS* 5.5 1.1 + - - +
335C PRO 3.9 5.9 + - - -
336C LEU* 3.3 43.6 - - + +
337C THR* 3.2 37.2 + - + +
339C GLY* 1.3 75.7 - - - +
341C GLN* 1.3 57.6 + - - +
343C VAL* 3.1 13.0 - - + +
344C VAL* 2.9 32.6 + - - +
373C VAL* 4.1 13.2 - - + +
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Residues in contact with GLN 341 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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100C PHE* 3.8 32.0 - - + -
103C LEU* 3.6 24.4 - - + +
104C ILE* 6.0 0.6 - - - +
107C ARG* 4.7 15.4 + - - -
336C LEU* 4.7 4.2 - - + +
337C THR 2.6 23.2 + - - +
338C LEU* 3.4 9.5 - - - +
340C GLN* 1.3 73.5 - - - +
342C LEU* 1.3 75.4 + - + +
344C VAL* 3.1 9.9 - - - +
345C VAL* 2.9 31.2 + - + +
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Residues in contact with LEU 342 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
338C LEU* 2.9 41.3 + - + +
339C GLY* 3.2 7.2 + - - +
341C GLN* 1.3 97.4 - - + +
343C VAL* 1.3 57.3 + - - +
345C VAL* 3.5 23.6 - - + +
346C LEU* 3.8 11.1 - - - +
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Residues in contact with VAL 343 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
127C ALA 4.8 0.9 - - - +
128C GLN* 4.4 23.1 - - + -
130C PRO* 3.8 38.3 - - + +
339C GLY 2.9 14.8 + - - +
340C GLN* 3.1 23.3 - - + +
342C LEU* 1.3 76.6 - - - +
344C VAL* 1.3 61.3 + - - +
345C VAL 3.3 0.4 - - - -
346C LEU* 3.2 7.6 + - + +
347C THR* 2.9 29.8 + - + +
373C VAL* 4.8 14.8 - - + -
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Residues in contact with VAL 344 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99C VAL* 4.6 1.1 - - + -
103C LEU* 3.7 19.1 - - + -
322C GLY* 5.2 8.5 - - - +
325C VAL* 3.9 28.7 - - + -
336C LEU* 4.4 11.4 - - + -
340C GLN 2.9 18.3 + - - +
341C GLN* 3.1 22.0 - - - +
343C VAL* 1.3 78.7 - - + +
345C VAL* 1.3 59.1 + - - +
347C THR* 3.6 6.5 - - + -
348C ALA* 2.9 34.1 + - + +
369C VAL* 4.2 16.4 - - + -
373C VAL* 4.9 5.4 - - + -
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Residues in contact with VAL 345 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96C ALA* 3.8 35.1 - - + +
99C VAL* 3.7 21.7 - - + +
100C PHE* 4.7 7.2 - - + +
103C LEU* 5.3 3.1 - - + -
341C GLN* 2.9 22.7 + - + +
342C LEU* 3.5 30.3 - - + +
344C VAL* 1.3 77.3 - - - +
346C LEU* 1.3 63.7 + - + +
349C VAL* 3.3 22.9 + - - +
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Residues in contact with LEU 346 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
130C PRO* 4.8 22.0 - - + -
132C LEU* 3.8 34.8 - - + -
342C LEU 3.8 13.5 - - - +
343C VAL* 3.2 10.0 + - + +
344C VAL 3.1 0.6 - - - -
345C VAL* 1.3 84.4 - - + +
347C THR* 1.3 60.6 + - - +
349C VAL* 4.0 4.8 + - + +
350C LEU* 3.6 28.2 + - + +
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Residues in contact with THR 347 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
130C PRO* 5.8 6.5 - - - -
343C VAL* 2.9 22.8 + - + +
344C VAL* 3.5 13.7 - - + +
346C LEU* 1.3 77.9 - - - +
348C ALA* 1.3 61.8 + - - +
349C VAL 3.3 0.9 - - - -
350C LEU* 3.4 8.7 + - - +
351C ALA* 2.9 27.8 + - - +
368C MET 4.1 6.8 + - - -
369C VAL* 3.6 11.7 - - + +
372C SER* 3.3 35.8 - - - +
373C VAL* 5.7 0.9 - - + -
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Residues in contact with ALA 348 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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99C VAL* 3.8 27.6 - - + -
318C ALA* 4.6 7.7 - - - +
321C GLN* 3.8 18.0 - - + +
322C GLY 5.0 2.0 - - - +
344C VAL* 2.9 21.5 + - + +
347C THR* 1.3 75.2 - - - +
349C VAL* 1.3 61.0 + - - +
351C ALA* 3.7 1.1 - - - -
352C SER* 2.9 33.7 + - - -
369C VAL* 4.4 8.7 - - + -
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Residues in contact with VAL 349 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92C LEU* 4.5 12.8 - - + +
95C SER* 4.1 16.4 - - - +
96C ALA* 4.1 30.1 - - + +
99C VAL* 4.6 3.8 - - + -
318C ALA* 5.5 0.2 - - - -
345C VAL 3.3 20.3 + - - +
346C LEU* 4.1 7.0 - - + +
347C THR 3.3 0.2 - - - -
348C ALA* 1.3 77.0 - - - +
350C LEU* 1.3 66.1 + - + +
352C SER* 3.2 6.8 + - - -
353C ILE* 2.9 54.9 + - + +
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Residues in contact with LEU 350 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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92C LEU* 6.3 0.7 - - + -
132C LEU* 4.8 13.9 - - + +
135C THR* 3.6 37.6 + - + +
136C LEU* 6.1 8.1 - - + -
346C LEU* 3.6 29.8 - - + +
347C THR* 3.4 9.0 + - - +
348C ALA 3.3 0.2 - - - -
349C VAL* 1.3 87.8 - - + +
351C ALA* 1.3 57.6 + - - +
352C SER 3.6 0.2 - - - -
353C ILE* 4.3 12.5 - - + +
354C GLY* 3.9 12.9 + - - -
365C MET* 5.0 2.1 - - - +
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Residues in contact with ALA 351 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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321C GLN* 3.5 19.2 + - - +
347C THR* 2.9 17.4 + - - +
348C ALA 3.9 0.4 - - - +
350C LEU* 1.3 79.4 - - - +
352C SER* 1.3 58.2 + - - +
354C GLY 4.4 0.7 - - - -
355C THR* 2.8 15.6 + - - -
365C MET* 3.2 40.4 - - + +
368C MET* 4.6 10.1 - - + +
369C VAL* 4.3 11.2 - - + -
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Residues in contact with SER 352 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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95C SER* 5.3 1.9 - - - -
312C ILE 4.6 1.6 + - - -
314C MET* 3.2 28.0 + - - +
317C THR* 4.4 9.9 - - - -
318C ALA* 3.8 34.3 - - - +
321C GLN* 4.0 5.4 + - - +
348C ALA 2.9 18.1 + - - -
349C VAL* 3.2 7.1 + - - -
351C ALA* 1.3 75.8 - - - +
353C ILE* 1.3 69.6 + - - +
354C GLY 3.3 0.4 - - - -
355C THR* 3.0 18.8 + - - -
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Residues in contact with ILE 353 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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91C TYR* 6.1 1.6 - - + -
92C LEU* 3.7 22.4 - - + -
95C SER* 5.2 6.1 - - - +
153C VAL* 5.3 2.4 - - - +
154C LEU* 4.0 27.5 - - + +
311C THR 3.4 17.2 - - - +
312C ILE* 3.5 45.6 - - + +
349C VAL* 2.9 41.8 + - + +
350C LEU* 4.6 11.7 - - + +
352C SER* 1.3 80.9 + - - +
354C GLY* 1.3 58.3 + - - +
355C THR 3.1 5.0 + - - +
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Residues in contact with GLY 354 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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153C VAL* 4.8 12.1 + - - +
154C LEU* 5.0 17.0 - - - +
350C LEU 3.9 12.7 + - - -
351C ALA 4.3 2.9 + - - -
352C SER 3.3 0.8 - - - -
353C ILE* 1.3 78.9 - - - +
355C THR* 1.3 61.1 + - - +
356C ALA 3.8 1.0 + - - -
365C MET* 4.5 13.0 - - - +
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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
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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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