Contacts of the helix formed by residues 328 - 341 (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 ALA 328 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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322A PHE* 3.5 33.4 - - + +
324A MET 3.3 2.2 + - - +
325A ASP* 3.3 19.2 + - - +
326A ALA 3.5 0.2 - - - -
327A PHE* 1.3 78.0 - - - +
329A HIS* 1.3 57.7 + - + +
330A GLY 3.4 1.8 - - - -
331A THR* 3.2 6.4 + - - +
332A LYS* 3.0 29.3 + - + +
360A PHE* 4.1 13.7 - - + -
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Residues in contact with HIS 329 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
294A ASP* 4.1 1.1 - - - +
300A ARG* 3.7 28.9 - - - +
325A ASP 3.6 14.8 + - - -
326A ALA* 3.7 23.4 + - - -
327A PHE 3.6 1.0 - - - -
328A ALA* 1.3 77.2 - - + +
330A GLY* 1.3 57.5 + - - +
332A LYS* 3.8 15.1 - - + +
333A ALA* 3.0 28.9 + - - +
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Residues in contact with GLY 330 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
294A ASP* 2.9 25.9 + - - -
295A ILE* 3.7 10.9 - - - +
300A ARG* 3.7 16.8 - - - +
319A MET* 4.0 7.0 - - - +
329A HIS* 1.3 74.0 - - - +
331A THR* 1.3 64.0 - - - +
333A ALA* 3.4 3.8 + - - +
334A ILE* 3.3 27.4 + - - +
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Residues in contact with THR 331 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
294A ASP* 4.2 1.0 + - - -
315A TRP* 3.9 23.8 - - + -
318A PRO* 3.7 14.3 - - + +
319A MET* 2.9 28.2 + - - +
320A GLY* 3.5 9.2 + - - -
322A PHE* 3.9 13.7 - - + +
327A PHE 5.0 0.5 + - - -
328A ALA 3.2 9.2 + - - -
330A GLY* 1.3 76.8 - - - +
332A LYS* 1.3 62.8 + - - +
334A ILE* 3.2 5.1 + - - +
335A ALA* 3.1 20.8 + - - +
356A ALA* 4.0 15.3 - - + -
360A PHE* 3.9 16.6 - - + -
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Residues in contact with LYS 332 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
328A ALA* 3.0 18.1 + - - +
329A HIS* 3.8 16.2 - - - +
331A THR* 1.3 78.0 - - - +
333A ALA* 1.4 56.9 + - - +
335A ALA* 3.2 1.6 + - - +
336A GLU* 2.8 62.7 + - + +
360A PHE* 3.6 48.5 - - + +
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Residues in contact with ALA 333 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
300A ARG* 3.9 31.4 - - + +
304A ARG* 5.5 1.9 + - - +
329A HIS 3.0 18.4 + - - +
330A GLY 3.7 5.8 - - - +
331A THR 3.3 0.2 - - - -
332A LYS* 1.4 77.4 - - - +
334A ILE* 1.3 61.4 - - + +
336A GLU* 3.5 9.8 + - - +
337A ALA* 3.0 29.1 + - - +
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Residues in contact with ILE 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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192A ILE* 3.8 27.8 - - + -
295A ILE* 4.5 4.5 - - + -
300A ARG* 5.0 5.6 - - - +
303A TYR* 3.8 38.1 - - + -
304A ARG* 5.2 0.7 - - + +
307A ILE* 4.0 9.2 - - + -
315A TRP* 4.1 27.8 - - + +
319A MET* 3.5 21.8 - - + -
330A GLY 3.3 14.1 + - - +
331A THR 3.2 7.2 + - - +
333A ALA* 1.3 76.3 - - + +
335A ALA* 1.3 68.7 + - - +
337A ALA* 3.2 5.9 + - + +
338A LEU* 3.0 25.1 + - + +
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Residues in contact with ALA 335 (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* 4.1 18.1 - - + -
331A THR 3.1 12.5 + - - +
332A LYS 3.7 6.7 - - - +
334A ILE* 1.3 78.5 - - - +
336A GLU* 1.3 62.0 + - - +
338A LEU* 3.3 2.8 + - - -
339A ALA* 3.0 19.2 + - - +
357A VAL* 4.4 6.7 - - + -
360A PHE* 4.1 14.1 - - + -
362A LEU* 3.7 18.8 - - + -
366A MET* 3.4 20.1 - - + +
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Residues in contact with GLU 336 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
304A ARG* 5.9 1.2 + - - -
332A LYS* 2.8 53.1 + - + +
333A ALA* 4.0 7.9 - - - +
335A ALA* 1.3 74.2 - - - +
337A ALA* 1.3 62.5 + - - +
339A ALA* 3.3 4.5 + - - +
340A GLU* 3.0 27.2 + - - +
362A LEU* 4.0 18.3 - - + +
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Residues in contact with ALA 337 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
304A ARG* 3.8 30.7 - - + +
307A ILE* 3.9 22.4 - - + +
333A ALA 3.0 18.9 + - - +
334A ILE* 3.2 6.2 + - + +
336A GLU* 1.3 75.4 - - - +
338A LEU* 1.3 57.8 + - - +
340A GLU* 2.9 27.9 - - - +
341A ALA* 3.1 19.1 + - - +
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Residues in contact with LEU 338 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
307A ILE* 3.7 26.2 - - + -
313A VAL* 3.8 30.5 - - + -
315A TRP* 3.7 36.6 - - + -
334A ILE* 3.0 22.4 + - + +
335A ALA* 3.7 4.5 - - - +
337A ALA* 1.3 73.8 - - - +
339A ALA* 1.3 64.3 + - - +
341A ALA* 3.3 19.4 + - - +
344A THR* 4.5 8.7 - - + +
346A SER* 4.2 17.4 + - - -
348A ILE* 4.0 16.8 - - + -
365A LYS 4.8 2.6 - - - +
366A MET* 4.1 14.1 - - - -
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Residues in contact with ALA 339 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
335A ALA 3.0 16.2 + - - +
336A GLU* 3.3 5.1 + - - +
338A LEU* 1.3 76.6 - - - +
340A GLU* 1.3 59.6 + - - +
341A ALA 4.7 1.7 - - - +
342A LEU* 5.7 1.4 - - - +
362A LEU* 4.0 19.5 - - + -
365A LYS* 3.5 58.4 + - + +
366A MET* 4.2 4.8 - - + +
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Residues in contact with GLU 340 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
304A ARG* 3.8 22.0 + - - +
308A ARG* 2.9 35.7 + - - +
336A GLU* 3.0 20.9 + - + +
337A ALA* 2.9 25.3 - - - +
339A ALA* 1.3 77.5 - - - +
341A ALA* 1.3 58.8 + - - +
342A LEU* 3.1 21.8 + - - +
365A LYS* 5.6 0.7 - - - +
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Residues in contact with ALA 341 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
307A ILE* 4.3 10.3 - - + -
308A ARG* 4.4 12.3 - - + +
337A ALA 3.1 16.7 + - - +
338A LEU 3.3 11.7 + - - +
339A ALA 4.7 1.6 - - - +
340A GLU* 1.3 77.9 - - - +
342A LEU* 1.3 66.0 - - - +
343A ASP 3.4 1.0 + - - +
344A THR* 3.3 40.7 + - - +
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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