Contacts of the helix formed by residues 281 - 293 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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116A TYR* 3.5 24.6 + - - +
148A ALA* 2.8 33.3 + - - +
149A GLY* 3.6 16.2 - - - +
150A GLU* 3.9 25.9 + - + +
280A ASN* 1.3 73.2 - - - +
282A GLY* 1.3 60.8 + - - +
283A LEU 3.2 0.4 - - - -
284A ILE* 3.1 5.4 + - - +
285A LEU* 3.0 38.2 + - + +
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Residues in contact with GLY 282 (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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280A ASN* 2.9 15.1 + - - +
281A ARG* 1.3 76.4 - - - +
283A LEU* 1.3 61.1 + - - +
285A LEU* 3.2 15.3 + - - +
286A ASP* 3.0 32.2 + - - +
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Residues in contact with LEU 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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110A SER* 5.8 0.2 - - - +
112A LEU* 3.5 49.8 - - + +
113A GLN* 2.9 43.3 + - + -
116A TYR* 4.1 7.6 - - + -
278A GLY 3.7 24.5 - - - +
279A LEU* 3.9 7.6 - - + -
280A ASN* 3.0 25.6 + - - +
282A GLY* 1.3 77.4 - - - +
284A ILE* 1.3 60.8 + - - +
286A ASP* 3.5 10.6 - - - +
287A LEU 3.4 4.2 + - - -
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Residues in contact with ILE 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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113A GLN* 4.1 14.8 - - + +
116A TYR* 3.3 39.5 - - + -
117A VAL* 3.9 24.7 - - + -
145A ILE* 3.7 32.3 - - + -
149A GLY* 3.6 22.2 - - - +
151A VAL* 4.5 3.6 - - + -
281A ARG 3.1 7.2 + - - +
283A LEU* 1.3 76.1 - - - +
285A LEU* 1.3 65.4 + - - +
286A ASP 3.2 0.2 - - - -
287A LEU* 3.0 27.1 + - + +
288A LEU* 3.2 13.6 + - + +
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Residues in contact with LEU 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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147A ASP 4.4 7.2 - - - +
148A ALA* 3.7 31.0 - - - +
149A GLY* 3.9 5.6 - - - +
281A ARG* 3.0 33.1 + - - +
282A GLY* 3.2 15.9 + - - +
284A ILE* 1.3 74.8 - - - +
286A ASP* 1.4 62.1 + - - +
288A LEU* 3.2 20.2 + - + +
289A ASP* 3.3 21.3 + - - +
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Residues in contact with ASP 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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113A GLN* 4.3 7.0 - - - +
282A GLY 3.0 22.8 + - - +
283A LEU* 3.5 17.2 - - - +
284A ILE 3.2 0.2 - - - -
285A LEU* 1.4 76.7 - - - +
287A LEU* 1.3 59.0 + - - +
288A LEU 3.4 0.2 - - - -
289A ASP* 3.5 16.0 + - - +
290A LYS* 3.5 25.3 + - - +
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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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99A LEU* 4.4 11.7 - - + -
102A ILE* 3.7 26.6 - - + +
106A THR* 3.8 23.4 - - + +
107A GLY 5.5 0.2 - - - +
108A SER 5.7 0.7 - - - +
109A LEU* 4.0 34.8 - - + -
113A GLN* 3.6 29.8 - - - +
283A LEU 3.4 3.0 + - - +
284A ILE* 3.0 26.1 + - + +
286A ASP* 1.3 77.5 - - - +
288A LEU* 1.3 64.3 + - + +
290A LYS* 3.5 13.9 + - + +
291A LEU* 3.4 18.7 + - - +
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Residues in contact with LEU 288 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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96A ALA* 3.6 28.7 - - + -
102A ILE* 4.2 11.0 - - + -
145A ILE* 3.8 12.8 - - + -
146A ASN 3.9 20.9 - - - +
147A ASP* 4.0 19.1 - - - +
149A GLY* 4.2 12.1 - - - +
284A ILE* 3.2 13.8 + - + +
285A LEU* 3.2 13.2 + - + +
287A LEU* 1.3 76.6 - - + +
289A ASP* 1.3 60.9 + - - +
290A LYS 3.5 0.2 - - - -
291A LEU* 3.5 13.5 + - + +
292A LYS* 3.2 27.4 + - - +
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Residues in contact with ASP 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 LEU* 3.3 17.2 + - - +
286A ASP* 3.7 19.9 - - - +
287A LEU 3.3 0.4 - - - -
288A LEU* 1.3 77.7 - - - +
290A LYS* 1.4 60.5 + - + +
291A LEU 3.2 0.2 - - - -
292A LYS* 3.2 5.1 + - - +
293A ASN* 2.9 40.2 + - - +
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Residues in contact with LYS 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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105A VAL* 5.1 0.9 - - - +
106A THR* 4.1 33.1 + - + +
108A SER 5.3 5.7 + - - -
113A GLN* 5.8 2.7 - - - +
286A ASP 3.5 14.7 + - - +
287A LEU* 3.5 16.5 + - + +
288A LEU 3.5 0.2 - - - -
289A ASP* 1.4 77.1 - - + +
291A LEU* 1.3 59.6 + - - +
293A ASN* 4.1 2.6 - - - +
294A PRO* 3.5 23.9 - - - +
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Residues in contact with LEU 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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96A ALA* 4.5 20.2 - - + +
101A ASP 4.5 1.8 - - - +
102A ILE* 4.1 36.6 - - + +
105A VAL* 3.7 37.0 - - + +
106A THR* 3.8 7.8 - - + +
287A LEU 3.4 10.8 + - - +
288A LEU* 3.6 15.9 - - + +
289A ASP 3.2 0.6 - - - -
290A LYS* 1.3 79.6 - - - +
292A LYS* 1.3 57.8 + - - +
294A PRO* 3.2 15.9 - - - +
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Residues in contact with LYS 292 (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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288A LEU 3.2 16.5 + - - +
289A ASP* 3.2 6.7 + - - +
291A LEU* 1.3 74.7 - - - +
293A ASN* 1.3 64.3 + - - +
294A PRO* 3.2 10.9 - - - +
295A GLY 5.1 0.3 + - - -
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Residues in contact with ASN 293 (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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289A ASP* 2.9 22.3 + - - +
290A LYS* 4.1 4.7 - - - -
292A LYS* 1.3 83.3 - - - +
294A PRO* 1.4 58.9 - - - +
295A GLY 3.5 9.0 - - - +
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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