Contacts of the helix formed by residues 325 - 344 (chain A) in PDB entry 4P22
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 ARG 325 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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315A PHE* 5.0 3.6 - - - -
323A PHE* 3.0 30.9 + - + -
324A SER* 1.3 88.9 + - - +
326A PRO* 1.3 79.8 - - - +
327A ALA* 3.4 33.7 - - - +
328A GLN* 3.1 43.1 - - + +
329A LEU 3.4 10.4 + - - -
375A GLN* 4.4 11.3 + - - +
379A ASP* 5.7 2.2 - - + +
382A LEU* 4.9 2.9 - - + -
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Residues in contact with PRO 326 (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 PHE* 3.7 36.6 - - + -
316A VAL 6.1 2.5 - - - -
323A PHE* 3.7 15.5 - - + +
324A SER 3.7 3.1 - - - +
325A ARG* 1.3 102.6 - - - +
327A ALA* 1.3 55.2 + - - +
328A GLN 3.2 0.2 + - - -
329A LEU* 3.2 3.0 + - + +
330A HIS* 2.7 34.7 + - - +
425A TYR* 3.9 28.7 - - + +
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Residues in contact with ALA 327 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
315A PHE* 3.7 23.0 - - + -
325A ARG* 3.4 21.7 - - - +
326A PRO* 1.3 77.4 - - - +
328A GLN* 1.3 58.5 + - - +
330A HIS* 3.2 3.4 - - - +
331A ILE* 2.9 32.6 + - - +
373A VAL* 4.1 16.3 - - + +
375A GLN* 3.8 21.3 - - - +
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Residues in contact with GLN 328 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
325A ARG* 3.1 41.2 + - + +
326A PRO 3.1 0.6 - - - -
327A ALA* 1.3 75.2 - - - +
329A LEU* 1.3 55.0 + - - +
331A ILE* 3.4 8.5 + - - +
332A GLY* 2.7 32.6 + - - -
375A GLN* 3.8 23.1 + - + +
377A ASN 4.4 4.4 + - - -
378A LEU* 3.1 17.8 - - + +
379A ASP* 2.8 43.3 + - + +
382A LEU* 4.0 14.8 - - + -
383A ILE* 4.0 10.0 - - + +
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Residues in contact with LEU 329 (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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195A PHE* 3.7 41.3 - - + -
196A GLY 4.9 0.2 - - - +
323A PHE* 3.4 35.4 - - + -
325A ARG 3.4 2.5 + - - +
326A PRO 3.2 5.3 + - - +
328A GLN* 1.3 75.4 - - - +
330A HIS* 1.3 56.4 + - - +
332A GLY* 4.2 0.9 - - - +
333A PHE* 2.6 47.5 + - + +
382A LEU* 4.1 13.9 - - + +
383A ILE* 6.5 0.4 - - + -
386A LEU* 5.1 10.8 - - + -
425A TYR* 3.5 34.5 - - + -
426A PHE 4.0 8.7 - - - +
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Residues in contact with HIS 330 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
310A LEU* 2.9 53.1 + - + +
313A PRO* 3.8 17.8 - - + +
315A PHE* 3.7 13.2 - + + -
326A PRO 2.7 17.2 + - - +
327A ALA 3.2 9.6 - - - +
328A GLN 3.2 0.2 - - - -
329A LEU* 1.3 74.5 - - - +
331A ILE* 1.3 65.5 + - - +
333A PHE* 3.2 2.8 + - - +
334A GLN* 3.1 21.5 + - + +
373A VAL* 4.5 13.2 - - + -
423A TRP* 3.6 24.4 - + - -
425A TYR* 2.7 33.7 + - + +
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Residues in contact with ILE 331 (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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327A ALA 2.9 21.5 + - - +
328A GLN* 3.6 10.8 - - + +
330A HIS* 1.3 75.4 - - + +
332A GLY* 1.3 65.4 + - - +
334A GLN* 3.1 5.4 + - - +
335A ALA* 3.0 20.8 + - - +
362A ALA* 3.5 35.2 - - + +
365A VAL* 3.6 22.8 - - + +
366A ASN* 3.7 28.5 - - + +
369A ALA* 5.4 0.9 - - + -
373A VAL* 3.9 20.4 - - + -
375A GLN* 4.1 19.5 - - + -
378A LEU* 4.6 8.1 - - + -
383A ILE* 5.0 0.4 - - + -
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Residues in contact with GLY 332 (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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328A GLN 2.7 21.9 + - - -
329A LEU* 3.4 2.7 - - - -
331A ILE* 1.3 74.6 - - - +
333A PHE* 1.3 55.8 + - - +
335A ALA* 3.4 6.3 + - - +
336A LEU* 3.0 22.0 + - - +
358A LEU* 4.7 1.4 - - - +
383A ILE* 3.7 20.6 - - - -
386A LEU* 3.4 22.9 - - - +
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Residues in contact with PHE 333 (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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190A ASP* 3.4 24.7 - - - -
192A ARG* 3.5 33.0 - - + -
195A PHE* 4.1 28.9 - - + -
196A GLY 4.7 1.1 - - - -
197A GLN* 3.6 47.6 - - + +
329A LEU* 2.6 31.7 + - + +
330A HIS 3.7 3.8 - - - +
332A GLY* 1.3 70.7 - - - +
334A GLN* 1.3 66.3 + - - +
336A LEU* 3.2 6.4 + - - +
337A HIS* 3.1 34.4 + + - +
386A LEU* 4.5 12.6 - - + -
425A TYR* 3.9 17.9 - + + -
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Residues in contact with GLN 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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169A LEU* 3.3 30.5 - - - +
310A LEU* 3.2 33.6 - - + +
330A HIS* 3.1 13.3 + - + +
331A ILE* 3.1 9.2 + - - +
333A PHE* 1.3 77.0 - - - +
335A ALA* 1.3 62.9 + - - +
337A HIS* 3.1 12.6 + - - +
338A GLN* 3.0 22.7 + - - +
365A VAL* 3.5 31.1 - - + +
368A ARG* 6.0 2.2 - - - -
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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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331A ILE 3.0 9.1 + - - +
332A GLY* 3.7 7.6 - - - +
334A GLN* 1.3 79.1 - - - +
336A LEU* 1.3 58.8 + - - +
338A GLN* 3.1 6.8 + - - +
339A PHE* 2.8 28.6 + - - +
358A LEU* 3.8 10.5 - - + +
361A LEU* 3.6 17.6 - - + +
362A ALA* 3.6 33.0 - - + +
365A VAL* 4.1 7.4 - - + -
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Residues in contact with LEU 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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192A ARG* 3.4 39.0 - - - +
332A GLY 3.0 15.9 + - - +
333A PHE* 3.5 9.2 - - - +
334A GLN 3.1 0.4 - - - -
335A ALA* 1.3 77.8 - - - +
337A HIS* 1.3 56.8 + - - +
339A PHE* 3.2 1.5 + - + -
340A CYS* 2.9 34.5 + - - -
346A PRO* 5.0 0.2 - - + -
347A PRO* 3.5 33.2 - - + -
358A LEU* 3.7 14.1 - - + +
386A LEU* 3.5 33.7 - - + -
390A ALA* 4.0 10.3 - - + -
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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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167A THR 4.1 4.4 + - - -
168A PRO* 4.8 3.1 - - + -
169A LEU* 3.7 50.8 - - + +
172A GLN* 3.7 26.1 + - - -
190A ASP* 4.3 9.9 + - - -
192A ARG* 4.0 22.0 + - - -
197A GLN* 4.8 10.8 - - - -
333A PHE* 3.1 27.9 + + + -
334A GLN* 3.5 7.3 - - - +
336A LEU* 1.3 71.4 - - - +
338A GLN* 1.3 67.5 + - - +
340A CYS* 4.0 6.6 - - + +
341A ALA* 2.9 26.9 + - - +
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Residues in contact with GLN 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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334A GLN* 3.0 15.8 + - + +
335A ALA* 3.1 9.6 + - - +
337A HIS* 1.3 77.1 - - - +
339A PHE* 1.3 63.0 + - - +
341A ALA* 3.8 4.9 - - - +
342A GLN* 3.0 24.0 + - + +
361A LEU* 3.5 29.9 - - + +
365A VAL* 4.3 11.6 - - - +
368A ARG* 3.9 24.2 + - - +
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Residues in contact with PHE 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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335A ALA 2.8 13.6 + - - +
336A LEU* 3.4 9.0 - - + +
337A HIS 3.2 0.2 - - - -
338A GLN* 1.3 76.3 - - - +
340A CYS* 1.3 58.3 + - - +
342A GLN* 3.0 7.6 + - - +
343A HIS* 2.9 54.9 + + + -
345A ARG* 3.5 23.6 - - - -
346A PRO 3.7 3.6 - - - -
347A PRO* 3.7 24.9 - - + -
354A ASP* 3.6 46.9 - - + -
357A GLU* 3.7 17.5 - - + -
358A LEU* 3.9 15.3 - - + -
361A LEU* 3.7 20.4 - - + +
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Residues in contact with CYS 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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192A ARG* 3.8 25.1 - - - +
336A LEU* 2.9 27.1 + - - +
337A HIS* 4.0 7.4 - - + +
339A PHE* 1.3 75.8 - - - +
341A ALA* 1.3 58.1 + - - +
344A GLY* 2.8 30.8 + - - -
345A ARG* 3.4 11.4 - - - +
346A PRO* 3.7 32.1 - - - -
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Residues in contact with ALA 341 (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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337A HIS 2.9 18.4 + - - +
338A GLN* 3.8 6.3 - - - +
340A CYS* 1.3 77.9 - - - +
342A GLN* 1.3 61.3 + - - +
344A GLY* 4.6 1.0 + - - -
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Residues in contact with GLN 342 (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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338A GLN* 3.0 13.8 + - + +
339A PHE* 3.0 9.3 + - - +
341A ALA* 1.3 80.3 - - - +
343A HIS* 1.3 87.4 + - + +
344A GLY 3.5 0.2 - - - -
357A GLU* 4.6 5.6 - - - +
361A LEU* 6.4 0.4 - - + -
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Residues in contact with HIS 343 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
339A PHE* 2.9 54.6 + + + +
342A GLN* 1.3 91.3 + - + +
344A GLY* 1.3 60.0 + - - +
345A ARG* 3.2 37.5 + - + +
357A GLU* 2.7 40.0 + - - -
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Residues in contact with GLY 344 (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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340A CYS* 2.8 18.1 + - - -
341A ALA 4.5 1.0 + - - -
342A GLN 3.5 1.4 - - - -
343A HIS* 1.3 77.4 - - - +
345A ARG* 1.3 58.5 + - - +
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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
------------------------------------------------------------
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