Contacts of the helix formed by residues 234 - 245 (chain A) in PDB entry 3VF1
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 ASP 234 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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231A TYR* 2.8 24.6 + - + +
232A TRP 4.1 0.7 - - - +
233A ARG* 1.3 76.4 - - - +
235A ASP* 1.3 71.6 + - - +
236A VAL* 3.0 26.5 + - - +
237A TRP* 3.1 9.2 + - + +
238A PHE* 2.8 28.9 + - - +
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Residues in contact with ASP 235 (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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233A ARG 3.4 1.9 + - - -
234A ASP* 1.3 75.9 + - - +
236A VAL* 1.3 57.9 + - + +
238A PHE* 3.5 4.9 - - - +
239A GLY* 3.0 23.7 + - - -
325A ILE 4.1 0.9 - - - +
326A ILE* 4.2 10.3 - - + -
327A PRO* 3.3 29.7 - - + +
345A PRO* 4.5 8.3 - - - +
353A TRP* 3.1 23.9 + - - -
357A LYS* 2.8 30.3 + - - +
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Residues in contact with VAL 236 (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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234A ASP* 3.0 18.0 + - - +
235A ASP* 1.3 76.9 - - + +
237A TRP* 1.3 65.2 + - - +
239A GLY* 3.5 1.2 + - - -
240A SER* 3.2 22.3 + - - -
320A LYS* 3.9 24.2 - - - +
324A ASP* 3.6 32.3 - - + +
325A ILE 4.0 3.9 - - - +
326A ILE* 4.0 15.3 - - + -
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Residues in contact with TRP 237 (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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227A HIS* 4.1 2.5 - - + -
228A ALA* 3.4 37.0 - - + -
231A TYR* 3.4 46.0 - + + +
232A TRP* 3.6 21.4 - - - +
234A ASP* 3.1 8.5 + - + +
236A VAL* 1.3 77.0 - - - +
238A PHE* 1.3 71.8 + + - +
240A SER* 2.7 26.0 + - - -
241A GLN* 3.1 38.7 + - + +
565A ALA 5.2 2.5 - - - -
572A ASN* 2.8 22.7 + - - -
663A SER* 4.0 30.7 - - - -
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Residues in contact with PHE 238 (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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232A TRP 4.7 10.5 - - - +
234A ASP 2.8 17.7 + - - +
235A ASP* 3.5 9.0 - - - +
237A TRP* 1.3 81.6 - - - +
239A GLY* 1.3 63.9 + - - +
241A GLN* 3.1 21.3 + - + +
242A PHE* 3.4 30.1 - + - -
317A PHE* 4.3 1.6 - + - -
327A PRO* 3.6 31.9 - - + -
330A ILE* 5.2 0.2 - - + -
357A LYS* 3.5 50.3 - - + +
360A LEU* 4.1 15.5 - - + -
361A ARG* 3.2 33.0 - - + -
572A ASN 5.9 0.4 - - - -
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Residues in contact with GLY 239 (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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235A ASP 3.0 12.0 + - - -
237A TRP 3.3 0.2 - - - -
238A PHE* 1.3 76.8 - - - +
240A SER* 1.3 61.3 + - - +
242A PHE* 3.2 15.4 + - - +
243A LEU 4.0 1.2 + - - -
317A PHE* 4.1 15.9 - - - -
325A ILE* 3.2 45.8 - - - +
327A PRO* 4.4 0.7 - - - -
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Residues in contact with SER 240 (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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236A VAL* 3.2 13.8 + - - -
237A TRP* 2.7 29.7 + - - -
239A GLY* 1.3 76.7 - - - +
241A GLN* 1.3 60.4 + - - +
242A PHE 3.1 0.4 - - - -
243A LEU* 3.1 12.2 + - - +
244A ASN* 2.7 49.0 + - - +
325A ILE* 4.4 2.3 + - - +
470A LYS 6.0 0.2 - - - -
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Residues in contact with GLN 241 (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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237A TRP* 3.1 57.1 + - + +
238A PHE* 3.1 13.1 + - + +
240A SER* 1.3 88.8 + - - +
242A PHE* 1.3 56.6 + - - +
243A LEU 3.2 1.3 - - - -
244A ASN* 4.8 5.1 + - - +
245A GLY* 3.3 34.8 + - - +
246A SER 4.5 1.9 + - - -
247A ASN* 4.7 4.2 + - - +
361A ARG* 3.8 31.3 + - - +
565A ALA 5.0 0.7 - - - +
566A THR* 4.6 6.4 + - - -
572A ASN* 3.3 24.6 + - - +
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Residues in contact with PHE 242 (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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238A PHE* 3.4 38.1 - + - -
239A GLY 3.2 9.3 + - - +
240A SER 3.1 0.6 - - - -
241A GLN* 1.3 77.1 - - - +
243A LEU* 1.3 64.6 + - - +
247A ASN 3.7 8.8 - - - +
248A PRO* 3.5 19.4 - - - +
250A VAL* 5.7 2.4 + - + -
251A ILE* 4.0 25.1 + - + +
290A THR* 3.9 21.3 - - + -
292A TYR* 3.3 26.5 - + - -
317A PHE* 3.9 12.3 - + - -
360A LEU* 4.0 23.6 - - + -
361A ARG* 3.6 35.7 - - - +
364A ASP* 4.1 9.2 - - + -
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Residues in contact with LEU 243 (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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239A GLY 4.3 1.8 - - - +
240A SER* 3.1 8.5 + - - +
242A PHE* 1.3 82.8 - - - +
244A ASN* 1.3 69.2 + - - +
245A GLY 3.6 1.6 - - - -
248A PRO* 3.5 11.2 - - - +
251A ILE* 3.8 28.5 - - + -
323A ASP 6.0 1.6 - - - +
325A ILE* 4.0 35.0 - - + +
468A LEU* 4.1 21.1 - - + -
470A LYS* 4.2 17.7 - - + +
471A PHE* 3.0 51.9 - - + -
473A TYR* 3.6 5.4 - - - +
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Residues in contact with ASN 244 (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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240A SER* 2.7 29.8 + - - +
241A GLN* 4.8 6.6 + - - +
243A LEU* 1.3 83.6 - - - +
245A GLY* 1.3 65.7 + - - +
470A LYS 3.1 22.8 + - - -
471A PHE* 3.6 1.4 - - - -
472A TYR* 2.9 45.1 + - + -
473A TYR* 3.3 5.9 + - - -
665A TYR* 3.8 26.6 - - + -
667A TRP* 4.9 3.8 + - - -
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Residues in contact with GLY 245 (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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241A GLN* 3.3 31.0 + - - -
242A PHE 5.0 0.2 - - - -
243A LEU 3.6 1.6 + - - -
244A ASN* 1.3 83.4 - - - +
246A SER* 1.3 63.9 + - - -
247A ASN 3.6 1.5 - - - +
248A PRO* 5.4 2.2 - - - +
361A ARG* 5.8 0.4 - - - -
558A ALA 4.1 3.6 - - - +
562A SER* 3.7 12.9 + - - -
566A THR* 3.9 11.0 - - - -
665A TYR* 4.4 7.1 + - - -
667A TRP* 4.9 0.4 - - - -
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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