Contacts of the helix formed by residues 285 - 294 (chain B) in PDB entry 6A5T
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 PRO 285 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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282B GLY 5.7 0.2 - - - +
283B VAL* 3.8 1.7 - - - -
284B VAL* 1.3 101.8 - - + +
286B ASP* 1.3 66.6 + - - +
287B GLY 3.3 1.1 - - - -
288B GLU* 3.3 27.5 + - - +
289B ILE* 3.6 9.1 + - - +
10I CYS 4.2 5.2 - - - +
11I ASN* 3.2 43.7 - - + +
12I ASN* 4.8 6.1 - - - +
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Residues in contact with ASP 286 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
279B ARG* 2.4 49.6 + - - -
284B VAL 3.2 4.8 - - - +
285B PRO* 1.3 69.9 - - - +
287B GLY* 1.3 58.2 + - - +
289B ILE* 2.5 35.3 + - - +
290B LEU* 2.9 17.5 + - + +
310B ILE* 3.3 37.2 - - + +
314B PHE* 4.6 5.2 - - - -
6I PHE* 4.8 0.4 - - + -
11I ASN 3.7 4.2 + - - +
12I ASN* 4.6 8.6 + - - +
13I MET* 5.1 12.6 + - + +
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Residues in contact with GLY 287 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
285B PRO 3.3 1.2 - - - -
286B ASP* 1.3 76.7 - - - +
288B GLU* 1.3 62.1 + - - +
290B LEU* 3.4 2.8 + - - +
291B GLN* 3.0 23.8 + - - +
6I PHE* 3.4 35.5 - - - -
11I ASN* 3.3 21.9 + - - -
12I ASN* 4.9 0.4 - - - +
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Residues in contact with GLU 288 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
282B GLY 5.5 0.7 - - - +
283B VAL* 4.8 13.8 - - + +
285B PRO* 3.3 21.7 + - - +
286B ASP 3.2 0.6 - - - -
287B GLY* 1.3 75.3 - - - +
289B ILE* 1.3 56.2 + - - +
291B GLN* 3.2 18.6 + - - +
292B HIS* 2.8 44.4 + - + +
11I ASN* 3.2 26.3 + - - +
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Residues in contact with ILE 289 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
275B VAL* 3.7 23.8 - - + -
278B PHE* 4.1 22.4 - - + -
279B ARG* 4.0 2.9 - - + -
283B VAL* 3.1 47.8 - - + +
285B PRO 3.9 2.5 - - - +
286B ASP* 2.5 41.4 + - - +
288B GLU* 1.3 72.6 - - - +
290B LEU* 1.3 69.8 + - + +
292B HIS* 2.8 21.4 + - + +
293B ILE* 2.9 21.7 + - + +
310B ILE* 4.8 2.9 - - + -
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Residues in contact with LEU 290 (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 ASP* 2.9 18.9 + - + +
287B GLY 4.1 0.2 - - - +
289B ILE* 1.3 78.5 - - + +
291B GLN* 1.3 57.3 + - - +
293B ILE* 4.3 5.2 - - - +
294B CYS* 2.8 37.6 + - + +
303B LEU* 3.6 17.3 - - + -
306B LEU* 4.0 17.5 - - + -
307B LYS* 3.5 32.3 - - - +
310B ILE* 3.5 35.7 - - + -
4I PHE 6.0 0.4 - - - +
6I PHE* 4.0 29.2 - - + -
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Residues in contact with GLN 291 (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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287B GLY 3.0 13.7 + - - +
288B GLU* 3.2 26.2 + - - +
290B LEU* 1.3 79.4 - - - +
292B HIS* 1.3 65.5 + - + +
293B ILE 3.2 0.7 + - - -
294B CYS 3.3 10.3 - - - +
563B ASP* 3.2 31.7 + - - -
564B PRO* 3.2 39.6 - - + +
565B ALA* 4.2 16.0 - - + +
6I PHE* 5.4 0.2 - - - -
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Residues in contact with HIS 292 (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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278B PHE* 6.4 2.7 - - + -
283B VAL* 4.2 21.3 - - + +
288B GLU* 2.8 33.5 + - + +
289B ILE* 2.8 13.0 + - + +
291B GLN* 1.3 77.9 - - + +
293B ILE* 1.3 63.1 + - + +
295B TYR* 3.1 27.2 + - - -
368B THR* 4.3 16.2 + - - +
369B PHE* 3.1 63.4 - + - -
372B GLY* 4.6 8.6 - - - -
564B PRO* 4.9 2.0 - - - -
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Residues in contact with ILE 293 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
278B PHE* 4.1 23.3 - - + -
289B ILE* 2.9 25.6 + - + +
290B LEU* 4.3 4.3 - - - +
292B HIS* 1.3 80.5 - - + +
294B CYS* 1.3 71.3 + - + +
295B TYR* 3.1 21.4 + - - -
302B MET* 5.0 2.6 - - - +
306B LEU* 5.0 18.4 - - + -
372B GLY* 4.1 19.7 - - - -
375B VAL* 3.5 36.8 - - + -
376B ASN* 4.4 16.7 + - - +
379B LEU* 4.8 10.1 - - + -
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Residues in contact with CYS 294 (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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290B LEU* 2.8 23.3 + - + +
291B GLN* 3.3 10.6 - - - +
293B ILE* 1.3 75.3 - - + +
295B TYR* 1.3 67.6 + - - +
296B ASP 3.0 33.7 - - - -
297B GLU* 4.1 7.4 - - - -
302B MET* 3.8 24.0 - - + -
303B LEU* 4.4 23.8 - - + -
306B LEU* 5.3 1.3 - - + -
564B PRO* 4.6 3.6 - - - +
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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