Contacts of the helix formed by residues 276 - 291 (chain A) in PDB entry 3KHU
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 CYS 276 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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224A ASN* 3.9 4.7 - - - +
274A GLY 3.2 1.8 - - - -
275A SER* 1.3 83.1 - - - +
277A PHE* 1.3 64.2 + - + +
278A GLN 3.6 1.3 - - - -
279A LYS* 3.6 1.2 + - - +
280A ASP* 2.8 40.8 + - - +
501A UPG 2.0 70.9 + - - +
502A UPG 3.6 23.1 - - - -
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Residues in contact with PHE 277 (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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224A ASN* 3.5 37.9 - - + -
227A LEU* 3.8 20.4 - - + -
228A ALA* 3.9 20.2 - - + -
231A ILE* 3.9 18.2 - - + -
265A PHE* 3.9 4.5 - + - -
272A PHE* 3.8 30.1 - + + -
273A GLY 4.7 4.9 + - - +
274A GLY 4.3 3.2 + - - +
276A CYS* 1.3 80.3 - - + +
278A GLN* 1.3 66.2 + - - +
280A ASP* 3.9 2.1 - - - +
281A VAL* 3.0 32.1 + - - +
501A UPG 3.4 57.4 - - - -
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Residues in contact with GLN 278 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
272A PHE* 4.1 8.8 - - + -
273A GLY 6.2 0.4 - - - -
274A GLY 4.8 3.4 + - - +
276A CYS 3.6 0.2 - - - -
277A PHE* 1.3 77.8 - - - +
279A LYS* 1.3 64.6 + - - +
281A VAL* 4.0 0.3 - - - +
282A LEU* 2.9 49.1 + - + +
304A ILE* 4.0 27.4 - - + +
307A ASN* 5.1 4.2 + - - -
308A ASP* 4.4 10.0 - - - +
311A ARG* 4.4 14.9 + - - -
347A GLU* 4.0 37.4 + - + +
352A TYR* 4.7 4.4 + - - -
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Residues in contact with LYS 279 (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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91A THR* 3.2 37.8 + - - +
92A PRO* 4.2 5.8 - - - -
93A THR* 3.7 24.9 - - - +
102A ARG 4.8 1.7 - - - +
104A ALA* 5.8 2.7 - - - +
131A THR* 4.8 11.7 + - - +
275A SER 3.8 25.5 - - - +
276A CYS 3.8 1.7 - - - +
277A PHE 3.3 0.2 - - - -
278A GLN* 1.3 79.5 - - - +
280A ASP* 1.3 68.8 + - - +
282A LEU* 3.8 5.5 - - - +
283A ASN* 3.0 28.7 + - + +
347A GLU* 6.1 0.8 - - - +
502A UPG 5.8 4.0 + - - -
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Residues in contact with ASP 280 (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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131A THR* 3.9 20.6 + - - +
220A LYS* 4.5 1.4 - - - -
221A LEU* 3.8 32.6 - - + +
224A ASN* 2.7 39.8 + - + +
276A CYS* 2.8 28.3 + - - +
277A PHE 4.1 1.3 - - - +
279A LYS* 1.3 87.1 + - - +
281A VAL* 1.3 60.8 + - - +
283A ASN* 3.1 5.3 + - - +
284A LEU* 2.8 28.8 + - - +
501A UPG 4.0 4.0 + - - -
502A UPG 6.0 1.4 - - - -
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Residues in contact with VAL 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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224A ASN 4.8 1.1 - - - +
225A ALA* 3.9 32.1 - - + +
228A ALA* 4.3 13.9 - - + -
277A PHE 3.0 22.1 + - - +
278A GLN 4.0 2.0 - - - +
280A ASP* 1.3 75.7 - - - +
282A LEU* 1.3 59.2 + - - +
284A LEU* 3.1 8.2 + - - +
285A VAL* 2.8 32.0 + - + +
300A TRP* 3.8 30.1 - - + +
303A VAL* 4.5 9.4 - - + -
304A ILE* 3.8 22.4 - - + -
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Residues in contact with LEU 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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101A GLY 3.8 17.3 - - - +
102A ARG* 3.9 31.3 - - + +
278A GLN* 2.9 47.2 + - + +
279A LYS* 3.9 4.3 - - - +
281A VAL* 1.3 77.1 - - - +
283A ASN* 1.3 57.3 + - - +
285A VAL* 3.5 5.0 + - + +
286A TYR* 3.0 27.7 + - - +
301A GLN* 3.7 24.2 - - - +
304A ILE* 4.1 20.9 - - + -
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Residues in contact with ASN 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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102A ARG 3.3 19.1 + - - +
103A ALA* 3.9 3.0 - - - +
104A ALA* 3.3 29.7 - - - +
133A PRO* 3.6 23.8 - - - +
134A VAL 4.7 0.5 + - - -
221A LEU* 3.6 20.7 - - + +
279A LYS* 3.0 17.1 + - + +
280A ASP* 3.1 11.6 + - - +
282A LEU* 1.3 74.3 - - - +
284A LEU* 1.3 59.6 + - - +
286A TYR* 3.3 6.8 + - - +
287A LEU* 2.8 29.2 + - - +
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Residues in contact with LEU 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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218A LEU* 3.9 27.6 - - + -
221A LEU* 4.4 16.3 - - + +
222A ALA* 4.7 5.8 - - - -
225A ALA* 3.9 28.3 - - + -
280A ASP 2.8 12.7 + - - +
281A VAL* 3.3 9.2 - - - +
283A ASN* 1.3 77.2 - - - +
285A VAL* 1.3 61.9 + - + +
287A LEU* 3.2 13.7 + - + +
288A CYS* 3.1 28.1 + - - -
300A TRP* 4.0 31.4 - - + +
237B ILE* 4.7 7.6 - - + -
240B LEU* 3.9 16.6 - - + -
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Residues in contact with VAL 285 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102A ARG* 3.8 18.8 - - - +
281A VAL* 2.8 24.9 + - + +
282A LEU* 3.7 8.1 - - + +
284A LEU* 1.3 75.2 - - - +
286A TYR* 1.3 62.4 + - - +
288A CYS* 3.2 9.7 + - - +
289A GLU* 3.1 30.0 + - - +
297A ALA* 3.9 17.9 - - + +
300A TRP* 4.0 10.1 - - + -
301A GLN* 3.7 48.0 - - - +
614A EDO 4.1 3.4 - - - -
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Residues in contact with TYR 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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98A MET* 4.6 6.4 + - - +
99A GLY* 3.7 24.9 - - - -
102A ARG* 4.0 35.0 - - + +
103A ALA* 3.6 26.0 - - + -
135A ARG* 5.6 4.5 - - - -
282A LEU 3.0 17.5 + - - +
283A ASN* 3.7 8.7 - - - +
285A VAL* 1.3 76.9 - - - +
287A LEU* 1.3 67.8 + - - +
289A GLU* 3.2 8.6 + - + +
290A ALA* 2.9 36.2 + - + +
320E ASP* 4.7 5.7 + - - -
324E ASN* 3.3 22.5 + - - -
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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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133A PRO* 6.6 0.2 - - + -
134A VAL* 3.7 44.2 - - + +
135A ARG* 4.0 25.8 - - - +
218A LEU* 4.7 0.9 - - + -
221A LEU* 5.1 2.5 - - + -
283A ASN* 2.8 20.4 + - - +
284A LEU* 3.2 23.5 + - + +
286A TYR* 1.3 77.0 - - - +
288A CYS* 1.3 57.8 + - - +
290A ALA* 3.2 5.4 + - - +
291A LEU* 3.0 53.4 + - + +
240B LEU* 4.2 18.8 - - + -
244B THR* 4.9 2.2 - - + -
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Residues in contact with CYS 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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284A LEU* 3.1 23.3 + - - -
285A VAL* 3.5 8.1 - - - +
286A TYR 3.2 0.2 - - - -
287A LEU* 1.3 75.7 - - - +
289A GLU* 1.3 61.3 + - - +
291A LEU* 3.1 6.9 + - - -
293A LEU* 2.9 47.2 + - + +
296A VAL* 3.6 30.1 - - - -
297A ALA* 3.7 11.7 - - + -
300A TRP* 5.1 1.1 - - - -
240B LEU* 3.7 26.2 - - - -
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Residues in contact with GLU 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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102A ARG* 2.9 41.0 + - - -
285A VAL* 3.1 13.7 + - - +
286A TYR* 3.7 8.5 - - + +
288A CYS* 1.3 77.1 - - - +
290A ALA* 1.3 60.8 - - - +
292A ASN* 3.1 17.7 + - - +
293A LEU 4.8 3.1 - - - +
294A PRO* 5.4 2.9 - - + -
297A ALA* 3.7 5.2 - - + -
614A EDO 2.7 45.7 + - - +
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Residues in contact with ALA 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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135A ARG* 4.2 24.5 + - - +
286A TYR* 2.9 29.9 + - + +
287A LEU* 3.5 9.2 - - - +
289A GLU* 1.3 76.8 - - - +
291A LEU* 1.3 62.9 + - - +
292A ASN* 3.3 7.9 + - - +
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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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135A ARG* 3.4 30.5 - - - +
287A LEU* 3.0 32.4 + - + +
288A CYS 3.1 4.1 + - - +
290A ALA* 1.3 77.4 - - - +
292A ASN* 1.3 73.4 + - - +
293A LEU* 3.3 15.8 + - + +
240B LEU* 3.9 13.5 - - + -
243B ALA* 4.0 23.1 - - + +
244B THR* 3.5 31.0 - - + -
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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