Contacts of the helix formed by residues 331 - 344 (chain W) in PDB entry 6G0L
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 ALA 331 (chain W).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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286W VAL* 6.3 0.4 - - + -
287W PRO* 3.8 19.5 - - + +
327W ILE* 3.2 14.9 + - + +
330W LEU* 1.3 97.7 - - + +
332W PRO* 1.3 66.2 - - - +
333W GLU* 3.2 4.2 + - + +
334W GLN* 3.4 23.3 + - + +
335W VAL* 3.7 8.1 + - - +
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Residues in contact with PRO 332 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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328W VAL* 3.3 31.0 - - + +
329W LYS 5.2 0.7 - - - -
330W LEU 3.3 10.1 - - - +
331W ALA* 1.3 88.7 - - - +
333W GLU* 1.3 63.8 - - + +
335W VAL* 3.3 3.6 + - - +
336W LYS* 3.1 23.1 + - - +
1202W PHE* 5.6 11.2 - - + -
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Residues in contact with GLU 333 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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331W ALA* 3.2 1.9 + - + -
332W PRO* 1.3 80.8 - - + +
334W GLN* 1.3 62.5 + - + +
336W LYS* 3.0 37.7 + - - +
337W HIS* 3.0 36.4 + - - +
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Residues in contact with GLN 334 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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287W PRO* 4.1 19.2 + - + +
288W GLU* 3.0 38.8 + - - +
289W ARG* 3.5 14.5 + - - +
290W ILE* 4.6 15.3 + - + +
312W ARG* 5.4 3.8 - - - +
331W ALA* 3.4 21.7 + - + +
332W PRO 3.3 0.4 - - - -
333W GLU* 1.3 80.6 - - + +
335W VAL* 1.3 61.8 + - + +
337W HIS* 3.5 6.0 + - - +
338W PHE* 2.7 28.6 + - - +
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Residues in contact with VAL 335 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
290W ILE* 5.0 4.0 - - + -
307W TYR* 4.9 12.3 - - + +
327W ILE* 3.8 29.2 - - + +
328W VAL* 3.3 36.6 - - + -
331W ALA 3.7 9.6 + - - +
332W PRO 3.3 4.8 + - - +
334W GLN* 1.3 77.7 - - + +
336W LYS* 1.3 58.5 + - - +
338W PHE* 3.2 9.3 - - + +
339W GLN* 3.0 45.2 + - + +
1201W PRO* 5.2 3.4 - - + -
1202W PHE* 5.2 7.2 - - + -
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Residues in contact with LYS 336 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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332W PRO 3.1 14.2 + - - +
333W GLU* 3.0 45.8 + - - +
335W VAL* 1.3 73.9 - - - +
337W HIS* 1.3 85.9 + - - +
339W GLN* 3.5 6.9 + - - +
340W ASN* 3.2 25.8 + - + +
1202W PHE* 6.2 2.4 - - + -
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Residues in contact with HIS 337 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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333W GLU* 3.0 25.5 + - - +
334W GLN* 3.9 7.2 - - - +
336W LYS* 1.3 95.0 - - - +
338W PHE* 1.4 54.5 + - - +
340W ASN* 2.9 37.7 + - + +
341W ARG* 3.2 22.0 + - + +
449W PRO* 4.8 19.4 + - - +
450W ASP* 6.1 1.1 - - - -
452W ASN* 6.3 3.1 - - + -
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Residues in contact with PHE 338 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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289W ARG* 5.9 2.0 - - - +
290W ILE* 3.2 48.0 - - + +
291W ILE 4.2 0.7 - - - -
292W ASP* 4.0 10.8 - - - -
293W SER* 3.5 28.3 - - - -
307W TYR* 4.2 10.8 - + - -
334W GLN 2.7 20.1 + - - +
335W VAL* 3.1 15.2 + - + +
337W HIS* 1.4 67.7 - - - +
339W GLN* 1.3 90.8 + - - +
341W ARG* 3.3 43.0 - - - +
342W GLU* 2.9 36.4 - - - +
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Residues in contact with GLN 339 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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307W TYR* 4.3 12.7 + - - -
335W VAL* 3.0 25.9 + - + +
336W LYS* 3.8 6.7 - - - +
338W PHE* 1.3 104.0 - - - +
340W ASN* 1.4 55.4 + - - +
342W GLU* 3.2 16.8 + - - +
343W ASN* 2.8 36.8 + - + +
1189W TYR* 5.8 6.5 - - - +
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Residues in contact with ASN 340 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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336W LYS* 3.2 17.6 + - + +
337W HIS* 2.9 30.5 + - - +
339W GLN* 1.4 79.2 - - - +
341W ARG* 1.3 55.0 + - - +
343W ASN* 3.6 5.4 + - - +
344W SER* 2.7 46.6 + - - -
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Residues in contact with ARG 341 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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289W ARG* 3.8 31.4 - - - +
290W ILE 2.3 32.5 + - - -
291W ILE* 3.5 12.7 + - - +
337W HIS* 3.2 16.7 + - + +
338W PHE* 3.3 36.3 + - - +
340W ASN* 1.3 75.8 - - - +
342W GLU* 1.3 73.9 + - + +
343W ASN 3.5 0.2 + - - -
344W SER* 3.6 20.8 - - - +
452W ASN* 4.5 24.4 - - + +
454W ILE* 4.9 3.2 - - - +
469W TYR* 4.0 27.4 + - - -
484W LYS* 4.3 11.7 + - - -
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Residues in contact with GLU 342 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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292W ASP* 5.6 1.7 - - - +
293W SER* 4.1 4.5 + - - -
338W PHE* 2.9 49.7 - - - +
339W GLN* 3.2 22.0 + - - +
341W ARG* 1.3 91.8 - - + +
343W ASN* 1.3 62.1 + - - +
345W LYS* 4.0 15.8 + - - +
484W LYS* 4.6 14.7 + - - +
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Residues in contact with ASN 343 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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339W GLN 2.8 17.9 + - - +
340W ASN* 3.9 5.3 + - - +
342W GLU* 1.3 76.1 - - - +
344W SER* 1.3 53.6 + - - +
345W LYS* 2.6 26.1 + - - +
1033W GLU* 2.8 35.9 + - - +
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Residues in contact with SER 344 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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340W ASN* 2.7 38.2 + - - -
341W ARG* 3.6 15.4 + - - +
342W GLU 3.6 0.6 - - - -
343W ASN* 1.3 67.3 + - - +
345W LYS* 1.3 59.9 + - - +
346W ILE* 2.9 30.8 + - - +
347W LEU* 5.8 1.0 - - - +
450W ASP 5.9 2.5 - - - -
484W LYS* 5.8 0.7 + - - -
1033W GLU* 4.0 7.3 + - - -
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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