Contacts of the helix formed by residues 235 - 246 (chain A) in PDB entry 4TVJ
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 235 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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228A ASN* 4.2 5.2 - - - +
233A SER 3.4 1.8 + - - -
234A MET* 1.3 76.2 - - - +
236A LEU* 1.3 59.2 + - - +
237A ARG* 2.8 48.1 + - - +
238A VAL* 3.2 18.4 + - + +
239A GLN* 2.9 24.3 + - - +
371A PRO* 3.6 21.3 - - + +
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Residues in contact with LEU 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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224A LEU* 3.7 43.1 - - + +
225A GLY* 4.0 10.3 - - - +
228A ASN* 4.0 22.4 + - + +
234A MET 3.3 1.3 + - - -
235A ASP* 1.3 75.1 + - - +
237A ARG* 1.3 60.0 + - + +
239A GLN* 3.5 29.2 - - + +
240A GLU* 3.1 33.9 + - + +
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Residues in contact with ARG 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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235A ASP* 2.8 23.5 + - - +
236A LEU* 1.3 72.1 - - + +
238A VAL* 1.3 63.8 + - - +
240A GLU* 3.3 7.5 + - - +
241A LEU* 3.1 21.8 + - - +
371A PRO* 3.5 23.8 + - + +
372A LEU 2.8 27.9 + - - +
373A ASP* 5.0 2.8 - - - +
374A HIS* 3.7 9.3 + - - -
403A ASP* 2.8 45.0 + - - +
405A PHE* 3.8 14.9 - - + -
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Residues in contact with VAL 238 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
234A MET* 3.7 24.2 - - + -
235A ASP* 3.2 16.0 + - + +
237A ARG* 1.3 74.7 - - - +
239A GLN* 1.3 66.7 + - - +
241A LEU* 3.1 4.5 + - + +
242A ILE* 2.9 32.8 + - + +
362A TYR* 4.4 20.4 - - + -
369A LEU* 3.5 26.5 - - + +
371A PRO* 3.8 23.1 - - + -
405A PHE* 4.2 11.0 - - + -
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Residues in contact with GLN 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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228A ASN* 4.0 1.4 - - - +
233A SER* 4.0 16.0 - - - -
234A MET* 2.7 46.3 + - + +
235A ASP 2.9 14.5 + - - +
236A LEU* 3.5 33.1 - - + +
237A ARG 3.3 0.2 - - - -
238A VAL* 1.3 76.4 - - - +
240A GLU* 1.3 60.9 + - - +
242A ILE* 3.4 2.0 + - - +
243A LYS* 2.9 42.4 + - - +
356A HIS* 5.2 6.4 + - - -
358A LEU* 3.9 21.6 - - + +
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Residues in contact with GLU 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 LEU* 3.1 23.2 + - + +
237A ARG* 3.3 7.4 + - - +
238A VAL 3.2 0.2 - - - -
239A GLN* 1.3 77.3 - - - +
241A LEU* 1.3 61.7 + - - +
243A LYS* 3.0 37.3 + - - +
244A LEU* 3.1 23.9 + - - +
574A LYS* 4.6 17.2 + - - +
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Residues in contact with LEU 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 ARG 3.1 13.5 + - - +
238A VAL* 3.1 9.2 + - - +
240A GLU* 1.3 74.0 - - - +
242A ILE* 1.3 65.9 + - - +
244A LEU* 3.1 11.5 + - + +
245A ILE* 3.0 31.7 + - + +
369A LEU* 3.8 29.8 - - + -
405A PHE* 4.0 40.6 - - + -
484A LEU* 4.0 35.4 - - + -
572A LEU* 4.1 14.1 - - + -
574A LYS* 5.5 7.8 - - + +
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Residues in contact with ILE 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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234A MET* 4.3 9.0 - - - -
238A VAL* 2.9 29.4 + - + +
239A GLN* 3.8 4.9 - - - +
241A LEU* 1.3 76.6 - - + +
243A LYS* 1.3 64.4 + - - +
245A ILE* 4.2 8.5 - - + -
246A CYS* 3.0 39.9 + - - +
358A LEU* 3.9 24.5 - - + +
361A HIS* 4.0 13.2 - - + -
362A TYR* 4.0 21.1 - - + +
365A LEU* 4.0 26.9 - - + -
369A LEU* 4.3 9.6 - - + -
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Residues in contact with LYS 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 GLN* 2.9 29.3 + - - +
240A GLU* 3.0 37.4 + - - +
242A ILE* 1.3 78.0 - - - +
244A LEU* 1.3 61.7 + - - +
246A CYS* 3.9 2.9 - - - -
247A ASN* 3.4 23.7 + - - +
358A LEU* 3.9 33.4 - - + -
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Residues in contact with LEU 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 GLU 3.1 13.9 + - - +
241A LEU* 3.1 12.1 + - + +
243A LYS* 1.3 81.0 - - - +
245A ILE* 1.3 63.0 + - + +
247A ASN* 3.4 20.3 + - + +
250A ALA* 5.2 5.3 - - + +
432A MET* 3.6 26.6 - - + +
482A THR* 4.0 30.3 - - + +
484A LEU* 4.9 5.8 - - + -
574A LYS* 4.1 21.3 - - + +
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Residues in contact with ILE 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 LEU* 3.0 30.7 + - + +
242A ILE* 3.8 11.0 - - + +
244A LEU* 1.3 79.2 - - + +
246A CYS* 1.3 63.8 + - - +
247A ASN 3.3 1.5 + - - +
251A MET* 3.3 22.5 - - - +
365A LEU* 4.5 13.0 - - + -
369A LEU* 5.4 0.7 - - + -
432A MET* 4.2 19.4 - - + +
433A SER 5.5 0.2 - - - +
435A TRP* 3.9 11.4 - - + -
436A VAL* 3.4 31.9 + - + +
439A LEU* 3.9 26.9 - - + -
484A LEU* 3.6 30.3 - - + -
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Residues in contact with CYS 246 (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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242A ILE* 3.0 37.4 + - - +
243A LYS* 3.9 3.6 - - - +
245A ILE* 1.3 81.8 - - - +
247A ASN* 1.3 60.8 + - - +
248A VAL* 3.2 14.7 + - - +
251A MET* 4.5 5.6 - - - +
346A LEU* 4.7 4.0 - - - -
347A VAL* 3.7 30.3 - - + +
361A HIS* 3.9 19.7 - - + +
365A LEU* 5.8 1.6 - - - -
436A VAL* 4.0 18.2 - - - -
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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
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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