Contacts of the helix formed by residues 280 - 290 (chain B) in PDB entry 2I65
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 ARG 280 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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248B GLU* 3.9 13.0 - - - +
277B ASN 4.0 4.0 + - - -
278B ILE* 3.2 12.5 - - - +
279B TYR* 1.3 122.6 - - + +
281B PRO* 1.3 60.5 - - - +
282B ASP* 3.2 2.9 + - + -
283B LYS* 4.1 26.8 - - + +
284B PHE* 2.9 45.5 + - - +
287B CYS* 6.3 1.0 - - - -
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Residues in contact with PRO 281 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
131B LEU* 4.3 16.4 - - + +
243B ILE* 3.7 20.2 - - + -
244B HIS 3.1 22.7 - - - +
245B GLY* 5.1 2.2 - - - -
246B GLY 5.8 1.8 - - - +
248B GLU* 3.8 8.5 - - - +
278B ILE* 4.3 6.0 - - + +
279B TYR 3.3 12.3 - - - +
280B ARG* 1.3 83.9 - - - +
282B ASP* 1.3 66.1 + - - +
284B PHE* 3.5 9.2 - - + +
285B LEU* 3.3 25.1 + - - +
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Residues in contact with ASP 282 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
280B ARG* 3.2 1.1 - - + -
281B PRO* 1.3 82.7 - - + +
283B LYS* 1.3 66.9 + - + +
285B LEU* 3.2 8.2 + - - +
286B GLN* 3.2 34.2 + - - +
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Residues in contact with LYS 283 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
280B ARG* 3.4 27.9 + - + +
282B ASP* 1.3 75.8 - - + +
284B PHE* 1.3 55.6 + - - +
286B GLN* 3.3 18.6 + - + +
287B CYS* 2.7 46.2 + - - -
295B SER* 4.1 35.0 + - - +
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Residues in contact with PHE 284 (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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131B LEU* 4.7 6.1 - - + -
135B PHE* 3.5 39.7 - + - -
207B MET* 3.8 17.5 - - + -
241B TRP* 3.9 14.1 - + - -
278B ILE* 3.6 45.5 - - + -
280B ARG* 2.9 27.2 + - - +
281B PRO 3.5 7.0 - - - +
283B LYS* 1.3 75.1 - - - +
285B LEU* 1.3 66.8 + - + +
287B CYS* 3.2 7.0 + - + +
288B VAL* 2.9 41.7 + - + +
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Residues in contact with LEU 285 (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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131B LEU* 3.5 31.6 - - + -
134B GLN* 3.8 35.0 - - + +
135B PHE* 4.0 25.4 - - + +
138B VAL* 4.3 15.6 - - + +
281B PRO 3.3 4.8 + - - +
282B ASP* 3.2 10.3 + - - +
284B PHE* 1.3 88.0 - - + +
286B GLN* 1.3 58.5 + - + +
288B VAL* 3.5 5.6 + - + +
289B LYS* 3.0 35.5 + - - +
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Residues in contact with GLN 286 (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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282B ASP* 3.2 24.5 + - - +
283B LYS* 3.6 23.0 - - + +
285B LEU* 1.3 76.4 - - + +
287B CYS* 1.3 54.8 + - - +
289B LYS* 3.2 8.8 + - + +
290B ASN* 2.8 45.8 + - - +
293B ASP* 4.9 13.6 - - + +
296B CYS* 5.4 0.2 - - - -
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Residues in contact with CYS 287 (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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280B ARG* 6.3 1.1 - - - -
283B LYS* 2.7 32.1 + - - +
284B PHE* 3.7 6.1 - - + +
286B GLN* 1.3 72.5 - - - +
288B VAL* 1.3 60.8 + - + +
290B ASN 3.8 2.2 - - - -
291B PRO* 3.1 28.3 - - - +
293B ASP* 5.3 0.7 - - - -
295B SER* 4.3 7.9 - - - -
296B CYS* 2.2 58.3 - - + -
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Residues in contact with VAL 288 (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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135B PHE* 3.6 32.1 - - + -
138B VAL* 3.7 13.2 - - + +
139B GLN* 3.6 42.2 - - + +
284B PHE* 2.9 35.8 + - + +
285B LEU* 3.9 7.2 - - + +
287B CYS* 1.3 77.0 - - + +
289B LYS* 1.3 66.5 + - - +
291B PRO* 3.8 10.1 - - - +
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Residues in contact with LYS 289 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
138B VAL* 3.4 34.9 - - + +
285B LEU* 3.0 24.0 + - - +
286B GLN* 3.3 10.5 - - + +
288B VAL* 1.3 78.3 - - - +
290B ASN* 1.3 68.0 + - - +
291B PRO* 4.0 2.8 - - - +
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Residues in contact with ASN 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 GLN* 2.8 22.1 + - - +
287B CYS* 3.5 7.4 - - - +
289B LYS* 1.3 87.3 - - - +
291B PRO* 1.4 69.1 - - - +
292B GLU 3.3 6.8 + - - +
293B ASP* 3.3 40.5 + - - +
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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