Contacts of the helix formed by residues 282 - 298 (chain B) in PDB entry 3UGV
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 GLY 282 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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85B TYR* 3.5 17.6 - - - -
102B MET* 3.3 18.8 - - - -
106B SER* 3.0 17.5 + - - -
109B ASP* 3.6 6.9 - - - +
278B PHE 3.8 0.2 + - - -
280B ARG 3.2 4.4 + - - -
281B ILE* 1.3 78.9 - - - +
283B GLY* 1.3 63.5 + - - +
285B SER 3.6 0.2 + - - -
286B GLY 2.9 19.7 + - - -
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Residues in contact with GLY 283 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
106B SER* 3.1 9.5 + - - -
109B ASP* 3.4 5.8 - - - -
110B MET* 4.0 14.6 - - - -
278B PHE* 2.9 28.7 + - - -
281B ILE* 3.7 3.8 - - - +
282B GLY* 1.3 76.4 - - - +
284B VAL* 1.3 59.0 + - - -
287B TRP* 3.1 27.0 + - - +
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Residues in contact with VAL 284 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
109B ASP* 2.7 7.3 + - - -
110B MET* 4.2 10.9 - - + +
113B TRP* 3.5 38.6 - - + +
124B LEU* 3.9 23.6 - - + -
128B LEU* 4.1 25.4 - - + -
278B PHE* 5.0 0.4 - - - -
283B GLY* 1.3 70.9 - - - -
285B SER* 1.3 58.3 + - - +
287B TRP* 3.7 5.1 - - - +
288B MET* 2.9 35.8 + - + +
309B VAL* 3.9 21.3 - - + -
313B VAL* 4.3 7.0 - - + -
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Residues in contact with SER 285 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81B PRO* 4.3 7.8 + - - +
82B ALA* 4.7 2.4 + - - +
85B TYR* 4.2 20.1 - - - +
109B ASP* 2.5 29.9 + - - -
113B TRP* 2.8 22.7 + - - +
282B GLY 3.9 1.6 - - - -
284B VAL* 1.3 75.0 - - - +
286B GLY* 1.3 64.9 + - - +
288B MET* 3.4 5.1 + - - +
289B ARG* 3.2 37.5 + - - +
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Residues in contact with GLY 286 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85B TYR* 4.4 6.6 - - - -
259B PRO* 3.6 12.1 - - - +
281B ILE* 3.2 26.9 - - - -
282B GLY* 2.9 17.1 + - - -
285B SER* 1.3 73.8 - - - +
287B TRP* 1.3 58.6 + - - +
289B ARG* 3.0 5.3 + - - +
290B ALA* 2.8 30.0 + - - +
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Residues in contact with TRP 287 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
276B PRO* 3.7 28.9 - - + -
278B PHE* 3.6 33.0 - + + -
281B ILE* 3.9 8.5 - - + +
283B GLY 3.1 19.2 + - - +
284B VAL* 3.7 4.5 - - - +
285B SER 3.3 0.2 - - - -
286B GLY* 1.3 75.4 - - - +
288B MET* 1.3 68.4 + - - +
290B ALA* 3.3 4.8 + - - +
291B ALA* 2.8 29.2 + - + +
301B MET* 3.5 34.5 - - + +
302B SER 3.1 29.2 - - - -
303B THR* 3.6 14.6 - - + -
313B VAL* 3.4 23.3 - - + +
314B MET* 4.0 15.3 - - - -
317B THR* 2.9 27.7 + - - -
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Residues in contact with MET 288 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
113B TRP* 6.0 2.2 - - + -
128B LEU* 4.3 25.4 - - + +
284B VAL* 2.9 30.6 + - + +
285B SER* 3.8 5.4 - - - +
286B GLY 3.2 0.2 - - - -
287B TRP* 1.3 94.5 - - - +
289B ARG* 1.3 62.0 + - + +
291B ALA* 3.4 9.6 + - + +
292B GLY* 3.2 16.3 + - - -
313B VAL* 4.4 3.6 - - - +
316B VAL* 3.7 39.3 - - + +
317B THR* 5.2 0.4 - - - -
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Residues in contact with ARG 289 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82B ALA* 4.6 20.2 + - - +
85B TYR* 3.4 34.8 - - - -
259B PRO* 3.7 20.2 - - + -
285B SER* 3.2 21.4 + - - +
286B GLY* 3.0 8.4 + - - +
288B MET* 1.3 76.3 - - + +
290B ALA* 1.3 64.0 + - - +
292B GLY* 3.0 12.6 + - - -
293B VAL* 3.1 15.2 + - - +
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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
----------------------------------------------------------
259B PRO* 4.0 11.7 - - + +
262B MET* 3.8 26.9 - - + +
281B ILE* 4.1 18.6 - - + -
286B GLY 2.8 19.0 + - - +
287B TRP 3.6 4.3 - - - +
289B ARG* 1.3 72.0 - - - +
291B ALA* 1.3 58.0 + - - +
293B VAL* 3.0 8.7 + - - +
294B ALA* 2.8 30.3 + - - +
301B MET* 3.9 9.0 - - + -
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Residues in contact with ALA 291 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
287B TRP* 2.8 23.7 + - + +
288B MET* 3.4 14.4 - - + +
289B ARG 3.2 0.2 - - - -
290B ALA* 1.3 76.6 - - - +
292B GLY* 1.3 57.0 + - - +
294B ALA* 4.2 0.2 - - - +
295B GLY* 3.0 25.5 + - - -
301B MET* 3.7 14.5 - - - +
316B VAL 5.7 0.4 - - - +
317B THR* 4.1 29.1 - - + +
318B GLU* 5.1 6.7 - - - +
319B THR* 5.3 1.2 + - - -
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Residues in contact with GLY 292 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
288B MET 3.2 8.8 + - - -
289B ARG* 3.0 10.1 + - - -
291B ALA* 1.3 75.8 - - - +
293B VAL* 1.3 64.4 + - - +
295B GLY* 3.5 1.1 + - - -
296B ALA* 3.2 22.5 + - - +
318B GLU* 6.1 0.4 - - - -
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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
----------------------------------------------------------
259B PRO* 4.7 11.2 - - + +
262B MET* 4.2 9.9 - - + -
263B HIS* 4.2 27.1 - - + +
266B LEU* 4.0 22.0 - - + -
289B ARG 3.1 11.3 + - - +
290B ALA* 3.0 12.0 + - - +
292B GLY* 1.3 75.7 - - - +
294B ALA* 1.3 62.9 + - - +
296B ALA* 3.1 14.8 + - - +
297B TRP* 3.2 22.1 + - + +
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Residues in contact with ALA 294 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
262B MET* 4.3 10.8 - - - -
266B LEU* 5.0 1.8 - - - -
274B VAL* 4.6 2.2 - - + -
290B ALA 2.8 19.7 + - - +
291B ALA 4.2 0.9 - - - +
293B VAL* 1.3 75.8 - - - +
295B GLY* 1.3 51.2 + - - +
297B TRP* 3.3 5.1 + - - +
298B GLY* 2.7 31.4 + - - -
299B ILE* 3.1 33.4 + - + +
301B MET* 3.9 23.1 - - + -
319B THR* 4.1 2.7 - - - +
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Residues in contact with GLY 295 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
291B ALA 3.0 18.8 + - - -
292B GLY 3.9 1.8 - - - -
294B ALA* 1.3 76.4 - - - +
296B ALA* 1.3 60.4 + - - +
298B GLY* 3.4 10.0 + - - -
318B GLU* 3.7 28.7 - - - +
319B THR* 3.7 19.2 + - - +
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Residues in contact with ALA 296 (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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235A ASN* 5.3 1.0 - - - +
237A ASP* 4.3 5.9 - - - +
292B GLY 3.2 12.8 + - - +
293B VAL* 3.1 11.5 + - - +
295B GLY* 1.3 79.2 - - - +
297B TRP* 1.3 62.8 + - + +
298B GLY 3.6 0.2 + - - -
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Residues in contact with TRP 297 (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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235A ASN* 3.3 17.1 + - - +
237A ASP* 3.6 51.1 - - + +
238A GLY* 4.7 1.2 + - - -
243B ARG* 6.3 1.6 - - - -
263B HIS* 5.0 9.4 + + - -
266B LEU* 3.3 59.2 - - + +
267B GLN* 3.9 20.6 - - + -
293B VAL* 3.2 28.5 + - + +
294B ALA 3.8 3.4 - - - +
296B ALA* 1.3 79.4 - - + +
298B GLY* 1.3 60.9 + - - +
299B ILE* 3.5 29.4 + - + +
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Residues in contact with GLY 298 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
209A MET* 3.6 20.3 + - - +
235A ASN* 4.0 13.7 + - - -
294B ALA 2.7 14.0 + - - -
295B GLY 3.4 8.2 + - - -
296B ALA 3.3 4.2 + - - -
297B TRP* 1.3 75.4 - - - +
299B ILE* 1.3 59.2 + - - +
300B PRO* 3.5 8.8 - - - +
319B THR* 4.3 9.9 - - - +
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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
------------------------------------------------------------
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