Contacts of the helix formed by residues 349 - 356 (chain A) in PDB entry 1PH3
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 349 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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235A GLU* 5.9 4.0 - - - -
347A SER 4.4 0.2 + - - -
348A THR* 1.3 79.1 - - - +
350A LEU* 1.3 59.1 + - - +
351A GLN* 3.4 8.0 + - - +
352A ASP* 3.2 26.9 + - - -
353A LEU* 3.0 25.9 + - - +
371A THR* 4.3 1.6 - - - -
419A ASP* 3.8 5.8 - - - -
421A SER* 3.4 21.2 - - - -
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Residues in contact with LEU 350 (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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348A THR 3.9 0.2 + - - -
349A SER* 1.3 70.2 - - - +
351A GLN* 1.3 58.6 + - - +
353A LEU* 4.0 7.6 - - + -
354A PHE* 2.8 60.9 + - + +
355A HIS* 4.5 0.2 - - - -
371A THR* 4.0 14.6 + - + +
372A GLN 4.4 1.6 - - - +
373A PHE* 4.0 11.7 - - + -
417A VAL* 3.7 20.4 - - + -
418A LYS* 3.3 16.8 - - - +
419A ASP* 2.9 55.2 + - + +
422A THR* 4.0 9.9 - - + +
429A TYR* 4.1 8.1 - - + -
431A VAL* 5.4 1.1 - - + -
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Residues in contact with GLN 351 (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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349A SER* 3.2 6.3 - - - +
350A LEU* 1.3 76.0 - - - +
352A ASP* 1.3 59.3 + - - +
355A HIS* 2.9 73.7 + - - +
356A HIS* 3.5 17.8 + - + +
421A SER* 3.1 41.2 + - - +
422A THR* 3.8 11.1 - - - +
425A ASN* 4.7 3.9 + - - +
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Residues in contact with ASP 352 (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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348A THR* 3.7 18.5 - - + +
349A SER* 3.2 14.9 + - - +
351A GLN* 1.3 79.4 - - - +
353A LEU* 1.3 59.4 + - - +
356A HIS* 3.1 26.6 + - - +
357A ALA* 2.8 32.2 + - - -
363A LEU* 3.5 25.0 - - + +
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Residues in contact with LEU 353 (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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348A THR* 3.5 43.1 - - + +
349A SER 3.0 10.0 + - - +
350A LEU* 3.2 11.2 + - + +
352A ASP* 1.3 79.0 - - - +
354A PHE* 1.3 70.0 + - + +
357A ALA* 3.1 13.0 - - + +
363A LEU* 5.4 0.9 - - + -
369A PHE* 3.9 25.6 - - + -
371A THR* 3.9 23.3 - - + +
479A VAL* 4.7 11.7 - - + -
486A TYR* 2.7 47.2 + - + +
185B VAL* 3.5 2.6 - - - +
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Residues in contact with PHE 354 (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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350A LEU* 2.8 42.5 + - + +
353A LEU* 1.3 86.2 - - + +
355A HIS* 1.3 59.1 + - + +
429A TYR* 3.3 54.1 - + + -
430A ARG 3.5 26.2 - - - -
431A VAL* 4.6 7.6 - - + -
484A GLY 5.9 0.9 - - - -
485A PHE* 6.5 0.4 - - - -
486A TYR* 3.6 25.1 - + - -
185B VAL* 3.7 36.2 - - - +
186B ASP* 4.0 6.8 - - - +
188B GLY* 4.2 15.5 - - - -
189B ILE* 3.8 17.5 - - + +
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Residues in contact with HIS 355 (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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351A GLN* 2.9 52.0 + - - +
354A PHE* 1.3 80.4 - - - +
356A HIS* 1.3 75.5 + - + +
357A ALA 3.8 0.4 - - - -
358A ASP 5.4 0.4 - - - -
359A SER* 3.9 6.1 + - - -
425A ASN* 4.4 2.2 + - - -
427A ASN* 3.9 12.7 + - - -
429A TYR* 2.8 34.4 + + - -
185B VAL* 5.7 0.4 - - - -
189B ILE* 3.6 24.4 - - + +
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Residues in contact with HIS 356 (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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351A GLN* 3.5 34.0 + - + +
352A ASP* 3.1 31.9 + - - +
355A HIS* 1.3 87.1 + - + +
357A ALA* 1.3 58.7 + - - +
358A ASP 3.1 6.1 - - - -
359A SER* 3.7 12.4 + - - +
360A ASP* 3.0 39.4 + - + +
363A LEU* 3.6 11.4 - - + -
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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