Contacts of the helix formed by residues 331 - 340 (chain A) 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 331 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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32A TYR* 3.3 19.1 + - - -
302A ASP* 3.4 22.0 + - - -
303A VAL* 3.9 12.8 + - - -
304A GLY* 5.0 1.8 - - - -
329A HIS 3.3 5.1 + - - -
330A GLY* 1.3 73.5 - - - -
332A SER* 1.4 72.1 + - - +
334A TYR* 3.2 23.9 + - - -
335A SER* 2.8 23.6 + - - -
364A PHE* 4.0 10.5 - - - -
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Residues in contact with SER 332 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
330A GLY* 3.7 2.4 + - - -
331A SER* 1.4 79.6 - - - +
333A VAL* 1.3 72.2 + - - +
335A SER* 3.0 4.2 + - - -
336A HIS* 2.9 42.4 + - - -
363A GLN* 4.1 14.6 + - - +
364A PHE* 3.8 16.6 - - - -
368A LEU* 4.2 3.4 - - - +
371A GLU* 2.4 41.5 + - - +
372A PRO 4.6 2.3 + - - -
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Residues in contact with VAL 333 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
332A SER* 1.3 82.2 + - - +
334A TYR* 1.3 77.1 + - + +
336A HIS* 3.5 12.3 - - + -
337A HIS* 3.1 30.5 + - + -
368A LEU* 4.3 5.4 - - + -
371A GLU* 5.1 0.2 - - + -
372A PRO* 3.5 37.9 - - + -
384A LEU* 4.8 6.1 - - + -
389A PHE* 3.5 41.8 - - + +
391A VAL* 4.0 20.2 - - + -
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Residues in contact with TYR 334 (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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83A PHE* 4.0 8.0 + - - -
84A ALA* 3.4 35.3 - - + -
85A VAL* 3.7 11.6 + - + -
142A LEU* 3.9 30.0 - - + +
303A VAL* 4.0 16.8 - - + +
304A GLY 5.8 0.2 - - - +
309A LEU* 4.9 1.7 - - - +
331A SER* 3.4 19.7 - - - +
332A SER 3.0 0.8 + - - -
333A VAL* 1.3 86.2 - - + +
335A SER* 1.3 59.1 + - - +
338A ALA* 4.2 9.9 + - - +
364A PHE* 3.7 28.7 - + - -
368A LEU* 3.6 22.1 - - + +
389A PHE* 3.7 51.4 - + + -
391A VAL* 4.4 3.9 - - + +
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Residues in contact with SER 335 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
303A VAL* 3.8 19.0 - - - +
328A PRO* 4.6 2.5 - - - -
329A HIS 3.9 9.7 + - - -
330A GLY* 3.8 2.6 - - - -
331A SER 2.8 32.1 + - - -
332A SER 3.0 9.8 + - - -
334A TYR* 1.3 78.3 - - - +
336A HIS* 1.3 70.4 + - - +
337A HIS 3.3 0.4 - - - -
338A ALA* 2.9 6.1 + - - +
339A VAL* 2.9 36.6 + - - +
348A SER* 4.8 5.0 + - - -
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Residues in contact with HIS 336 (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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168A ILE* 3.7 19.4 - - + +
170A PHE* 3.4 37.0 - + - -
332A SER* 2.9 44.1 + - - -
333A VAL* 3.2 17.9 + - + +
335A SER* 1.3 79.3 + - - +
337A HIS* 1.3 62.7 + - - +
339A VAL* 4.1 1.8 - - - -
340A ILE* 3.1 30.3 + - - +
348A SER* 5.0 2.4 + - - -
349A GLU 5.2 2.5 - - - -
350A PHE* 6.0 4.0 - + - -
372A PRO* 4.9 6.4 + - + -
374A PRO* 6.0 0.2 - - - +
379A ILE* 3.4 22.7 - - + +
384A LEU* 3.8 21.3 - - + +
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Residues in contact with HIS 337 (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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155A PRO* 3.5 7.4 - - + -
156A VAL* 3.3 14.6 + - + -
157A TYR* 3.1 50.5 + + + +
160A LEU* 3.8 3.9 - - - +
333A VAL* 3.1 24.7 + - + +
336A HIS* 1.3 77.8 - - - +
338A ALA* 1.3 58.4 + - - +
340A ILE* 3.7 1.1 - - - +
341A THR* 3.4 9.2 - - - +
384A LEU* 3.1 51.0 + - + +
386A LYS 4.3 1.3 - - - -
388A GLY 3.3 18.2 - - - -
389A PHE* 3.8 33.0 + + + -
390A GLY* 5.3 0.2 - - - -
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Residues in contact with ALA 338 (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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160A LEU* 4.0 10.3 - - - -
309A LEU* 3.6 19.2 - - + +
312A LEU* 3.5 31.0 - - + -
334A TYR 4.2 5.0 + - - +
335A SER 2.9 8.1 + - - +
337A HIS* 1.3 77.2 - - - +
339A VAL* 1.3 60.9 + - - +
341A THR* 2.8 31.0 + - - -
342A PHE* 3.5 16.0 - - + -
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Residues in contact with VAL 339 (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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165A ARG* 2.9 21.2 + - - -
168A ILE* 4.1 18.6 - - + -
328A PRO* 3.6 40.2 - - + -
335A SER* 2.9 30.3 + - - +
336A HIS* 3.8 6.5 - - - +
338A ALA* 1.3 75.0 - - + +
340A ILE* 1.3 63.4 + - - +
341A THR 3.0 1.3 + - - -
342A PHE* 3.1 20.5 + - + +
345A THR* 3.6 16.5 - - + +
347A PHE 5.9 0.2 - - - -
348A SER* 4.2 21.5 - - - +
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Residues in contact with ILE 340 (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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157A TYR* 3.7 35.0 - - + -
163A ALA* 3.3 4.1 - - + -
164A VAL* 2.8 34.5 + - - +
165A ARG* 3.7 30.9 + - + +
167A GLU* 4.6 4.5 - - - -
168A ILE* 4.0 18.4 - - + -
336A HIS 3.1 19.6 + - - +
337A HIS 3.7 1.1 - - - +
339A VAL* 1.3 79.9 - - - +
341A THR* 1.4 54.6 + - + +
342A PHE 3.5 0.2 - - - -
379A ILE 5.0 0.7 - - - +
381A LYS* 3.4 40.6 - - + +
384A LEU* 3.9 12.6 - - + -
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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