Contacts of the helix formed by residues 282 - 298 (chain A) 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 A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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85A TYR* 3.4 18.5 - - - -
102A MET* 3.5 17.9 - - - -
106A SER* 3.1 16.8 + - - -
109A ASP* 3.6 3.3 - - - +
280A ARG 3.2 4.8 + - - -
281A ILE* 1.3 79.3 - - - +
283A GLY* 1.3 62.2 + - - +
285A SER 3.6 2.9 + - - -
286A GLY 2.9 19.5 + - - -
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Residues in contact with GLY 283 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
106A SER* 3.2 8.2 + - - -
109A ASP* 3.7 4.7 - - - -
110A MET* 4.0 15.5 - - - -
278A PHE* 2.7 33.9 + - - -
281A ILE* 3.6 4.0 - - - +
282A GLY* 1.3 69.7 - - - +
284A VAL* 1.3 61.7 + - - -
287A TRP* 3.0 28.4 + - - +
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Residues in contact with VAL 284 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
109A ASP* 2.9 4.4 + - - -
110A MET* 4.2 11.5 - - + +
113A TRP* 3.5 39.7 - - + +
124A LEU* 4.0 16.2 - - + -
128A LEU* 4.2 24.9 - - + -
278A PHE* 5.0 0.4 - - - -
283A GLY* 1.3 71.2 - - - -
285A SER* 1.3 57.2 + - - +
287A TRP* 3.2 7.2 + - - +
288A MET* 2.9 36.9 + - + +
309A VAL* 3.8 27.4 - - + -
313A VAL* 4.4 5.4 - - + -
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Residues in contact with SER 285 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81A PRO* 4.4 8.0 + - - +
82A ALA* 4.7 2.5 + - - +
85A TYR* 4.2 19.2 - - - +
109A ASP* 2.8 29.4 + - - -
113A TRP* 2.9 22.9 + - - +
282A GLY 4.0 1.8 - - - -
284A VAL* 1.3 78.1 - - - +
286A GLY* 1.3 63.4 + - - +
288A MET* 3.4 5.8 + - - +
289A ARG* 3.2 37.5 + - - +
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Residues in contact with GLY 286 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85A TYR* 4.3 6.6 + - - -
259A PRO* 3.7 14.5 - - - +
281A ILE* 3.3 26.9 - - - -
282A GLY* 2.9 14.8 + - - -
285A SER* 1.3 73.1 - - - +
287A TRP* 1.3 59.8 + - - +
289A ARG* 3.2 2.3 + - - -
290A ALA* 2.8 30.7 + - - +
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Residues in contact with TRP 287 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
276A PRO* 3.8 27.4 - - + -
278A PHE* 3.5 33.4 - + + -
281A ILE* 3.8 6.3 - - + +
283A GLY 3.0 19.2 + - - +
284A VAL* 3.2 5.6 + - - +
286A GLY* 1.3 75.9 - - - +
288A MET* 1.3 64.3 + - - +
290A ALA* 2.9 7.3 + - - +
291A ALA* 2.6 35.4 + - + +
301A MET* 3.5 33.6 - - + +
302A SER 3.2 28.5 - - - -
303A THR* 3.7 13.9 - - + -
313A VAL* 3.4 24.3 - - + +
314A MET* 4.0 15.3 - - - -
317A THR* 2.9 30.5 + - + +
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Residues in contact with MET 288 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
113A TRP* 6.1 2.2 - - + -
128A LEU* 4.3 24.7 - - + +
284A VAL* 2.9 30.1 + - + +
285A SER* 3.9 6.5 - - - +
287A TRP* 1.3 94.3 - - - +
289A ARG* 1.3 63.7 + - + +
291A ALA* 3.3 10.4 + - + +
292A GLY* 3.2 16.6 + - - -
313A VAL* 4.4 3.6 - - - +
316A VAL* 3.6 40.2 - - + +
317A THR* 5.1 0.2 - - - -
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Residues in contact with ARG 289 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82A ALA* 4.4 23.6 + - - +
85A TYR* 3.3 37.0 - - - -
259A PRO* 3.7 24.2 - - + -
285A SER* 3.2 21.9 + - - +
286A GLY* 3.7 2.5 - - - +
287A TRP 3.2 0.4 - - - -
288A MET* 1.3 77.5 - - + +
290A ALA* 1.3 62.5 + - - +
292A GLY* 3.1 11.5 + - - -
293A VAL* 3.2 16.5 + - - +
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Residues in contact with ALA 290 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
259A PRO* 4.1 12.5 - - + +
262A MET* 3.7 25.6 - - + +
281A ILE* 4.1 15.9 - - + -
286A GLY 2.8 18.0 + - - +
287A TRP 3.4 4.5 - - - +
289A ARG* 1.3 74.9 - - - +
291A ALA* 1.3 60.4 + - - +
293A VAL* 3.2 6.4 + - - +
294A ALA* 2.9 30.8 + - - +
301A MET* 3.9 9.4 - - + -
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Residues in contact with ALA 291 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
287A TRP* 2.6 28.0 + - + +
288A MET* 3.6 15.9 - - + +
289A ARG 3.3 0.2 - - - -
290A ALA* 1.3 71.6 - - - +
292A GLY* 1.3 52.8 + - - +
294A ALA* 3.9 0.3 - - - +
295A GLY* 2.7 32.2 + - - -
301A MET* 3.8 12.5 - - - +
316A VAL 5.6 0.2 - - - +
317A THR* 3.9 29.5 - - + +
318A GLU* 5.2 6.3 - - - +
319A THR* 5.2 1.4 + - - -
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Residues in contact with GLY 292 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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288A MET 3.2 9.2 + - - -
289A ARG* 3.1 8.8 + - - -
290A ALA 3.1 0.8 - - - -
291A ALA* 1.3 75.3 - - - +
293A VAL* 1.3 64.7 + - - +
295A GLY* 3.4 1.5 + - - -
296A ALA* 3.1 23.0 + - - +
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Residues in contact with VAL 293 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
259A PRO* 4.6 16.4 - - + +
262A MET* 4.4 7.4 - - - -
263A HIS* 4.3 23.6 - - + +
266A LEU* 4.2 11.4 - - + -
289A ARG 3.2 16.0 + - - +
290A ALA* 3.2 9.8 + - - +
292A GLY* 1.3 73.5 - - - +
294A ALA* 1.3 65.4 + - - +
296A ALA* 3.2 6.1 + - - +
297A TRP* 3.2 39.9 + - + +
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Residues in contact with ALA 294 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
262A MET* 4.2 9.8 - - - -
266A LEU* 4.9 0.2 - - - -
274A VAL* 4.7 1.1 - - + -
290A ALA 2.9 16.8 + - - +
291A ALA 3.9 0.7 - - - +
293A VAL* 1.3 77.0 - - - +
295A GLY* 1.3 53.7 + - - +
297A TRP* 3.3 1.1 + - - -
298A GLY* 2.8 31.0 + - - -
299A ILE* 3.1 40.8 + - + +
301A MET* 3.8 23.8 - - + -
319A THR* 4.1 3.1 - - - +
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Residues in contact with GLY 295 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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291A ALA 2.7 24.0 + - - -
292A GLY* 3.7 2.5 - - - -
293A VAL 3.2 0.2 - - - -
294A ALA* 1.3 73.1 - - - +
296A ALA* 1.3 60.4 + - - +
298A GLY* 3.2 13.0 + - - -
318A GLU* 3.9 30.4 - - - +
319A THR* 4.1 14.1 + - - +
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Residues in contact with ALA 296 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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292A GLY 3.1 12.7 + - - +
293A VAL* 3.2 9.4 + - - +
295A GLY* 1.3 76.4 - - - +
297A TRP* 1.3 64.9 + - + +
298A GLY 3.5 0.3 + - - -
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Residues in contact with TRP 297 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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243A ARG* 6.3 0.9 - - - -
263A HIS* 5.0 8.8 + - - -
266A LEU* 3.4 60.2 - - + +
267A GLN* 4.0 17.3 - - + -
293A VAL* 3.2 32.6 + - + +
294A ALA 3.9 2.9 - - - +
296A ALA* 1.3 80.8 - - + +
298A GLY* 1.3 62.5 + - - +
299A ILE* 3.6 15.4 + - + +
209D MET* 5.8 0.9 - - - +
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Residues in contact with GLY 298 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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294A ALA 2.8 7.7 + - - -
295A GLY 3.2 12.5 + - - -
296A ALA 3.2 0.2 - - - -
297A TRP* 1.3 79.9 - - - +
299A ILE* 1.3 59.7 + - - +
300A PRO* 3.8 2.6 - - - +
319A THR* 4.3 11.2 - - - +
209D MET* 3.6 26.1 + - - +
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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
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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