Contacts of the helix formed by residues 283 - 296 (chain B) in PDB entry 5TWV
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 283 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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281B PRO 4.5 0.2 - - - -
282B GLN* 1.3 75.7 - - - +
284B ALA* 1.3 58.1 + - - -
285B ARG* 3.1 3.4 - - - -
286B ALA* 3.3 15.8 - - - +
287B ILE* 2.6 37.7 + - - +
611B SER* 5.0 2.0 - - - -
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Residues in contact with ALA 284 (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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283B GLY* 1.3 70.8 - - - -
285B ARG* 1.3 57.6 + - - +
287B ILE* 3.6 4.4 + - - +
288B TRP* 3.0 29.1 + - - +
607B VAL* 4.7 11.4 - - + +
608B GLN* 5.6 2.5 - - - -
611B SER* 3.6 31.5 - - - -
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Residues in contact with ARG 285 (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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283B GLY* 3.1 0.6 - - - -
284B ALA* 1.3 78.9 - - - +
286B ALA* 1.3 55.1 + - - +
288B TRP* 3.4 6.0 - - - +
289B ARG* 2.8 38.0 + - - +
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Residues in contact with ALA 286 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
280B SER* 5.6 2.5 - - - +
281B PRO 3.8 13.2 - - - +
282B GLN* 4.2 1.3 - - - -
283B GLY* 3.1 26.5 + - - +
285B ARG* 1.3 80.5 - - - +
287B ILE* 1.3 57.6 + - - +
289B ARG* 4.6 2.4 - - - +
290B ALA* 2.9 30.0 + - - +
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Residues in contact with ILE 287 (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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282B GLN* 6.6 0.2 - - + -
283B GLY 2.6 23.2 + - - +
284B ALA* 4.1 4.3 - - - +
286B ALA* 1.3 70.8 - - - +
288B TRP* 1.3 59.4 + - - +
290B ALA* 4.2 4.6 - - - +
291B LEU* 2.9 29.1 + - - +
611B SER* 6.2 2.7 - - - -
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Residues in contact with TRP 288 (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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284B ALA 3.0 19.8 + - - +
285B ARG* 3.1 8.7 + - - +
287B ILE* 1.3 75.1 - - - +
289B ARG* 1.3 64.8 + - + +
291B LEU* 3.0 8.5 + - + +
292B CYS* 2.9 30.2 + - + +
432B PHE* 6.1 6.3 - + - -
603B ALA* 4.2 25.1 - - + -
604B LEU* 5.4 1.3 - - - -
607B VAL* 3.6 33.9 - - + -
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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
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285B ARG 2.8 18.4 + - - +
286B ALA* 4.6 2.0 - - - +
288B TRP* 1.3 75.1 - - + +
290B ALA* 1.3 61.5 + - - +
292B CYS* 3.8 8.7 - - - +
293B HIS* 2.9 28.1 + - - +
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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
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275B ARG* 3.4 35.0 - - + +
276B LYS* 4.1 8.5 - - + +
286B ALA 2.9 22.1 + - - +
287B ILE* 4.2 4.5 - - - +
289B ARG* 1.3 76.4 - - - +
291B LEU* 1.3 52.9 + - - +
293B HIS* 3.1 6.0 + - - -
294B ALA* 2.6 36.0 + - - +
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Residues in contact with LEU 291 (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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287B ILE 2.9 20.9 + - - +
288B TRP* 3.0 8.2 + - + +
290B ALA* 1.3 78.3 - - - +
292B CYS* 1.3 55.8 + - - +
294B ALA* 3.0 8.8 + - - +
295B PHE* 3.0 45.0 + - + -
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Residues in contact with CYS 292 (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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288B TRP* 2.9 19.9 + - + +
289B ARG* 3.9 8.7 - - - +
290B ALA 3.3 0.2 - - - -
291B LEU* 1.3 76.8 - - - +
293B HIS* 1.3 61.3 + - - +
294B ALA 3.6 0.2 + - - -
295B PHE* 3.9 8.9 + - - +
296B GLY* 3.7 15.8 + - - +
299B LEU* 5.1 5.2 - - - +
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Residues in contact with HIS 293 (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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275B ARG* 4.3 22.2 - - + -
289B ARG 2.9 18.7 + - - +
290B ALA* 3.5 6.3 - - - +
292B CYS* 1.3 75.6 - - - +
294B ALA* 1.3 65.1 + - - +
296B GLY* 3.6 11.2 + - - +
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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
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271B ASP* 4.5 20.2 - - + +
272B ALA* 4.5 10.8 - - + -
275B ARG* 3.4 21.1 - - + -
290B ALA 2.6 19.5 + - - +
291B LEU* 3.0 12.5 + - - +
293B HIS* 1.3 74.2 - - - +
295B PHE* 1.3 70.9 + - + +
296B GLY* 3.3 1.4 + - - -
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Residues in contact with PHE 295 (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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268B VAL* 5.3 9.6 - - + -
291B LEU* 3.0 28.7 + - + +
292B CYS* 4.3 7.4 - - - +
294B ALA* 1.3 82.9 - - + +
296B GLY* 1.3 62.0 + - - +
297B ARG 3.2 3.6 + - - -
298B ARG* 4.1 7.8 + - + +
299B LEU* 4.8 15.5 - - + +
383B THR* 3.8 30.7 - - + -
386B ASN* 5.0 4.0 - - + -
387B LEU* 3.5 34.3 - - + -
432B PHE* 3.8 34.8 - + - -
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Residues in contact with GLY 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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292B CYS 3.7 8.7 + - - +
293B HIS* 3.6 13.1 + - - -
294B ALA 3.2 3.7 - - - -
295B PHE* 1.3 76.1 - - - +
297B ARG* 1.3 65.1 + - - +
298B ARG 3.5 0.6 + - - -
299B LEU* 3.9 11.3 + - - +
300B ILE* 4.5 4.3 + - - +
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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