Contacts of the helix formed by residues 350 - 360 (chain A) in PDB entry 1PHP
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 GLY 350 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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316A ASN* 3.6 8.1 - - - -
349A GLY* 1.3 71.6 - - - -
351A GLY* 1.3 60.8 + - - +
352A ASP 3.5 2.2 - - - -
353A SER 3.4 0.9 + - - -
354A ALA* 2.9 33.8 + - - +
370A SER* 5.4 3.6 + - - -
373A GLY* 4.6 15.6 + - - +
376A SER* 5.0 0.4 - - - -
377A LEU* 4.2 11.4 - - - +
396A ADP 3.6 14.6 - - - -
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Residues in contact with GLY 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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350A GLY* 1.3 71.3 - - - +
352A ASP* 1.3 63.3 + - - +
354A ALA* 3.4 4.7 + - - +
355A ALA* 3.1 23.1 + - - +
373A GLY* 4.6 11.5 - - - -
396A ADP 3.3 6.1 + - - -
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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
----------------------------------------------------------
318A PRO* 4.0 8.3 - - + -
322A PHE* 3.8 15.3 - - + -
323A GLU* 4.4 6.8 - - - +
351A GLY* 1.3 73.2 - - - -
353A SER* 1.3 58.1 + - - +
355A ALA* 3.4 7.8 + - - +
356A ALA* 2.9 30.5 + - - +
395A MG 2.0 30.3 - - - -
396A ADP 2.9 43.1 + - - +
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Residues in contact with SER 353 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
315A TRP* 4.9 9.9 - - - -
316A ASN* 4.8 0.7 - - - -
317A GLY* 2.7 30.7 + - - -
318A PRO* 4.5 4.2 - - - +
348A ILE* 3.8 13.0 - - - -
349A GLY 3.6 17.2 + - - -
350A GLY 3.7 0.4 - - - -
352A ASP* 1.3 74.3 - - - +
354A ALA* 1.4 65.5 + - - +
356A ALA* 3.4 7.0 + - - +
357A VAL* 3.2 28.6 + - - +
396A ADP 2.6 22.4 + - - -
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Residues in contact with ALA 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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348A ILE* 4.2 4.4 - - + +
349A GLY 5.9 0.4 - - - -
350A GLY 2.9 18.2 + - - +
351A GLY* 3.8 5.8 - - - +
353A SER* 1.4 74.8 - - - +
355A ALA* 1.3 61.9 + - - +
357A VAL* 3.3 5.4 + - - +
358A GLU* 3.0 38.2 + - - +
369A ILE* 3.8 29.2 - - + -
370A SER 4.7 7.0 - - - +
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Residues in contact with ALA 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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322A PHE* 4.7 8.1 - - + -
351A GLY 3.1 17.2 + - - +
352A ASP* 3.5 9.4 - - - +
354A ALA* 1.3 77.1 - - - +
356A ALA* 1.3 56.8 + - - +
358A GLU* 3.3 10.1 + - - +
359A LYS* 2.8 34.0 + - - +
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Residues in contact with ALA 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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315A TRP* 5.5 0.7 - - + -
318A PRO* 5.1 0.9 - - + -
322A PHE* 3.7 31.6 - - + -
331A THR* 4.0 23.3 - - + -
352A ASP 2.9 20.5 + - - +
353A SER* 3.5 9.2 - - - +
355A ALA* 1.3 74.7 - - - +
357A VAL* 1.3 62.4 + - + +
359A LYS* 3.3 2.9 + - - +
360A PHE* 3.0 33.1 + - + -
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Residues in contact with VAL 357 (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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315A TRP* 3.9 27.4 - - + -
335A ALA* 4.4 9.2 - - + -
348A ILE* 4.4 12.8 - - + -
353A SER 3.2 14.4 + - - +
354A ALA* 3.7 7.6 - - - +
356A ALA* 1.3 76.3 - - - +
358A GLU* 1.3 60.8 + - - +
360A PHE* 3.6 6.8 + - - -
361A GLY 3.4 3.1 + - - -
362A LEU* 3.0 33.5 + - + +
363A ALA* 3.5 28.0 - - - +
366A MET* 4.0 13.2 - - + -
369A ILE* 3.9 13.9 - - + -
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Residues in contact with GLU 358 (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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35A THR* 5.9 4.0 - - - +
354A ALA* 3.0 34.7 + - - +
355A ALA* 3.6 10.9 + - - +
357A VAL* 1.3 74.5 - - - +
359A LYS* 1.3 61.8 + - - +
361A GLY* 2.9 22.4 + - - -
363A ALA* 4.0 25.4 - - + +
369A ILE* 4.1 14.2 - - - +
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Residues in contact with LYS 359 (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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322A PHE* 3.5 48.7 + - + +
323A GLU* 4.7 12.0 + - - +
325A ASP* 5.6 4.9 - - - -
355A ALA* 2.8 17.6 + - - +
356A ALA 3.4 2.9 - - - +
358A GLU* 1.3 78.6 - - - +
360A PHE* 1.3 72.1 + - + +
361A GLY 3.4 0.7 + - - -
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Residues in contact with PHE 360 (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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315A TRP* 5.7 0.2 - + - -
322A PHE* 4.4 13.0 - + + -
328A ALA* 4.1 17.5 - - + -
331A THR* 3.9 21.3 - - + -
332A LYS* 3.6 64.1 - - + +
335A ALA* 4.1 14.1 - - + -
356A ALA* 3.0 23.2 + - + +
357A VAL* 4.1 4.5 - - - +
358A GLU 3.2 0.4 - - - -
359A LYS* 1.3 92.2 - - + +
361A GLY* 1.3 59.9 + - - +
362A LEU* 3.7 19.4 + - + +
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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