Contacts of the helix formed by residues 325 - 337 (chain B) in PDB entry 6XAV
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 SER 325 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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333A GLU* 6.0 2.2 - - - -
272B ARG* 3.5 28.4 + - - -
323B THR* 3.2 7.6 + - - -
324B GLY* 1.3 78.3 + - - +
326B LYS* 1.3 64.8 + - - +
327B MET* 3.3 17.5 + - - +
328B ASP* 3.4 15.9 + - - +
329B GLU* 3.7 8.8 + - - +
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Residues in contact with LYS 326 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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286B THR* 6.0 5.4 - - + -
287B GLY* 4.2 22.0 - - - +
324B GLY 4.1 3.1 + - - +
325B SER* 1.3 70.9 + - - +
327B MET* 1.3 63.7 + - - +
329B GLU* 3.4 9.1 + - - +
330B VAL* 3.3 27.4 + - + +
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Residues in contact with MET 327 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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272B ARG* 3.4 45.1 - - + +
275B ASN* 4.1 18.4 - - - -
287B GLY 3.3 19.5 + - - +
288B GLY* 3.8 17.9 - - - +
289B VAL* 3.7 18.4 - - + -
325B SER* 3.2 9.9 + - - +
326B LYS* 1.3 79.3 - - - +
328B ASP* 1.3 62.5 + - - +
330B VAL* 3.3 3.8 + - - +
331B ILE* 3.1 37.5 + - + +
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Residues in contact with ASP 328 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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268B THR* 3.3 26.5 + - + +
269B ARG* 5.2 2.3 + - - -
272B ARG* 2.6 47.0 + - - +
320B LEU 4.2 10.9 - - - +
321B ILE* 5.8 1.3 - - - -
323B THR* 2.7 34.4 + - + +
325B SER* 3.4 5.3 + - - +
326B LYS 3.4 0.2 - - - -
327B MET* 1.3 78.0 - - - +
329B GLU* 1.3 58.0 + - - +
331B ILE* 3.8 8.1 - - - +
332B TYR* 2.9 30.5 + - - +
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Residues in contact with GLU 329 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
321B ILE* 4.6 12.0 - - - +
322B ASP* 4.9 9.5 + - - +
325B SER 3.7 6.2 + - - +
326B LYS* 3.4 14.7 + - - +
327B MET 3.2 1.0 - - - -
328B ASP* 1.3 76.1 - - - +
330B VAL* 1.3 61.2 + - + +
332B TYR* 3.4 17.4 + - - +
333B GLU* 2.8 46.3 + - + +
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Residues in contact with VAL 330 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
285B LEU* 6.3 4.0 - - + -
286B THR* 3.4 32.3 - - + +
287B GLY* 4.6 1.1 - - - -
289B VAL* 4.3 17.7 - - + -
294B LEU* 5.0 5.6 - - + +
326B LYS* 3.3 17.1 + - + +
327B MET 3.3 5.6 + - - +
329B GLU* 1.3 77.7 - - + +
331B ILE* 1.3 58.5 + - - +
333B GLU* 3.4 5.9 + - - +
334B GLU* 3.0 30.2 + - + +
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Residues in contact with ILE 331 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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267B ILE 4.9 3.4 - - - +
268B THR* 4.6 14.4 - - + +
271B ALA* 3.7 31.6 - - + -
272B ARG* 4.7 2.9 - - + +
275B ASN* 6.1 1.8 - - + -
289B VAL* 4.5 9.0 - - + -
294B LEU* 3.9 20.2 - - + -
327B MET* 3.1 35.9 + - + +
328B ASP* 3.8 13.5 - - - +
329B GLU 3.3 0.2 - - - -
330B VAL* 1.3 77.5 - - - +
332B TYR* 1.3 61.7 + - - +
334B GLU* 3.4 4.6 + - - +
335B PHE* 3.1 50.8 + - + -
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Residues in contact with TYR 332 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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175B LEU* 6.0 2.9 - - + -
177B VAL* 3.6 31.9 - - + +
268B THR* 6.0 0.9 - - - +
319B ALA* 4.1 20.0 - - + -
320B LEU 4.3 4.5 - - - +
321B ILE* 3.5 29.4 - - + +
328B ASP 2.9 19.0 + - - +
329B GLU* 3.8 13.7 - - - +
331B ILE* 1.3 78.7 - - - +
333B GLU* 1.3 78.9 + - - +
335B PHE* 3.4 4.8 + - + -
336B LYS* 3.0 54.6 + - + +
344B HIS* 3.7 21.3 + - - -
362B ARG* 5.2 3.5 + - - -
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Residues in contact with GLU 333 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
329B GLU* 2.8 31.6 + - + +
330B VAL* 4.0 6.3 - - + +
332B TYR* 1.3 96.6 - - - +
334B GLU* 1.3 61.3 + - - +
336B LYS* 3.8 30.2 + - - +
337B GLY 4.5 2.1 + - - -
269C ARG* 5.9 0.9 + - - -
323C THR 2.8 31.4 - - - +
324C GLY* 3.3 23.7 - - - +
325C SER* 4.5 6.7 - - - +
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Residues in contact with GLU 334 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
294B LEU* 4.2 25.4 - - + +
298B LYS* 4.4 17.1 + - + +
330B VAL* 3.0 20.2 + - + +
331B ILE 3.9 3.4 - - - +
333B GLU* 1.3 78.1 - - - +
335B PHE* 1.3 71.6 + - + +
336B LYS 3.2 0.9 + - - -
337B GLY* 3.9 5.7 + - - -
338B THR* 3.3 11.8 + - - -
210C ASP* 5.2 2.3 - - - +
269C ARG* 3.6 17.4 + - - +
272C ARG* 3.0 29.8 + - - -
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Residues in contact with PHE 335 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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175B LEU* 3.3 26.4 - - + +
267B ILE* 4.0 32.8 - - + -
271B ALA* 4.6 2.5 - - + -
294B LEU* 4.4 20.6 - - + -
297B PRO* 3.8 27.1 - - + -
298B LYS* 3.7 34.3 - - + -
301B PHE* 4.9 10.5 - + + -
331B ILE* 3.1 36.4 + - + +
332B TYR* 3.7 4.0 - - - +
334B GLU* 1.3 85.1 - - + +
336B LYS* 1.3 64.1 + - - +
337B GLY 3.4 0.2 - - - -
338B THR* 3.2 21.8 + - - +
339B GLY 3.8 0.7 + - - -
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Residues in contact with LYS 336 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
175B LEU* 4.6 7.1 - - - +
332B TYR* 3.0 46.2 + - + +
333B GLU* 3.8 29.1 + - - +
334B GLU 3.2 0.8 - - - -
335B PHE* 1.3 79.0 - - - +
337B GLY* 1.3 58.5 + - - +
338B THR 3.3 3.6 + - - -
339B GLY 4.2 3.1 + - - +
342B GLU* 3.3 32.8 - - + +
344B HIS* 5.3 8.6 - - - -
362B ARG* 5.8 3.4 - - - +
180C PRO* 5.8 11.5 - - - +
181C LYS* 5.4 13.7 - - - +
212C ARG* 4.8 0.2 + - - -
323C THR 6.2 0.4 - - - -
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Residues in contact with GLY 337 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
333B GLU 4.5 2.4 + - - -
334B GLU 3.9 6.7 + - - -
335B PHE 3.4 0.4 - - - -
336B LYS* 1.3 76.3 - - - +
338B THR* 1.3 55.5 + - - +
366B ARG* 6.3 0.4 - - - -
211C GLU* 5.7 0.3 - - - +
212C ARG* 2.8 27.6 + - - +
269C ARG* 5.1 12.7 + - - -
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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