Contacts of the helix formed by residues 280 - 291 (chain A) in PDB entry 6MOL
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 HIS 280 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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243A ALA 3.5 22.0 - - - -
244A ARG 4.1 0.6 + - - -
245A ALA 3.5 27.0 + - - -
246A GLY* 3.7 14.3 + - - -
275A ALA* 3.2 11.2 + - + +
278A ALA* 3.4 32.6 - - + +
279A GLY* 1.3 80.8 + - - +
281A LEU* 1.3 65.0 + - - +
282A GLU* 3.2 11.3 + - - +
283A ILE* 3.2 23.3 + - + -
284A VAL* 3.0 24.6 + - - +
312A ILE* 3.6 3.9 - - - +
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Residues in contact with LEU 281 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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279A GLY 3.9 2.6 + - - -
280A HIS* 1.3 72.9 - - - +
282A GLU* 1.3 70.9 + - + +
284A VAL* 4.1 2.7 - - + +
285A GLU* 3.3 35.6 + - + +
311A GLU* 3.6 52.9 - - + +
312A ILE* 4.0 15.9 - - + +
315A VAL* 3.7 18.2 - - + -
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Residues in contact with GLU 282 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
248A LEU* 3.7 26.0 - - + +
280A HIS* 4.1 9.9 + - - +
281A LEU* 1.3 93.0 + - + +
283A ILE* 1.3 78.7 + - + +
285A GLU* 3.6 9.0 + - - +
286A VAL* 3.3 26.3 + - - +
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Residues in contact with ILE 283 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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243A ALA* 3.9 12.1 - - + -
246A GLY* 4.0 25.8 - - - +
248A LEU* 4.1 26.0 - - + +
251A VAL* 4.0 25.4 - - + -
275A ALA* 3.7 21.1 - - + -
280A HIS* 3.2 20.3 + - + -
282A GLU* 1.3 92.7 - - - +
284A VAL* 1.3 67.3 + - - +
286A VAL* 3.1 4.1 + - - +
287A LEU* 2.9 36.9 + - + +
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Residues in contact with VAL 284 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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272A LEU* 3.8 21.8 - - + -
275A ALA* 3.7 9.4 - - + +
276A ALA* 3.7 33.9 - - + +
280A HIS 3.0 21.1 + - - +
281A LEU* 4.1 6.1 - - + +
283A ILE* 1.3 78.4 - - - +
285A GLU* 1.3 61.9 + - - +
287A LEU* 3.5 1.7 + - - +
288A LEU* 3.1 38.3 + - + +
312A ILE* 4.4 18.4 - - + -
315A VAL* 4.2 11.4 - - + -
316A LEU* 4.7 4.7 - - + -
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Residues in contact with GLU 285 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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281A LEU* 3.3 36.2 + - - +
282A GLU* 3.9 7.8 - - - +
283A ILE 3.2 0.6 - - - -
284A VAL* 1.3 78.9 - - - +
286A VAL* 1.3 61.3 + - + +
288A LEU* 3.6 3.0 + - - +
289A LYS* 3.2 40.0 + - - +
315A VAL* 3.9 33.4 - - + +
319A TYR* 4.1 4.1 + - + +
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Residues in contact with VAL 286 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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248A LEU* 3.8 17.0 - - + -
251A VAL* 4.8 4.5 - - + -
252A GLU* 4.0 25.6 - - + +
255A LEU* 3.9 19.7 - - + -
282A GLU 3.3 16.4 - - - +
283A ILE* 3.1 7.0 + - - +
285A GLU* 1.3 78.6 - - + +
287A LEU* 1.3 65.3 + - - +
289A LYS* 3.2 20.5 + - + +
290A TYR* 3.3 29.4 - - + -
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Residues in contact with LEU 287 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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239A LEU* 4.3 12.8 - - + -
243A ALA* 4.3 1.1 - - + -
251A VAL* 3.8 23.6 - - + -
255A LEU* 3.8 9.9 - - + -
261A VAL* 3.6 27.0 - - + +
271A PRO* 3.7 36.1 - - + +
272A LEU* 3.9 12.6 - - + +
275A ALA* 4.1 3.4 - - + -
283A ILE* 2.9 35.8 + - + +
284A VAL 3.9 3.8 - - - +
286A VAL* 1.3 76.6 - - - +
288A LEU* 1.3 60.5 + - - +
290A TYR* 3.6 0.9 + - - -
291A GLY 3.3 6.9 + - - -
292A ALA* 3.1 27.3 + - + +
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Residues in contact with LEU 288 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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272A LEU* 3.7 27.4 - - + -
284A VAL* 3.1 27.4 + - + +
285A GLU 4.0 0.7 - - - +
287A LEU* 1.3 73.5 - - - +
289A LYS* 1.3 65.5 + - - +
291A GLY* 3.4 10.9 + - - -
292A ALA* 3.8 20.2 + - + +
294A VAL* 4.1 15.3 - - + -
315A VAL* 3.7 18.6 - - + +
316A LEU* 4.4 10.1 - - + -
319A TYR* 3.5 57.2 - - + -
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Residues in contact with LYS 289 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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285A GLU* 3.2 29.5 + - - +
286A VAL* 3.2 13.6 + - + +
288A LEU* 1.3 79.1 - - - +
290A TYR* 1.3 67.7 + - + +
291A GLY* 3.4 0.7 + - - -
319A TYR* 3.2 20.9 - - - +
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Residues in contact with TYR 290 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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252A GLU* 4.6 2.8 + - + +
255A LEU* 3.8 51.4 - - + -
256A LYS* 3.3 35.2 - - + +
261A VAL* 4.9 5.9 - - + +
286A VAL* 3.3 35.7 + - + +
287A LEU 3.6 4.0 + - - +
289A LYS* 1.3 84.1 - - + +
291A GLY* 1.3 57.0 + - - +
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Residues in contact with GLY 291 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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261A VAL* 3.3 8.9 - - - +
262A ASN* 3.3 20.3 + - - -
287A LEU 3.3 2.6 + - - -
288A LEU 3.4 6.2 + - - -
289A LYS 3.2 3.9 - - - -
290A TYR* 1.3 80.1 - - - +
292A ALA* 1.3 67.5 + - - +
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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