Contacts of the helix formed by residues 276 - 291 (chain E) 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 E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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224E ASN* 3.8 5.6 - - - +
274E GLY 3.2 1.2 - - - -
275E SER* 1.3 81.0 - - - +
277E PHE* 1.3 63.6 + - + +
278E GLN 3.6 1.6 - - - -
279E LYS* 3.5 1.7 + - - +
280E ASP* 2.8 40.4 + - - +
501E UPG 2.1 70.0 + - - +
502E UPG 3.4 27.6 - - - -
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Residues in contact with PHE 277 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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224E ASN* 3.6 41.1 - - + -
227E LEU* 3.8 19.7 - - + -
228E ALA* 4.0 16.4 - - + -
231E ILE* 3.9 14.1 - - + -
265E PHE* 3.9 4.3 - + - -
272E PHE* 3.6 34.5 - + + -
273E GLY 4.5 4.9 + - - +
274E GLY 4.4 3.4 + - - -
276E CYS* 1.3 78.7 - - + +
278E GLN* 1.3 68.9 + - - +
280E ASP* 3.9 1.9 - - - +
281E VAL* 2.9 31.3 + - - +
501E UPG 3.5 58.3 - - - -
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Residues in contact with GLN 278 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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272E PHE* 4.1 8.1 - - + -
274E GLY 4.9 3.9 + - - +
276E CYS 3.6 0.2 - - - -
277E PHE* 1.3 78.8 - - - +
279E LYS* 1.3 64.8 + - - +
281E VAL* 3.9 0.5 - - - +
282E LEU* 2.9 48.1 + - + +
304E ILE* 4.0 31.2 - - + +
307E ASN* 5.1 4.5 + - - -
308E ASP* 4.4 8.8 - - - +
311E ARG* 4.4 12.5 + - - -
347E GLU* 3.9 37.2 + - + +
352E TYR* 4.6 4.7 + - - -
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Residues in contact with LYS 279 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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91E THR* 3.1 38.4 + - - +
92E PRO* 4.2 3.1 - - - -
93E THR* 3.7 29.7 + - - +
102E ARG 4.8 1.4 - - - +
104E ALA* 5.9 1.8 - - - +
131E THR* 4.8 11.5 + - - +
274E GLY 5.7 0.4 + - - -
275E SER 3.9 19.0 - - - +
276E CYS 3.5 7.3 + - - +
278E GLN* 1.3 79.8 - - - +
280E ASP* 1.3 70.8 + - - +
282E LEU* 3.6 6.0 + - - +
283E ASN* 3.0 29.3 + - + +
347E GLU* 6.1 0.4 - - - +
502E UPG 6.0 0.2 + - - -
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Residues in contact with ASP 280 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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131E THR* 3.8 21.9 + - - +
220E LYS* 4.4 1.2 - - - -
221E LEU* 3.9 32.1 - - + +
224E ASN* 2.7 39.3 + - + +
276E CYS* 2.8 26.9 + - - +
277E PHE 4.1 1.8 - - - +
279E LYS* 1.3 86.7 + - - +
281E VAL* 1.3 65.1 + - - +
283E ASN* 3.2 4.3 + - - +
284E LEU* 2.9 22.7 + - - +
501E UPG 4.2 2.9 + - - -
502E UPG 6.0 0.3 - - - -
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Residues in contact with VAL 281 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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224E ASN 4.7 0.9 - - - +
225E ALA* 3.9 29.8 - - + +
228E ALA* 4.3 14.1 - - + -
277E PHE 2.9 23.6 + - - +
280E ASP* 1.3 76.1 - - + +
282E LEU* 1.3 58.9 + - - +
284E LEU* 3.1 10.3 + - + +
285E VAL* 2.9 31.4 + - + +
300E TRP* 3.7 32.8 - - + +
303E VAL* 4.5 8.7 - - + -
304E ILE* 3.9 22.7 - - + -
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Residues in contact with LEU 282 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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101E GLY 3.8 17.7 - - - +
102E ARG* 4.0 31.2 - - + +
278E GLN* 2.9 46.0 + - + +
279E LYS* 4.0 5.4 - - - +
281E VAL* 1.3 76.4 - - - +
283E ASN* 1.3 57.1 + - - +
285E VAL* 3.4 6.2 + - + +
286E TYR* 3.0 28.4 + - - +
301E GLN* 3.8 26.7 - - - +
304E ILE* 4.0 19.3 - - + -
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Residues in contact with ASN 283 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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102E ARG 3.5 11.6 + - - +
103E ALA* 4.0 2.6 - - - +
104E ALA* 3.3 38.3 - - - +
133E PRO* 3.6 20.5 - - - +
134E VAL 4.7 0.3 + - - -
221E LEU* 3.6 23.3 - - + +
279E LYS* 3.0 19.4 + - + +
280E ASP* 3.5 8.3 - - - +
281E VAL 3.1 0.2 - - - -
282E LEU* 1.3 74.4 - - - +
284E LEU* 1.3 61.0 + - - +
286E TYR* 3.4 6.6 + - - +
287E LEU* 2.9 27.9 + - - +
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Residues in contact with LEU 284 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
218E LEU* 3.9 18.8 - - + -
221E LEU* 4.6 19.2 - - + +
222E ALA* 4.7 5.8 - - - -
225E ALA* 3.9 27.6 - - + -
280E ASP 2.9 13.0 + - - +
281E VAL* 3.2 10.1 - - - +
283E ASN* 1.3 77.6 + - - +
285E VAL* 1.3 63.6 + - + +
287E LEU* 3.1 13.2 + - + +
288E CYS* 3.0 27.0 + - - -
300E TRP* 4.1 31.2 - - + +
237F ILE* 4.9 4.3 - - + -
240F LEU* 3.9 24.0 - - + -
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Residues in contact with VAL 285 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102E ARG* 3.9 9.0 - - - +
281E VAL* 2.9 21.4 + - + +
282E LEU* 3.6 10.3 - - + +
283E ASN 3.3 0.2 - - - -
284E LEU* 1.3 75.1 - - - +
286E TYR* 1.3 64.3 + - - +
288E CYS* 3.1 9.9 + - - +
289E GLU* 3.0 40.1 + - - +
297E ALA* 3.9 18.3 - - + +
300E TRP* 4.0 9.4 - - + -
301E GLN* 3.7 49.8 - - + +
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Residues in contact with TYR 286 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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320C ASP* 5.1 4.2 + - - -
324C ASN* 3.3 20.9 + - - -
98E MET* 4.7 4.2 + - - +
99E GLY* 3.7 25.9 + - - -
102E ARG* 4.0 36.7 - - + +
103E ALA* 3.6 25.8 - - + -
282E LEU 3.0 16.7 + - - +
283E ASN* 3.7 8.1 - - - +
285E VAL* 1.3 75.2 - - - +
287E LEU* 1.3 69.4 + - - +
289E GLU* 3.2 8.5 + - + +
290E ALA* 2.9 36.7 + - + +
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Residues in contact with LEU 287 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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134E VAL* 3.7 49.1 - - + +
135E ARG* 6.1 0.7 - - + -
218E LEU* 4.7 1.1 - - + -
221E LEU* 5.2 2.2 - - + -
283E ASN* 2.9 16.3 + - - +
284E LEU* 3.1 22.9 + - + +
286E TYR* 1.3 81.9 - - - +
288E CYS* 1.3 63.5 + - - +
290E ALA* 3.2 7.0 + - + +
291E LEU* 3.0 55.0 + - + +
240F LEU* 4.3 17.5 - - + -
244F THR* 5.0 1.8 - - + -
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Residues in contact with CYS 288 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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284E LEU* 3.0 23.3 + - - -
285E VAL* 3.1 7.6 + - - +
287E LEU* 1.3 77.0 - - - +
289E GLU* 1.3 62.1 + - - +
291E LEU* 3.1 7.1 + - - -
293E LEU* 2.9 46.8 + - + +
296E VAL* 3.5 31.6 - - - -
297E ALA* 3.7 11.0 - - + +
300E TRP* 5.0 1.1 - - - -
240F LEU* 3.7 26.5 - - - -
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Residues in contact with GLU 289 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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102E ARG* 2.8 44.7 + - - -
285E VAL* 3.0 22.8 + - - +
286E TYR* 3.2 9.2 + - + +
288E CYS* 1.3 74.7 - - - +
290E ALA* 1.3 62.6 + - - +
292E ASN* 3.0 18.7 + - - +
293E LEU 4.8 3.1 - - - +
294E PRO* 5.4 4.0 - - + -
297E ALA* 3.8 14.9 - - + +
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Residues in contact with ALA 290 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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286E TYR* 2.9 36.0 + - + +
287E LEU* 3.6 9.6 - - + +
289E GLU* 1.3 76.4 - - - +
291E LEU* 1.3 65.8 + - + +
292E ASN* 3.3 7.9 + - - -
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Residues in contact with LEU 291 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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287E LEU* 3.0 37.3 + - + +
288E CYS 3.1 3.1 + - - +
289E GLU 3.1 0.6 - - - -
290E ALA* 1.3 82.2 - - + +
292E ASN* 1.3 72.0 + - - +
293E LEU* 3.3 17.1 + - + +
240F LEU* 3.9 14.6 - - + -
243F ALA* 4.2 22.5 - - + +
244F THR* 3.7 28.9 - - + -
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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