Contacts of the helix formed by residues 289 - 306 (chain B) in PDB entry 4U7C
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 SER 289 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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208B LEU* 3.8 0.9 - - - -
287B GLY 3.5 0.4 - - - -
288B THR* 1.3 80.8 + - - +
290B ALA* 1.3 66.3 + - - +
291B GLN* 3.8 9.4 + - - +
292B GLU* 3.0 27.0 + - - +
293B VAL* 2.9 23.0 + - - +
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Residues in contact with ALA 290 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102B THR* 3.9 18.2 - - + +
204B ILE* 4.4 2.4 - - + +
208B LEU* 3.6 32.9 - - + +
289B SER* 1.3 72.5 - - - +
291B GLN* 1.3 64.3 + - - +
293B VAL* 3.2 5.7 + - - +
294B VAL* 2.9 26.2 + - - +
313B ILE* 4.2 7.9 - - + -
334B GLN* 4.1 18.4 - - - +
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Residues in contact with GLN 291 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
289B SER* 3.9 10.0 - - - +
290B ALA* 1.3 78.1 - - - +
292B GLU* 1.3 59.4 + - + +
294B VAL 3.3 0.3 + - - -
295B LYS* 3.0 44.5 + - + +
313B ILE* 3.9 11.2 - - - +
332B GLN* 3.1 34.4 + - - +
333B TYR* 4.7 3.2 - - - +
334B GLN* 3.1 42.8 + - - +
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Residues in contact with GLU 292 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
285B VAL 4.6 1.4 - - - +
286B PHE* 3.4 17.4 - - - +
287B GLY* 2.5 48.1 + - - +
289B SER* 3.0 23.8 + - - +
291B GLN* 1.3 79.4 - - + +
293B VAL* 1.3 65.4 + - - +
295B LYS* 3.2 29.1 + - - +
296B GLU* 2.9 24.3 + - - +
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Residues in contact with VAL 293 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
188B TYR* 3.8 15.9 - - + -
204B ILE* 4.0 16.4 - - + -
207B HIS* 3.7 23.1 - - + +
208B LEU* 3.6 17.7 - - + -
211B ARG* 3.5 34.1 - - - +
287B GLY 4.7 0.4 + - - -
289B SER 2.9 18.9 + - - +
290B ALA 3.4 7.2 - - - +
292B GLU* 1.3 74.6 - - - +
294B VAL* 1.3 58.6 + - - +
296B GLU* 3.2 9.2 + - - +
297B ILE* 2.9 37.1 + - + +
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Residues in contact with VAL 294 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
104B VAL* 3.8 32.8 - - + -
106B ILE* 5.9 1.6 - - + -
204B ILE* 4.8 2.9 - - + -
290B ALA 2.9 11.2 + - - +
291B GLN 3.5 7.4 - - - +
293B VAL* 1.3 75.1 - - + +
295B LYS* 1.3 59.7 + - - +
297B ILE* 3.1 11.2 + - + +
298B ARG* 2.9 29.4 + - + +
311B ALA* 3.6 25.1 - - + -
313B ILE* 3.6 22.9 - - + -
332B GLN* 3.3 26.2 - - - +
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Residues in contact with LYS 295 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
286B PHE* 3.9 14.2 - - + -
291B GLN* 3.0 28.2 + - + +
292B GLU* 3.3 38.4 + - - +
294B VAL* 1.3 74.4 - - - +
296B GLU* 1.3 57.2 + - - +
298B ARG* 3.9 11.1 + - - +
299B PHE* 2.9 29.3 + - - +
332B GLN* 3.3 32.3 + - - +
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Residues in contact with GLU 296 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
188B TYR* 2.8 24.6 + - - +
211B ARG* 2.6 40.5 + - - -
214B TRP* 5.4 1.2 - - - -
218B LYS 4.8 1.7 - - - +
219B ARG* 4.2 4.0 - - - -
221B TYR* 3.3 32.4 + - + -
286B PHE* 3.3 35.6 - - + +
292B GLU 2.9 13.6 + - - +
293B VAL* 3.2 10.5 - - - +
295B LYS* 1.3 77.3 - - - +
297B ILE* 1.3 57.0 + - - +
299B PHE* 3.1 3.5 + - - +
300B ARG* 2.9 34.1 + - - +
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Residues in contact with ILE 297 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
104B VAL* 5.5 0.9 - - + -
106B ILE* 4.2 13.7 - - + -
184B ILE* 4.1 9.8 - - + +
185B LEU* 3.8 23.6 - - + -
188B TYR* 3.5 48.0 - - + -
202B LEU* 4.2 17.0 - - + -
204B ILE* 5.2 2.7 - - + -
293B VAL* 2.9 26.5 + - + +
294B VAL* 3.1 14.1 + - + +
296B GLU* 1.3 75.9 - - - +
298B ARG* 1.3 63.6 + - + +
300B ARG* 3.4 4.4 + - - +
301B ILE* 2.9 33.4 + - + +
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Residues in contact with ARG 298 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
106B ILE* 5.0 5.6 - - + -
294B VAL* 2.9 25.0 + - + +
295B LYS* 3.9 12.4 - - - +
297B ILE* 1.3 76.1 - - + +
299B PHE* 1.3 57.4 + - - +
301B ILE* 3.4 11.0 + - - +
302B GLU* 2.9 28.6 + - - +
307B LEU 5.0 0.2 - - - +
308B THR* 5.9 0.5 - - - -
309B ALA* 3.0 31.1 + - + +
311B ALA* 4.1 14.8 - - + -
330B ASN* 2.5 49.7 + - - +
331B GLY* 3.1 12.3 + - - +
332B GLN* 2.7 45.0 + - - +
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Residues in contact with PHE 299 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
221B TYR* 4.0 24.5 - - + -
222B PHE 4.1 6.5 - - - -
223B ILE* 4.0 25.1 - - + -
284B VAL* 4.0 14.6 - - + -
286B PHE* 3.6 26.2 - + + -
295B LYS 2.9 19.4 + - - +
296B GLU 3.3 4.5 - - - +
298B ARG* 1.3 73.1 - - - +
300B ARG* 1.3 71.3 + - + +
302B GLU* 3.0 11.0 + - + +
303B GLN* 2.9 58.8 + - + +
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Residues in contact with ARG 300 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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183B GLU 5.3 0.2 + - - -
184B ILE* 3.4 36.8 - - + +
187B ASP* 2.8 31.5 + - - +
188B TYR* 3.0 36.8 + - - -
221B TYR* 3.3 47.1 + - + -
296B GLU* 2.9 23.9 + - + +
297B ILE 3.8 4.0 - - - +
299B PHE* 1.3 79.6 - - + +
301B ILE* 1.3 57.5 + - - +
303B GLN* 3.2 5.9 + - - +
304B LYS* 2.9 33.4 + - - +
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Residues in contact with ILE 301 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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106B ILE* 4.4 18.4 - - + -
108B MET* 4.2 18.2 - - + -
181B VAL* 4.0 28.7 - - + -
184B ILE* 3.6 19.1 - - + -
185B LEU* 4.8 2.5 - - + -
297B ILE* 2.9 35.1 + - + +
298B ARG* 3.5 9.2 - - - +
300B ARG* 1.3 76.7 - - - +
302B GLU* 1.3 55.3 + - - +
305B THR* 2.7 45.5 + - - +
307B LEU 3.3 17.3 - - - +
309B ALA* 4.4 12.3 - - + +
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Residues in contact with GLU 302 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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298B ARG 2.9 13.8 + - - +
299B PHE* 3.0 11.6 + - + +
301B ILE* 1.3 76.7 - - - +
303B GLN* 1.3 71.6 + - - +
306B THR* 2.9 27.7 + - + +
307B LEU 3.4 19.5 - - - +
308B THR* 4.0 25.5 - - + +
330B ASN* 4.4 10.0 + - - +
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Residues in contact with GLN 303 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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427A LYS* 5.4 1.6 - - - -
222B PHE 4.4 6.1 - - - +
223B ILE* 3.6 7.2 - - - +
224B LYS* 2.7 48.7 + - + +
299B PHE* 2.9 54.2 + - + +
300B ARG* 3.7 8.3 - - - +
302B GLU* 1.3 92.6 + - - +
304B LYS* 1.3 63.3 + - - +
306B THR* 4.2 5.2 + - - -
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Residues in contact with LYS 304 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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427A LYS* 3.6 21.8 - - - +
429A GLU* 3.6 20.4 - - - -
180B GLU* 3.4 37.6 + - + +
183B GLU* 2.7 32.1 + - - +
184B ILE* 3.9 24.7 - - + +
300B ARG 2.9 16.4 + - - +
301B ILE 4.2 0.7 - - - +
303B GLN* 1.3 79.0 - - + +
305B THR* 1.3 61.5 + - + +
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Residues in contact with THR 305 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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427A LYS* 4.5 0.4 - - - -
108B MET* 4.9 0.2 - - - +
118B ARG* 2.8 32.9 + - - +
177B VAL* 4.5 4.9 - - + -
180B GLU* 4.0 31.0 - - + +
181B VAL* 4.0 20.2 - - + +
184B ILE* 5.5 0.2 - - + -
301B ILE* 2.7 28.7 + - + +
304B LYS* 1.3 85.5 - - + +
306B THR* 1.3 70.2 + - - +
307B LEU* 3.3 28.0 + - - +
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Residues in contact with THR 306 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
427A LYS* 3.5 19.8 + - - -
118B ARG* 3.8 19.1 - - + +
302B GLU* 2.9 24.8 + - + +
303B GLN 4.2 3.3 + - - -
304B LYS 3.8 0.4 - - - -
305B THR* 1.3 81.0 + - - +
307B LEU* 1.3 68.4 + - - +
308B THR* 6.0 0.2 - - - -
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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