Contacts of the helix formed by residues 281 - 293 (chain B) in PDB entry 7KAC
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 281 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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116B TYR* 3.4 22.7 + - - +
148B ALA* 2.9 43.9 + - - +
149B GLY 3.4 19.3 - - - +
150B GLU* 4.3 16.3 + - - +
280B ASN* 1.3 72.0 - - + +
282B GLY* 1.3 59.0 + - - +
284B ILE* 3.0 7.7 + - - +
285B LEU* 2.9 40.6 + - + +
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Residues in contact with GLY 282 (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 ASN* 2.9 15.6 + - - -
281B ARG* 1.3 80.5 - - - +
283B LEU* 1.3 56.2 + - - +
285B LEU* 3.3 15.6 + - - +
286B ASP* 3.0 37.9 + - - +
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Residues in contact with LEU 283 (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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112B LEU* 3.4 46.4 - - + +
113B GLN* 3.0 42.0 + - + -
116B TYR* 3.9 7.2 - - + -
278B GLY 3.7 23.8 - - - +
279B LEU* 3.9 12.3 - - + -
280B ASN* 3.0 23.6 + - - +
282B GLY* 1.3 77.9 - - - +
284B ILE* 1.3 59.1 + - - +
286B ASP* 3.5 11.0 - - - +
287B LEU 3.4 5.5 + - - -
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Residues in contact with ILE 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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99B LEU* 4.9 1.8 - - + -
102B ILE* 5.5 0.2 - - + -
109B LEU* 4.5 1.8 - - + -
113B GLN* 4.0 35.2 - - + +
116B TYR* 3.5 28.0 - - + -
117B VAL* 4.0 13.0 - - + -
145B ILE* 3.6 36.6 - - + -
149B GLY* 3.9 11.9 - - - +
151B VAL* 4.9 2.0 - - + -
281B ARG 3.0 8.7 + - - +
283B LEU* 1.3 75.4 - - - +
285B LEU* 1.4 59.1 + - - +
286B ASP 3.2 0.9 - - - -
287B LEU* 3.0 22.8 + - + +
288B LEU* 2.9 31.3 + - + +
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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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147B ASP 3.4 26.2 - - - +
148B ALA* 3.9 13.0 - - - +
149B GLY* 3.9 2.6 - - - +
281B ARG* 2.9 37.7 + - + +
282B GLY* 3.7 15.7 - - - +
284B ILE* 1.4 74.0 - - - +
286B ASP* 1.3 58.1 + - - +
288B LEU* 3.2 12.0 + - + +
289B ASP* 3.0 36.8 + - - +
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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
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113B GLN* 4.4 6.3 - - - +
282B GLY 3.0 23.3 + - - +
283B LEU* 3.5 16.4 - - - +
284B ILE 3.2 0.2 - - - -
285B LEU* 1.3 77.7 - - - +
287B LEU* 1.3 59.1 + - - +
289B ASP* 3.5 16.6 + - - +
290B LYS* 3.5 18.4 + - - +
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Residues in contact with LEU 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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99B LEU* 4.4 7.2 - - + -
102B ILE* 3.7 24.2 - - + -
106B THR* 3.6 29.0 - - - +
107B GLY 5.1 0.9 - - - +
108B SER 5.3 1.8 - - - +
109B LEU* 3.8 36.1 - - + -
113B GLN* 3.6 27.8 - - - +
283B LEU 3.4 3.1 + - - +
284B ILE* 3.0 28.4 + - + +
286B ASP* 1.3 78.1 - - - +
288B LEU* 1.4 63.0 + - + +
290B LYS* 3.3 10.4 + - + +
291B LEU* 3.2 15.8 + - - +
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Residues in contact with LEU 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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96B ALA* 3.5 29.4 - - + -
102B ILE* 3.7 21.1 - - + -
145B ILE* 4.2 7.6 - - + -
146B ASN 3.8 22.2 - - - +
147B ASP* 4.5 14.4 - - - +
149B GLY 4.8 1.6 - - - +
284B ILE* 2.9 21.0 + - + +
285B LEU* 3.2 15.9 + - + +
287B LEU* 1.4 76.0 - - + +
289B ASP* 1.4 59.6 + - - +
291B LEU* 3.1 16.8 + - + +
292B LYS* 3.0 28.8 + - - +
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Residues in contact with ASP 289 (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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285B LEU* 3.0 21.4 + - - +
286B ASP* 3.7 20.2 - - - +
287B LEU 3.3 0.4 - - - -
288B LEU* 1.4 76.1 - - - +
290B LYS* 1.4 57.6 + - - +
292B LYS* 3.3 6.0 + - - +
293B ASN* 2.9 34.3 + - + +
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Residues in contact with LYS 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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105B VAL* 5.1 3.5 - - - +
106B THR* 4.2 17.1 - - + +
286B ASP 3.5 8.2 + - - +
287B LEU* 3.3 14.0 + - + +
288B LEU 3.3 0.6 - - - -
289B ASP* 1.4 78.1 - - - +
291B LEU* 1.3 58.5 + - - +
293B ASN* 3.1 21.4 - - - +
294B PRO* 5.1 1.0 - - - +
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Residues in contact with LEU 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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96B ALA* 4.7 11.4 - - + +
101B ASP 4.6 1.6 - - - +
102B ILE* 4.1 28.5 - - + +
105B VAL* 3.7 41.8 - - + +
106B THR* 3.8 7.6 - - + +
287B LEU 3.2 11.2 + - - +
288B LEU* 3.1 31.6 + - + +
290B LYS* 1.3 78.9 - - - +
292B LYS* 1.3 59.9 + - - +
293B ASN 5.1 0.9 - - - +
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Residues in contact with LYS 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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288B LEU 3.0 14.9 + - - +
289B ASP* 3.3 6.9 + - - +
291B LEU* 1.3 78.3 - - - +
293B ASN* 1.3 58.1 + - + +
294B PRO* 4.0 6.1 - - - +
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Residues in contact with ASN 293 (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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289B ASP* 2.9 15.6 + - + +
290B LYS* 3.1 19.3 - - - +
291B LEU 5.1 0.9 - - - -
292B LYS* 1.3 77.8 - - + +
294B PRO* 1.4 70.9 - - + +
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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