Contacts of the helix formed by residues 276 - 291 (chain F) 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 F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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224F ASN* 3.7 6.5 - - - +
274F GLY* 3.2 1.4 - - - -
275F SER* 1.3 86.8 - - - +
277F PHE* 1.3 64.1 + - + +
278F GLN 3.5 1.1 - - - -
279F LYS* 3.5 1.7 + - - +
280F ASP* 2.8 40.3 + - - +
501F UPG 1.9 68.9 - - - +
502F UPG 3.9 22.7 - - - -
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Residues in contact with PHE 277 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
224F ASN* 3.6 40.8 - - + -
227F LEU* 3.8 18.2 - - + -
228F ALA* 4.1 16.4 - - + -
231F ILE* 4.0 8.5 - - + -
265F PHE* 3.9 13.9 - + - -
272F PHE* 3.7 33.0 - + + -
273F GLY 4.5 6.7 + - - +
274F GLY 4.3 3.0 + - - -
276F CYS* 1.3 82.0 - - + +
278F GLN* 1.3 65.4 + - - +
280F ASP* 3.9 2.4 - - - +
281F VAL* 2.9 32.0 + - - +
501F UPG 3.6 57.4 - - - -
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Residues in contact with GLN 278 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
272F PHE* 4.2 8.7 - - + -
273F GLY 6.2 0.2 - - - -
274F GLY 4.8 4.0 + - - +
276F CYS 3.5 0.2 - - - -
277F PHE* 1.3 78.5 - - - +
279F LYS* 1.3 58.6 + - - +
281F VAL* 3.8 0.3 - - - +
282F LEU* 2.9 53.6 + - + +
304F ILE* 4.1 28.4 - - + +
307F ASN* 5.0 4.7 + - - -
308F ASP* 4.4 12.3 - - - +
311F ARG* 4.4 12.0 + - - -
347F GLU* 3.9 36.9 + - + +
352F TYR* 4.7 3.8 + - - -
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Residues in contact with LYS 279 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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91F THR* 3.2 37.1 + - - +
92F PRO* 4.2 7.2 - - - -
93F THR* 3.7 25.3 + - - +
102F ARG 4.8 1.7 - - - +
104F ALA* 5.9 2.1 - - - +
131F THR* 4.9 11.1 + - - +
275F SER 3.9 20.8 - - - +
276F CYS 3.5 6.9 + - - +
277F PHE 3.3 0.6 - - - -
278F GLN* 1.3 80.3 - - - +
280F ASP* 1.3 70.5 + - - +
282F LEU* 3.9 5.6 - - - +
283F ASN* 3.0 28.8 + - + +
347F GLU* 6.1 0.6 - - - +
502F UPG 5.8 5.1 + - - -
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Residues in contact with ASP 280 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
131F THR* 3.9 22.4 + - - +
220F LYS* 4.4 1.9 - - - +
221F LEU* 3.9 30.8 - - + +
224F ASN* 2.7 39.0 + - + +
276F CYS* 2.8 27.9 + - - +
277F PHE 4.1 1.8 - - - +
279F LYS* 1.3 87.4 + - - +
281F VAL* 1.3 59.8 + - - +
283F ASN* 3.3 5.1 + - - +
284F LEU* 2.9 27.4 + - - +
501F UPG 4.1 3.3 + - - -
502F UPG 6.2 0.2 - - - -
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Residues in contact with VAL 281 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
224F ASN 4.7 1.1 - - - +
225F ALA* 3.9 33.0 - - + +
228F ALA* 4.3 13.5 - - + -
277F PHE 2.9 23.4 + - - +
280F ASP* 1.3 74.8 - - + +
282F LEU* 1.3 65.0 + - - +
284F LEU* 3.0 8.9 + - - +
285F VAL* 2.9 22.5 + - + +
300F TRP* 3.7 32.1 - - + +
303F VAL* 4.5 6.7 - - + -
304F ILE* 3.7 26.0 - - + -
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Residues in contact with LEU 282 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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101F GLY 3.8 17.3 - - - +
102F ARG* 3.9 32.1 - - + +
278F GLN* 2.9 48.6 + - + +
279F LYS* 4.0 5.4 - - - +
281F VAL* 1.3 79.0 - - - +
283F ASN* 1.3 55.1 + - - +
285F VAL* 3.3 5.4 + - + +
286F TYR* 2.9 28.9 + - - +
301F GLN* 3.7 27.1 - - - +
304F ILE* 4.0 19.3 - - + -
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Residues in contact with ASN 283 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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102F ARG 3.4 11.8 + - - +
103F ALA* 3.9 2.2 - - - +
104F ALA* 3.3 40.3 - - - +
133F PRO* 3.6 22.5 - - - +
134F VAL 4.7 0.5 + - - -
221F LEU* 3.6 19.4 - - + +
279F LYS* 3.0 20.4 + - + +
280F ASP* 3.5 7.9 - - - +
281F VAL 3.2 0.2 - - - -
282F LEU* 1.3 74.1 - - - +
284F LEU* 1.3 59.8 + - - +
286F TYR* 3.2 6.2 + - - +
287F LEU* 2.8 30.5 + - - +
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Residues in contact with LEU 284 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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237E ILE* 4.7 7.2 - - + -
240E LEU* 3.7 27.1 - - + -
218F LEU* 3.9 19.3 - - + -
221F LEU* 4.6 14.7 - - + +
222F ALA* 4.9 4.5 - - - -
225F ALA* 3.9 28.0 - - + -
280F ASP 2.9 13.1 + - - +
281F VAL* 3.3 9.2 - - - +
283F ASN* 1.3 77.4 + - - +
285F VAL* 1.3 63.9 + - + +
287F LEU* 3.2 12.9 + - + +
288F CYS* 3.0 28.0 + - - -
300F TRP* 3.9 33.7 - - + +
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Residues in contact with VAL 285 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102F ARG* 3.8 9.0 - - - +
281F VAL* 2.9 20.1 + - + +
282F LEU* 3.6 10.8 - - + +
284F LEU* 1.3 74.9 - - - +
286F TYR* 1.3 62.8 + - - +
288F CYS* 3.2 9.2 + - - +
289F GLU* 3.0 42.5 + - - +
297F ALA* 3.7 17.7 - - + +
300F TRP* 4.0 11.2 - - + +
301F GLN* 3.7 48.5 - - + +
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Residues in contact with TYR 286 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
320B ASP* 5.0 5.0 + - - -
324B ASN* 3.5 20.5 + - - -
98F MET* 4.7 4.0 + - - +
99F GLY* 3.6 26.9 + - - -
102F ARG* 4.0 36.6 - - + +
103F ALA* 3.7 27.1 - - + -
282F LEU 2.9 16.3 + - - +
283F ASN* 3.7 8.1 - - - +
284F LEU 3.2 0.2 - - - -
285F VAL* 1.3 75.5 - - - +
287F LEU* 1.3 69.3 + - - +
289F GLU* 3.3 7.0 + - + +
290F ALA* 3.0 35.7 + - + +
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Residues in contact with LEU 287 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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240E LEU* 4.0 23.1 - - + -
244E THR* 4.9 2.9 - - + -
133F PRO* 6.6 0.2 - - + -
134F VAL* 3.8 48.5 - - + +
135F ARG* 5.3 4.9 - - + -
218F LEU* 4.8 0.7 - - + -
221F LEU* 5.2 2.0 - - + -
283F ASN* 2.8 16.9 + - - +
284F LEU* 3.4 19.5 - - + +
286F TYR* 1.3 81.8 - - - +
288F CYS* 1.3 64.0 + - - +
290F ALA* 3.1 8.1 + - + +
291F LEU* 3.0 51.9 + - + +
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Residues in contact with CYS 288 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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240E LEU* 3.7 25.8 - - - -
284F LEU* 3.0 25.5 + - - -
285F VAL* 3.2 8.0 + - - +
287F LEU* 1.3 75.5 - - - +
289F GLU* 1.3 64.8 + - - +
291F LEU* 3.0 8.2 + - - -
293F LEU* 2.9 45.8 + - + +
296F VAL* 3.6 30.1 - - - -
297F ALA* 3.6 11.7 - - + +
300F TRP* 5.0 1.1 - - - -
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Residues in contact with GLU 289 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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102F ARG* 2.8 45.6 + - - -
285F VAL* 3.0 26.0 + - - +
286F TYR* 3.8 6.0 - - + +
287F LEU 3.3 0.2 - - - -
288F CYS* 1.3 78.4 - - - +
290F ALA* 1.3 62.2 + - - +
292F ASN* 3.2 17.3 + - - +
293F LEU 4.8 3.4 - - - +
294F PRO* 5.3 4.3 - - + -
297F ALA* 3.7 15.6 - - + +
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Residues in contact with ALA 290 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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286F TYR* 3.0 37.2 + - + +
287F LEU* 3.6 8.3 - - + +
289F GLU* 1.3 75.9 - - - +
291F LEU* 1.3 63.8 + - + +
292F ASN* 3.3 7.7 + - - +
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Residues in contact with LEU 291 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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240E LEU* 3.7 16.6 - - + -
243E ALA* 3.9 23.5 - - + +
244E THR* 3.5 29.8 - - + -
287F LEU* 3.0 35.2 + - + +
288F CYS 3.0 3.5 + - - +
290F ALA* 1.3 81.5 - - + +
292F ASN* 1.3 72.8 + - - +
293F LEU* 3.3 16.1 + - + +
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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
------------------------------------------------------------
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