Contacts of the helix formed by residues 327 - 345 (chain A) in PDB entry 6PI7
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 327 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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326A VAL* 1.4 79.7 - - - +
328A SER* 1.3 64.4 + - - -
329A ARG 3.2 2.7 - - - -
330A SER* 2.8 20.7 + - - -
331A LEU* 3.1 20.1 + - - +
58C TYR* 5.1 5.2 - - - -
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Residues in contact with SER 328 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
327A GLY* 1.3 70.8 - - - -
329A ARG* 1.3 65.5 + - - +
331A LEU* 3.3 13.8 + - - +
332A GLN* 2.9 48.2 + - - +
602A UNX 3.5 21.4 - - - -
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Residues in contact with ARG 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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325A ILE* 3.6 25.8 - - + +
326A VAL 5.9 0.2 - - - +
327A GLY 3.2 0.6 - - - -
328A SER* 1.3 80.2 + - - +
330A SER* 1.3 58.5 + - - +
332A GLN* 2.7 34.8 + - - +
333A LEU* 2.9 28.9 + - - +
412A LEU* 3.6 11.3 - - - +
413A PRO* 3.9 29.6 - - - +
415A GLN* 3.3 31.7 + - - +
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Residues in contact with SER 330 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
311A TYR* 4.3 6.5 - - - -
324A GLN* 6.3 2.5 - - - -
325A ILE 3.2 4.5 + - - -
326A VAL* 3.0 13.0 - - - -
327A GLY 2.8 27.0 + - - -
329A ARG* 1.3 76.3 - - - +
331A LEU* 1.3 57.5 + - - +
333A LEU* 3.5 3.0 + - - +
334A ASP* 3.1 35.4 + - - +
415A GLN* 5.3 1.1 - - - +
58C TYR* 3.4 23.5 + - - -
104C TYR* 4.5 0.2 - - - -
105C ARG* 3.3 16.3 + - - +
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Residues in contact with LEU 331 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
327A GLY 3.1 16.4 + - - +
328A SER* 3.6 14.1 - - - +
330A SER* 1.3 73.2 - - - +
332A GLN* 1.3 66.1 + - + +
334A ASP* 3.5 10.9 + - + +
335A LYS* 3.2 22.2 + - - +
58C TYR* 3.3 43.5 - - + +
60C SER* 5.8 3.6 - - - +
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Residues in contact with GLN 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 SER* 2.9 37.8 + - - +
329A ARG* 2.7 38.1 + - - +
331A LEU* 1.3 77.6 - - + +
333A LEU* 1.4 54.8 + - - +
335A LYS* 3.5 9.5 + - - +
336A LEU* 3.0 26.2 + - - +
412A LEU* 3.1 19.7 - - + +
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Residues in contact with LEU 333 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
324A GLN* 3.6 29.4 - - + +
329A ARG 2.9 17.1 + - - +
330A SER* 3.7 7.4 - - - +
331A LEU 3.3 0.2 - - - -
332A GLN* 1.4 72.6 - - - +
334A ASP* 1.3 61.0 + - - +
336A LEU* 3.1 7.7 + - + +
337A VAL* 2.9 41.5 + - + +
390A ASP* 3.7 33.2 - - + +
391A PHE* 4.2 12.1 - - + -
412A LEU* 3.7 13.9 - - + +
415A GLN* 4.0 20.4 - - + +
105C ARG* 3.9 15.3 - - - +
107C TRP* 5.3 0.4 - - + -
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Residues in contact with ASP 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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330A SER 3.1 14.0 + - - +
331A LEU* 3.6 11.4 - - + +
333A LEU* 1.3 77.1 - - - +
335A LYS* 1.3 58.9 + - - +
337A VAL* 3.5 1.6 + - - +
338A ASN* 2.5 36.6 + - - +
36C TYR* 5.5 0.3 + - - -
58C TYR* 4.4 2.9 - - - -
104C TYR* 2.4 36.9 + - - -
105C ARG* 2.7 35.5 + - - -
107C TRP* 3.3 17.9 - - + +
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Residues in contact with LYS 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 LEU 3.2 12.0 + - - +
332A GLN* 3.5 12.3 - - - +
334A ASP* 1.3 78.4 - - - +
336A LEU* 1.3 52.5 + - - +
338A ASN* 3.4 5.0 + - - +
339A GLU* 2.7 69.8 + - + +
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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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332A GLN 3.0 14.8 + - - +
333A LEU* 3.1 13.2 + - + +
335A LYS* 1.3 72.8 - - - +
337A VAL* 1.3 60.7 + - + +
339A GLU* 3.6 9.4 - - - +
340A MET* 2.9 46.7 + - - +
372A ARG* 3.5 43.1 - - + +
390A ASP* 4.1 6.5 - - - +
409A PHE* 3.7 40.6 - - + +
412A LEU* 4.0 18.6 - - + -
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Residues in contact with VAL 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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333A LEU* 2.9 33.0 + - + +
334A ASP 3.9 4.3 - - - +
336A LEU* 1.3 74.9 - - + +
338A ASN* 1.3 55.5 + - - +
340A MET* 5.5 0.7 - - - -
341A THR* 2.7 35.5 + - - -
369A SER* 3.9 21.8 - - - +
370A TRP 3.7 11.8 - - - +
371A TYR* 3.9 21.3 - - + -
391A PHE* 4.2 1.6 - - + -
107C TRP* 3.5 49.6 - - + -
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Residues in contact with ASN 338 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
334A ASP* 2.5 30.9 + - - +
335A LYS* 3.8 4.7 - - + +
336A LEU 3.2 0.4 - - - -
337A VAL* 1.3 73.9 - - - +
339A GLU* 1.3 64.3 + - - +
341A THR* 3.4 7.3 + - - -
342A GLN* 3.1 24.8 + - - +
369A SER* 5.7 0.5 + - - -
93B PHE* 3.8 34.3 - - + +
107C TRP* 3.4 35.6 - - - +
112C TYR* 5.0 1.7 + - - -
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Residues in contact with GLU 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 LYS* 2.7 64.4 + - + +
336A LEU* 3.6 11.6 - - - +
338A ASN* 1.3 68.6 - - - +
340A MET* 1.3 60.3 + - - +
342A GLN* 3.2 15.9 + - - +
343A HIS* 3.0 29.6 + - - +
406A ARG* 4.6 6.8 + - - -
408A ASP* 5.3 0.7 - - - +
409A PHE* 3.9 24.4 - - + -
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Residues in contact with MET 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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336A LEU* 2.9 37.0 + - - +
337A VAL* 3.8 3.6 - - - +
339A GLU* 1.3 71.4 - - - +
341A THR* 1.3 56.8 + - - +
343A HIS* 3.3 1.4 + - - +
344A TYR* 2.9 39.7 + - + +
361A ALA* 4.0 10.5 - - + -
370A TRP* 3.9 13.5 - - + +
371A TYR 3.5 37.9 - - - +
372A ARG* 3.7 21.8 - - - +
405A LEU* 3.7 23.8 - - + -
409A PHE* 3.8 33.0 - - + -
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Residues in contact with THR 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 VAL 2.7 23.1 + - - -
338A ASN* 3.5 9.6 - - - -
340A MET* 1.3 76.7 - - - +
342A GLN* 1.3 55.3 + - - +
345A GLU* 2.8 50.7 + - + +
368A GLY 4.0 18.6 - - - +
369A SER* 3.3 14.1 + - - +
370A TRP* 3.1 25.1 + - + +
31B SER* 4.0 16.6 - - - -
93B PHE* 4.4 7.9 - - + -
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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 ASN 3.1 14.0 + - - +
339A GLU* 3.2 18.1 + - - +
341A THR* 1.3 76.0 - - - +
343A HIS* 1.3 62.1 + - - +
345A GLU* 3.8 17.8 - - - +
346A ASN 5.3 0.2 + - - -
29B SER* 5.6 2.4 + - - -
93B PHE* 4.4 18.4 - - + -
94B TRP* 4.1 25.5 - - - -
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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
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339A GLU 3.0 15.5 + - - +
340A MET 3.7 2.7 - - - +
342A GLN* 1.3 79.8 - - - +
344A TYR* 1.3 110.9 + + - +
345A GLU 3.8 0.2 + - - -
346A ASN 4.6 1.4 + - - -
347A SER* 4.1 13.1 + - - -
404A ALA 5.4 0.2 - - - -
406A ARG* 3.5 41.3 - - + +
409A PHE* 3.9 11.1 - + + -
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Residues in contact with TYR 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 MET* 2.9 32.0 + - + +
343A HIS* 1.3 106.0 - + - +
345A GLU* 1.3 66.6 - - - +
346A ASN 3.3 2.9 - - - -
347A SER* 2.7 27.8 + - - +
350A GLU* 5.7 0.9 - - - -
361A ALA* 3.5 21.3 - - + -
370A TRP* 3.4 37.1 - + + -
403A ARG* 3.7 23.3 - - + -
404A ALA 2.8 27.6 + - - -
405A LEU* 3.3 3.1 - - - -
406A ARG 2.9 19.8 + - - -
409A PHE* 3.6 20.2 - + - -
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Residues in contact with GLU 345 (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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341A THR* 2.8 34.8 + - + +
342A GLN* 3.8 15.0 - - - +
343A HIS 3.5 0.4 - - - -
344A TYR* 1.3 75.2 - - - +
346A ASN* 1.3 67.3 + - - +
347A SER 3.9 0.7 + - - +
368A GLY 5.5 2.2 - - - +
370A TRP* 3.8 14.2 + - - +
29B SER* 2.4 38.3 + - - +
30B VAL 5.0 0.2 - - - -
31B SER* 3.4 31.1 + - - -
67B ARG* 3.6 21.8 + - - +
93B PHE* 4.7 4.2 - - - -
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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