Contacts of the helix formed by residues 332 - 340 (chain B) in PDB entry 2P3Z
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 SER 332 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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330B GLY* 3.6 2.6 - - - -
331B SER* 1.3 80.6 - - - +
333B VAL* 1.3 76.2 + - - +
335B SER* 3.1 2.6 + - - -
336B HIS* 3.0 44.2 + - - -
363B GLN* 3.9 15.5 + - - +
364B PHE* 3.7 18.6 - - - -
368B LEU* 4.4 0.3 - - - +
371B GLU* 2.7 40.3 + - - +
372B PRO 4.8 1.4 + - - -
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Residues in contact with VAL 333 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
332B SER* 1.3 89.5 + - - +
334B TYR* 1.3 82.1 + - + +
336B HIS* 3.4 9.9 - - + -
337B HIS* 3.0 32.1 + - + -
368B LEU* 4.8 2.7 - - + -
371B GLU* 5.0 0.2 - - + -
372B PRO* 3.8 36.3 - - + -
384B LEU* 4.7 6.3 - - + -
386B LYS* 6.2 0.2 - - - +
389B PHE* 3.5 40.1 - - + +
391B VAL* 3.9 16.4 - - + -
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Residues in contact with TYR 334 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83B PHE* 4.2 6.8 + - - -
84B ALA* 3.5 32.1 - - + -
85B VAL* 3.7 15.7 + - + -
142B LEU* 4.0 28.5 - - + -
303B VAL* 4.0 20.9 - - + +
309B LEU* 4.8 2.1 - - - +
331B SER* 3.4 19.7 - - - +
332B SER 3.2 0.8 + - - -
333B VAL* 1.3 86.8 - - + +
335B SER* 1.3 59.4 + - - +
338B ALA* 4.1 10.4 + - - +
364B PHE* 3.6 28.3 - + - -
368B LEU* 4.2 17.4 - - + +
389B PHE* 3.6 51.5 - + + -
391B VAL* 4.4 4.4 - - + +
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Residues in contact with SER 335 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
303B VAL* 3.8 19.1 - - - +
328B PRO* 3.6 13.5 + - - +
330B GLY* 5.1 1.0 - - - -
331B SER* 3.6 18.2 + - - -
332B SER 3.1 7.9 + - - -
334B TYR* 1.3 75.8 - - - +
336B HIS* 1.4 71.1 + - - +
337B HIS 3.2 0.2 - - - -
338B ALA* 2.8 8.0 + - - +
339B VAL* 2.8 45.8 + - - +
348B SER* 4.1 8.6 + - - -
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Residues in contact with HIS 336 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
168B ILE* 3.7 18.2 - - + +
170B PHE* 3.3 38.9 - + - -
330B GLY* 6.4 0.2 - - - -
331B SER 5.8 0.4 - - - -
332B SER* 3.0 46.3 + - - -
333B VAL* 3.1 19.0 + - + +
335B SER* 1.4 78.3 - - - +
337B HIS* 1.3 62.3 + - - +
339B VAL* 3.7 1.7 - - - +
340B ILE* 3.2 28.9 + - - +
348B SER* 4.9 5.2 + - - -
349B GLU 5.3 2.5 - - - -
350B PHE* 6.0 3.4 - + - -
372B PRO* 4.7 6.7 + - + -
379B ILE* 3.6 20.4 - - + +
384B LEU* 3.9 19.9 - - + +
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Residues in contact with HIS 337 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
155B PRO* 3.6 6.7 - - + -
156B VAL* 3.5 4.2 + - + -
157B TYR* 3.1 54.3 + + + +
160B LEU* 3.6 5.6 - - - +
333B VAL* 3.0 30.2 + - + +
336B HIS* 1.3 76.8 - - - +
338B ALA* 1.3 56.8 - - - +
340B ILE* 4.2 0.9 - - - -
341B THR* 3.4 9.0 - - - +
384B LEU* 3.1 50.3 + - + +
386B LYS 4.2 1.3 - - - -
388B GLY 3.5 16.4 - - - -
389B PHE* 3.6 46.0 + + + -
390B GLY* 4.9 0.8 - - - -
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Residues in contact with ALA 338 (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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160B LEU* 4.1 8.1 - - - -
309B LEU* 3.7 18.5 - - + +
312B LEU* 3.5 31.6 - - + -
334B TYR 4.1 5.0 + - - +
335B SER 2.8 9.3 + - - +
337B HIS* 1.3 77.7 - - - +
339B VAL* 1.3 60.8 + - - +
340B ILE 3.1 1.8 - - - -
341B THR* 2.9 28.9 + - - -
342B PHE* 3.4 17.1 - - + -
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Residues in contact with VAL 339 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
165B ARG* 2.9 22.3 + - - -
168B ILE* 3.9 15.7 - - + -
328B PRO* 3.6 19.5 - - + -
335B SER* 2.8 42.9 + - - +
336B HIS* 3.7 12.8 - - - +
338B ALA* 1.3 66.1 - - + +
340B ILE* 1.3 65.6 + - - +
341B THR 3.0 2.2 - - - -
342B PHE* 3.0 22.5 + - + +
345B THR* 3.5 30.4 - - + +
348B SER* 4.4 15.7 - - - +
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Residues in contact with ILE 340 (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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157B TYR* 3.6 37.5 - - + -
163B ALA* 3.8 3.1 - - + -
164B VAL* 2.9 27.9 + - - +
165B ARG* 3.4 32.0 + - + +
166B ASP 4.5 2.0 - - - +
167B GLU* 4.6 3.4 - - - -
168B ILE* 4.1 17.5 - - + -
336B HIS 3.2 19.6 + - - +
337B HIS* 4.0 0.9 - - - +
338B ALA 3.1 1.0 - - - -
339B VAL* 1.3 79.1 - - - +
341B THR* 1.3 62.0 + - + +
379B ILE 4.8 0.7 - - - +
381B LYS* 3.6 38.4 - - + +
384B LEU* 4.0 13.5 - - + -
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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
------------------------------------------------------------
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