Contacts of the helix formed by residues 325 - 337 (chain F) 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 F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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333E GLU* 5.5 7.6 - - - -
272F ARG* 4.4 8.8 + - - -
323F THR* 3.3 6.1 + - - -
324F GLY* 1.3 79.3 + - - +
326F LYS* 1.3 64.3 + - - +
327F MET* 3.4 21.7 + - - +
328F ASP* 3.5 27.5 + - - +
329F GLU* 3.8 7.4 + - - +
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Residues in contact with LYS 326 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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286F THR* 4.9 20.1 - - - +
287F GLY* 4.9 11.2 - - - +
324F GLY 4.4 0.4 + - - -
325F SER* 1.3 71.4 + - - +
327F MET* 1.3 64.8 + - - +
329F GLU* 3.1 20.1 + - + +
330F VAL* 3.2 21.7 + - + +
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Residues in contact with MET 327 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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272F ARG* 3.4 45.8 - - + +
275F ASN* 4.7 11.7 - - - -
287F GLY* 3.4 34.7 - - - +
288F GLY 4.7 6.3 - - - +
289F VAL* 3.7 22.0 - - + -
325F SER* 3.2 11.4 + - - +
326F LYS* 1.3 79.5 - - - +
328F ASP* 1.3 64.2 + - - +
330F VAL* 3.3 5.5 + - - +
331F ILE* 3.1 34.2 + - + +
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Residues in contact with ASP 328 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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268F THR* 3.3 24.9 + - + +
272F ARG* 2.8 36.6 + - - -
320F LEU 3.9 17.1 - - - +
321F ILE* 5.6 1.1 - - - -
322F ASP 6.2 0.2 - - - +
323F THR* 2.5 33.3 + - - +
325F SER* 3.5 9.8 + - - +
326F LYS 3.3 0.6 - - - -
327F MET* 1.3 82.5 - - - +
329F GLU* 1.3 58.9 + - - +
331F ILE* 3.8 9.1 - - - +
332F TYR* 2.9 28.9 + - - +
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Residues in contact with GLU 329 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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321F ILE* 4.2 15.6 - - - +
322F ASP* 4.9 6.4 + - - +
325F SER 3.8 4.3 + - - +
326F LYS* 3.1 21.7 + - + +
328F ASP* 1.3 76.8 - - - +
330F VAL* 1.3 61.4 + - + +
332F TYR* 3.3 23.6 + - - +
333F GLU* 2.8 34.6 + - + +
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Residues in contact with VAL 330 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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285F LEU* 6.1 5.4 - - + -
286F THR* 3.5 45.1 - - - +
289F VAL* 5.5 7.2 - - + -
294F LEU* 5.5 5.8 - - + -
326F LYS* 3.2 26.3 + - + +
327F MET* 3.3 5.6 + - - +
329F GLU* 1.3 78.0 - - + +
331F ILE* 1.3 57.5 + - + +
333F GLU* 3.4 6.9 + - + +
334F GLU* 2.9 31.5 + - + +
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Residues in contact with ILE 331 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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267F ILE* 4.0 10.5 - - + +
268F THR* 5.1 6.3 - - - +
271F ALA* 3.7 31.4 - - + +
272F ARG* 4.8 5.6 - - + +
275F ASN* 6.2 0.9 - - + -
289F VAL* 4.4 13.7 - - + -
294F LEU* 4.3 16.4 - - + -
327F MET* 3.1 35.5 + - + +
328F ASP* 3.8 11.4 - - - +
329F GLU 3.3 0.2 - - - -
330F VAL* 1.3 78.1 - - - +
332F TYR* 1.3 57.3 + - - +
334F GLU* 3.4 4.5 + - - +
335F PHE* 3.0 58.8 + - + -
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Residues in contact with TYR 332 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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175F LEU* 5.5 4.9 - - + -
177F VAL* 3.6 30.3 - - + -
267F ILE* 5.4 6.9 - - + +
319F ALA* 4.0 15.3 - - + -
320F LEU 4.8 3.4 - - - +
321F ILE* 3.5 29.8 - - + +
328F ASP 2.9 18.8 + - - +
329F GLU* 3.7 19.5 - - - +
330F VAL 3.3 0.2 - - - -
331F ILE* 1.3 78.4 - - - +
333F GLU* 1.3 72.7 + - - +
335F PHE* 3.5 3.6 + - - +
336F LYS* 3.0 58.1 + - + +
342F GLU* 5.6 0.7 - - + -
344F HIS* 3.1 27.2 + - - -
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Residues in contact with GLU 333 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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329F GLU* 2.8 27.6 + - + +
330F VAL* 3.9 7.0 - - + +
332F TYR* 1.3 90.0 - - + +
334F GLU* 1.3 61.4 + - - +
336F LYS* 3.8 21.1 + - - +
337F GLY* 4.0 4.3 + - - -
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Residues in contact with GLU 334 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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294F LEU* 3.9 30.5 - - + +
298F LYS* 5.5 10.6 + - + +
330F VAL* 2.9 20.2 + - + +
331F ILE 3.9 3.1 - - - +
333F GLU* 1.3 76.1 - - - +
335F PHE* 1.3 71.8 + - + +
336F LYS 3.4 0.3 + - - -
337F GLY* 3.6 9.5 + - - -
338F THR* 3.7 10.6 + - - -
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Residues in contact with PHE 335 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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175F LEU* 3.5 21.0 - - + +
267F ILE* 4.1 36.3 - - + -
271F ALA* 4.4 2.9 - - + -
294F LEU* 4.0 34.8 - - + -
297F PRO* 3.6 34.8 - - + -
298F LYS* 4.5 11.7 - - + -
301F PHE* 4.4 15.0 - + + -
331F ILE* 3.0 36.6 + - + +
332F TYR* 4.2 3.4 - - - +
334F GLU* 1.3 81.6 - - + +
336F LYS* 1.3 64.8 + - - +
338F THR* 3.3 19.7 + - - -
339F GLY 3.6 6.4 + - - -
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Residues in contact with LYS 336 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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175F LEU* 4.0 9.2 - - + +
332F TYR* 3.0 51.5 + - + +
333F GLU* 3.9 18.5 + - - +
334F GLU 3.2 0.4 - - - -
335F PHE* 1.3 78.6 - - - +
337F GLY* 1.3 56.3 + - - +
338F THR 3.1 4.3 + - - -
339F GLY 3.7 8.1 + - - +
342F GLU* 3.3 39.3 - - + +
344F HIS* 4.6 8.8 + - - -
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Residues in contact with GLY 337 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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333F GLU 4.0 4.9 + - - -
334F GLU 3.6 7.7 + - - -
335F PHE 3.3 0.8 - - - -
336F LYS* 1.3 77.7 - - - +
338F THR* 1.3 60.4 + - - +
339F GLY 4.4 2.3 - - - +
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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