Contacts of the helix formed by residues 322 - 332 (chain B) in PDB entry 4TR8
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 VAL 322 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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268B PHE* 3.5 43.1 - - + +
272B ALA* 3.6 21.8 - - + -
280B ARG* 2.8 46.9 + - + +
282B ILE* 3.9 24.0 - - + -
320B PHE 3.3 3.9 + - - -
321B ASN* 1.3 71.2 + - - +
323B SER* 1.4 59.1 + - - +
325B LEU* 3.1 6.4 + - + +
326B LEU* 2.9 33.1 + - + +
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Residues in contact with SER 323 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
176B ARG* 5.5 0.5 + - - -
280B ARG* 5.4 5.4 - - - +
321B ASN* 2.8 27.6 + - - -
322B VAL* 1.4 78.0 - - - +
324B TYR* 1.3 64.5 + - - -
326B LEU* 3.3 10.5 + - - +
327B ASP* 2.9 42.1 + - - +
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Residues in contact with TYR 324 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
173B ASP* 4.3 3.4 + - - -
175B HIS* 3.4 45.1 + + + +
176B ARG* 3.5 46.1 + - + +
321B ASN* 3.3 42.6 + - + +
323B SER* 1.3 89.6 + - - +
325B LEU* 1.3 62.0 + - - +
327B ASP* 3.6 2.4 + - - +
328B VAL* 3.3 28.6 + - - +
362B VAL* 3.6 30.0 - - + +
363B MET 4.8 5.4 - - - -
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Residues in contact with LEU 325 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
268B PHE* 3.7 34.1 - - + -
282B ILE* 3.9 19.3 - - + -
284B LEU* 4.4 4.7 - - + -
320B PHE* 3.7 44.9 - - + -
321B ASN 3.5 8.9 + - - +
322B VAL* 3.1 7.5 + - - +
324B TYR* 1.3 72.3 - - - +
326B LEU* 1.4 59.9 + - - +
328B VAL* 3.3 7.1 + - + +
329B LEU* 3.0 34.9 + - + +
339B PHE* 4.3 21.9 - - + -
348B ALA* 5.6 1.1 - - + -
350B VAL* 5.8 0.7 - - + -
362B VAL* 4.4 16.2 - - + -
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Residues in contact with LEU 326 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
265B ARG* 2.9 78.2 + - + +
268B PHE* 3.9 15.9 - - + -
269B SER* 3.9 20.9 - - - +
280B ARG* 5.1 8.1 - - - +
322B VAL* 2.9 34.3 + - + +
323B SER* 3.7 9.2 - - - +
325B LEU* 1.4 74.8 - - - +
327B ASP* 1.3 62.7 + - - +
329B LEU 3.4 0.7 + - - -
330B GLY* 3.0 9.0 + - - -
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Residues in contact with ASP 327 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
144B PHE* 3.4 37.3 - - + +
176B ARG* 2.8 29.8 + - - +
265B ARG* 5.2 2.1 + - - +
323B SER* 2.9 26.2 + - - +
324B TYR 3.8 4.5 - - - +
325B LEU 3.4 0.2 - - - -
326B LEU* 1.3 77.3 - - - +
328B VAL* 1.4 61.8 + - - +
330B GLY* 3.4 9.6 + - - -
331B VAL* 3.6 14.4 + - - +
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Residues in contact with VAL 328 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
144B PHE* 4.1 20.2 - - + -
176B ARG* 6.1 1.1 - - + -
177B LEU 5.5 0.9 - - - +
324B TYR 3.3 13.4 + - - +
325B LEU* 3.3 10.2 + - + +
327B ASP* 1.4 75.1 - - - +
329B LEU* 1.3 66.9 + - + +
331B VAL* 3.1 20.4 + - - +
332B ILE* 3.4 10.5 + - + +
339B PHE* 5.6 1.3 - - + -
350B VAL* 3.8 33.2 - - + -
360B TYR* 3.8 34.1 - - + -
361B VAL 5.5 0.4 - - - +
362B VAL* 3.9 17.7 - - + -
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Residues in contact with LEU 329 (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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261B ARG* 2.9 36.9 + - + +
264B LEU* 3.9 4.5 - - + -
265B ARG* 3.5 49.1 - - + +
268B PHE* 3.7 28.3 - - + -
325B LEU 3.0 17.4 + - - +
328B VAL* 1.3 76.8 - - + +
330B GLY* 1.3 60.2 + - - +
331B VAL 3.2 1.0 + - - -
332B ILE* 3.3 12.0 + - + -
337B VAL* 3.9 39.3 - - + -
339B PHE* 4.1 13.0 - - + -
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Residues in contact with GLY 330 (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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261B ARG* 4.3 3.8 + - - -
265B ARG* 3.5 15.8 - - - +
326B LEU 3.0 16.0 + - - -
327B ASP* 3.4 3.8 + - - -
328B VAL 3.2 0.6 - - - -
329B LEU* 1.3 76.3 - - - +
331B VAL* 1.4 62.5 + - - +
332B ILE 3.7 2.1 - - - +
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Residues in contact with VAL 331 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
140B ASP 3.6 21.5 - - - +
141B ARG* 3.3 31.8 + - - +
144B PHE* 3.5 31.4 - - + -
327B ASP 3.6 3.3 + - - +
328B VAL 3.1 13.2 + - - +
330B GLY* 1.4 78.8 - - - +
332B ILE* 1.3 64.7 + - - +
333B GLY 3.4 2.8 + - - -
360B TYR* 3.3 33.1 + - + +
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Residues in contact with ILE 332 (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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261B ARG* 3.3 29.3 + - + -
328B VAL* 3.4 16.8 - - + +
329B LEU* 3.3 13.5 + - - +
330B GLY 5.0 1.7 - - - +
331B VAL* 1.3 75.9 - - - +
333B GLY* 1.3 59.6 + - - +
334B THR* 3.5 30.5 - - - +
336B GLN 4.0 7.2 - - - +
337B VAL* 4.0 18.6 - - + -
350B VAL* 4.3 3.1 - - + -
351B HIS 3.8 27.8 - - - +
352B GLU* 3.8 11.4 - - + +
360B TYR* 3.9 26.2 - - + -
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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