Contacts of the helix formed by residues 276 - 291 (chain C) 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 C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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224C ASN* 3.9 6.1 - - - +
274C GLY 3.2 1.6 - - - -
275C SER* 1.3 84.6 - - - +
277C PHE* 1.3 64.9 + - + +
278C GLN 3.6 0.9 - - - -
279C LYS* 3.6 1.5 + - - +
280C ASP* 2.9 40.4 + - - +
501C UPG 1.9 68.6 - - - +
502C UPG 3.9 25.6 - - - -
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Residues in contact with PHE 277 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
224C ASN* 3.6 37.0 - - + -
227C LEU* 3.8 17.9 - - + -
228C ALA* 4.1 16.4 - - + -
231C ILE* 3.9 18.4 - - + -
265C PHE* 3.9 5.2 - + - -
272C PHE* 3.7 34.1 - + + -
273C GLY 4.6 4.9 + - - +
274C GLY 4.3 3.0 + - - -
276C CYS* 1.3 79.4 - - + +
278C GLN* 1.3 68.9 + - - +
280C ASP* 3.8 1.9 - - - +
281C VAL* 2.9 32.3 + - - +
501C UPG 3.5 61.7 + - - -
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Residues in contact with GLN 278 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
272C PHE* 4.1 8.1 - - + -
274C GLY 4.9 3.4 + - - +
276C CYS 3.6 0.2 - - - -
277C PHE* 1.3 78.8 - - - +
279C LYS* 1.3 64.3 + - - +
281C VAL* 3.9 0.5 - - - +
282C LEU* 2.9 47.4 + - + +
304C ILE* 4.1 27.4 - - + +
307C ASN* 5.2 4.2 + - - -
308C ASP* 4.4 9.5 - - - +
311C ARG* 4.4 14.4 + - - -
347C GLU* 3.9 39.3 + - + +
352C TYR* 4.6 4.3 + - - -
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Residues in contact with LYS 279 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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91C THR* 3.2 37.1 + - - +
92C PRO* 4.1 4.0 - - - -
93C THR* 3.7 28.4 + - - +
102C ARG 4.8 2.1 - - - +
104C ALA* 6.2 0.7 - - - -
131C THR* 4.8 10.9 + - - +
274C GLY 5.7 0.2 + - - -
275C SER 3.8 24.8 + - - +
276C CYS 3.6 1.3 + - - +
277C PHE 3.3 0.4 - - - -
278C GLN* 1.3 80.5 - - - +
280C ASP* 1.3 70.2 + - - +
282C LEU* 4.0 5.5 - - - +
283C ASN* 3.1 27.5 + - + +
347C GLU* 6.1 0.6 - - - +
502C UPG 5.7 5.1 + - - -
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Residues in contact with ASP 280 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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131C THR* 3.8 22.9 + - - +
220C LYS* 4.4 2.1 - - - +
221C LEU* 3.8 30.8 - - + +
224C ASN* 2.8 37.0 + - + +
276C CYS* 2.9 23.8 + - - +
277C PHE 4.0 1.1 - - - +
279C LYS* 1.3 86.9 + - - +
281C VAL* 1.3 61.5 + - - +
283C ASN* 3.2 5.6 + - - +
284C LEU* 2.9 27.9 + - - +
501C UPG 4.2 3.5 + - - -
502C UPG 5.8 1.3 - - - -
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Residues in contact with VAL 281 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
224C ASN 4.7 1.1 - - - +
225C ALA* 4.0 30.5 - - + +
228C ALA* 4.4 13.2 - - + -
277C PHE 2.9 22.6 + - - +
278C GLN 4.0 1.8 - - - +
280C ASP* 1.3 73.7 - - + +
282C LEU* 1.3 60.7 + - - +
284C LEU* 3.1 9.8 + - + +
285C VAL* 2.9 31.8 + - + +
300C TRP* 3.9 25.1 - - + +
303C VAL* 4.4 7.2 - - + -
304C ILE* 3.8 27.1 - - + -
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Residues in contact with LEU 282 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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101C GLY 3.9 17.0 - - - +
102C ARG* 3.9 31.2 - - + +
278C GLN* 2.9 47.2 + - + +
279C LYS* 4.0 4.9 - - - +
281C VAL* 1.3 76.7 - - - +
283C ASN* 1.3 57.4 + - - +
285C VAL* 3.3 4.5 + - + +
286C TYR* 3.0 29.1 + - - +
301C GLN* 3.8 26.2 - - - +
304C ILE* 4.1 17.7 - - + -
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Residues in contact with ASN 283 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102C ARG 3.4 11.2 + - - +
103C ALA* 3.9 3.0 - - - +
104C ALA* 3.3 38.2 - - - +
132C VAL 5.9 0.2 - - - -
133C PRO* 3.6 23.3 - - - +
134C VAL 4.6 0.3 + - - -
221C LEU* 3.6 20.7 - - + +
279C LYS* 3.1 16.7 + - + +
280C ASP* 3.4 11.0 - - - +
281C VAL 3.1 0.2 - - - -
282C LEU* 1.3 78.7 - - - +
284C LEU* 1.3 62.3 + - - +
286C TYR* 3.3 6.1 + - - +
287C LEU* 2.9 24.9 + - - +
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Residues in contact with LEU 284 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
218C LEU* 3.8 20.4 - - + -
221C LEU* 4.6 19.0 - - + +
222C ALA* 4.8 5.6 - - - +
225C ALA* 3.9 28.0 - - + -
280C ASP 2.9 13.2 + - - +
281C VAL* 3.3 9.9 - - - +
283C ASN* 1.3 77.8 + - - +
285C VAL* 1.3 62.6 + - + +
287C LEU* 3.1 13.9 + - + +
288C CYS* 3.0 27.9 + - - -
300C TRP* 4.0 33.4 - - + +
237D ILE* 4.8 3.8 - - + -
240D LEU* 3.8 26.0 - - + -
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Residues in contact with VAL 285 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102C ARG* 3.8 19.5 - - - +
281C VAL* 2.9 20.3 + - + +
282C LEU* 3.6 10.3 - - + +
283C ASN 3.3 0.2 - - - -
284C LEU* 1.3 76.1 - - - +
286C TYR* 1.3 61.0 + - - +
288C CYS* 3.3 9.1 + - - +
289C GLU* 3.0 30.3 + - - +
297C ALA* 3.8 12.5 - - + +
300C TRP* 3.9 11.7 - - + -
301C GLN* 3.7 47.1 - - - +
616C EDO 4.0 8.3 - - - +
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Residues in contact with TYR 286 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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320A ASP* 4.9 5.5 + - - -
324A ASN* 3.3 22.7 + - - -
98C MET* 4.7 4.3 + - - +
99C GLY* 3.7 26.4 + - - -
102C ARG* 4.0 36.6 - - + +
103C ALA* 3.7 25.4 - - + -
135C ARG* 4.9 8.5 - - - -
282C LEU 3.0 16.1 + - - +
283C ASN* 3.7 9.2 - - - +
285C VAL* 1.3 73.7 - - - +
287C LEU* 1.3 71.8 + - + +
289C GLU* 3.0 9.8 + - + +
290C ALA* 2.9 36.2 + - + +
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Residues in contact with LEU 287 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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134C VAL* 3.7 45.1 - - + +
135C ARG* 4.0 26.9 - - - +
218C LEU* 4.8 0.9 - - + -
221C LEU* 5.1 2.2 - - + -
283C ASN* 2.9 16.6 + - - +
284C LEU* 3.1 22.4 + - + +
286C TYR* 1.3 82.4 - - - +
288C CYS* 1.3 57.8 + - - +
290C ALA* 3.3 4.7 + - - +
291C LEU* 3.0 54.3 + - + +
240D LEU* 4.3 17.3 - - + -
244D THR* 5.0 2.5 - - + -
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Residues in contact with CYS 288 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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284C LEU* 3.0 22.7 + - - -
285C VAL* 3.4 7.9 - - - +
287C LEU* 1.3 75.7 - - - +
289C GLU* 1.3 63.4 + - - +
291C LEU* 3.2 6.5 + - - -
293C LEU* 2.8 48.6 + - + +
296C VAL* 3.4 32.3 - - - -
297C ALA* 3.7 12.6 - - + +
300C TRP* 5.0 0.9 - - - -
240D LEU* 3.7 26.2 - - - -
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Residues in contact with GLU 289 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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102C ARG* 2.9 41.7 + - - -
285C VAL* 3.0 15.6 + - - +
286C TYR* 3.0 9.6 + - + +
288C CYS* 1.3 77.2 - - - +
290C ALA* 1.3 61.6 + - - +
292C ASN* 3.1 18.0 + - - +
293C LEU 4.8 2.9 - - - +
294C PRO* 5.5 4.7 - - + -
297C ALA* 3.8 13.0 - - + -
616C EDO 2.7 27.2 + - - -
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Residues in contact with ALA 290 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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135C ARG* 4.2 24.6 + - - +
286C TYR* 2.9 28.6 + - + +
287C LEU* 3.6 8.3 - - - +
289C GLU* 1.3 76.6 - - - +
291C LEU* 1.3 62.5 + - - +
292C ASN* 3.3 7.7 + - - -
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Residues in contact with LEU 291 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
135C ARG* 3.8 23.1 - - - +
287C LEU* 3.0 33.3 + - + +
288C CYS 3.2 3.6 + - - +
289C GLU 3.2 0.4 - - - -
290C ALA* 1.3 76.7 - - - +
292C ASN* 1.3 71.8 + - - +
293C LEU* 3.3 16.2 + - + +
240D LEU* 3.9 15.0 - - + -
243D ALA* 4.1 21.9 - - + +
244D THR* 3.5 30.5 - - + -
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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
------------------------------------------------------------
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