Contacts of the helix formed by residues 362 - 376 (chain A) in PDB entry 1P1K
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 362 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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192A ALA* 3.9 11.2 - - + -
193A ALA 5.4 0.9 - - - +
194A ASN* 5.4 1.6 - - - +
359A ASN 3.5 5.5 + - - +
360A LEU 2.9 12.4 - - - +
361A SER* 1.3 81.7 + - - +
363A PRO* 1.3 69.3 - - + +
364A LYS 3.3 0.9 - - - +
365A GLN* 3.1 31.3 + - - +
366A PHE* 3.1 16.2 + - - +
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Residues in contact with PRO 363 (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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361A SER 3.9 5.1 - - - +
362A ALA* 1.3 85.4 - - + +
364A LYS* 1.3 60.6 + - + +
366A PHE* 4.0 10.7 - - + +
367A ARG* 3.1 26.5 + - - +
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Residues in contact with LYS 364 (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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189A ASP* 4.7 11.1 + - - +
249A ARG* 4.0 40.1 - - + +
250A TYR 4.9 0.7 + - - -
362A ALA* 3.3 1.2 - - - +
363A PRO* 1.3 80.7 - - + +
365A GLN* 1.3 81.2 + - - +
367A ARG* 3.5 15.3 - - - +
368A SER* 3.8 9.4 + - - -
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Residues in contact with GLN 365 (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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189A ASP 5.5 0.3 - - - +
190A PHE 3.7 16.5 - - - +
191A ILE* 3.8 4.1 + - - -
192A ALA* 3.3 22.0 - - - +
247A THR* 3.3 34.4 - - + +
248A GLU 4.7 0.7 - - - -
249A ARG* 3.9 6.9 + - - +
359A ASN* 2.9 46.0 - - - +
360A LEU* 3.9 8.5 - - - +
362A ALA* 3.1 32.3 + - - +
364A LYS* 1.3 87.3 - - - +
366A PHE* 1.3 67.0 + - - +
367A ARG 3.1 2.3 + - - -
368A SER 3.3 9.5 + - - -
369A LYS 3.6 3.5 + - - -
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Residues in contact with PHE 366 (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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360A LEU* 3.3 25.2 + - + +
362A ALA 3.1 9.3 + - - +
363A PRO* 4.1 10.1 - - + +
365A GLN* 1.3 77.5 - - - +
367A ARG* 1.3 53.8 + - - +
369A LYS* 3.2 7.1 + - - +
370A GLU* 2.8 66.2 + - + +
400A ILE* 3.1 28.9 - - + -
401A VAL* 4.4 0.7 - - - -
402A ILE* 3.4 55.6 - - + -
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Residues in contact with ARG 367 (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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250A TYR* 5.9 4.9 - - + -
363A PRO 3.1 19.6 + - - +
364A LYS* 3.5 12.6 - - - +
365A GLN 3.1 0.2 - - - -
366A PHE* 1.3 76.6 - - - +
368A SER* 1.3 66.3 + - - +
370A GLU* 3.0 35.2 + - - +
371A ILE* 3.0 61.6 + - + +
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Residues in contact with SER 368 (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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247A THR* 3.9 3.4 - - - -
248A GLU 3.0 20.4 + - - -
250A TYR* 3.2 39.9 + - - -
297A PRO* 3.5 26.9 - - - +
298A GLN* 4.2 0.2 - - - -
364A LYS 3.8 7.1 + - - -
365A GLN 3.3 7.4 + - - -
367A ARG* 1.3 76.9 - - - +
369A LYS* 1.3 63.3 + - - +
371A ILE* 3.2 13.0 + - - +
372A SER* 3.3 13.2 + - - -
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Residues in contact with LYS 369 (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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297A PRO* 3.7 15.1 - - - +
320A ASP* 2.9 36.4 + - - +
356A ASP* 5.2 1.0 + - - -
360A LEU* 4.0 18.8 - - + -
365A GLN 3.6 5.5 + - - +
366A PHE* 3.3 13.5 - - - +
368A SER* 1.3 79.6 - - - +
370A GLU* 1.3 58.8 + - - +
371A ILE 3.0 0.7 + - - -
372A SER* 3.1 6.9 + - - -
373A LYS* 2.9 46.7 + - + +
402A ILE* 3.3 31.4 - - + -
489A LYS* 4.6 3.2 - - - +
650A NAI 2.7 37.3 + - - -
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Residues in contact with GLU 370 (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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366A PHE* 2.8 54.2 + - + +
367A ARG* 3.0 35.6 + - - +
369A LYS* 1.3 73.1 - - - +
371A ILE* 1.3 57.9 + - - +
373A LYS* 4.3 5.8 - - - +
374A SER* 2.8 35.5 + - - +
399A CYS* 6.0 0.3 - - - -
400A ILE* 4.4 16.3 + - + +
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Residues in contact with ILE 371 (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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250A TYR* 3.5 28.9 - - + +
367A ARG* 3.0 61.4 + - + +
368A SER* 3.4 8.3 - - - +
369A LYS 3.0 0.8 - - - -
370A GLU* 1.3 79.2 - - - +
372A SER* 1.3 61.7 + - - +
374A SER* 4.1 1.1 - - - -
375A SER* 3.4 26.2 + - - -
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Residues in contact with SER 372 (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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250A TYR* 5.7 1.3 - - - -
297A PRO* 3.5 14.2 - - - +
320A ASP* 2.7 31.0 + - - -
368A SER 3.3 2.8 + - - -
369A LYS 3.1 10.7 + - - -
371A ILE* 1.3 78.2 - - - +
373A LYS* 1.3 58.1 + - - +
374A SER 3.1 5.8 + - - -
375A SER* 3.6 11.2 + - - -
376A VAL* 4.1 4.9 + - - +
489A LYS* 3.0 24.5 - - - +
490A ALA* 3.5 29.6 - - - -
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Residues in contact with LYS 373 (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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323A SER* 3.7 8.1 + - - -
325A GLN* 2.8 35.9 - - - +
326A THR* 3.2 21.4 + - - +
329A LYS* 3.9 7.2 + - - +
348A SER* 5.9 1.1 - - - -
350A ASN* 4.4 7.1 - - - +
369A LYS* 2.9 41.9 + - + +
372A SER* 1.3 74.6 + - - +
374A SER* 1.3 56.3 + - - +
376A VAL* 3.7 14.0 - - - +
398A HIS* 3.9 4.7 - - - -
400A ILE* 3.0 39.7 - - + +
402A ILE* 4.0 9.9 - - + -
412A LYS* 4.8 2.0 - - - +
489A LYS* 3.2 26.7 - - + +
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Residues in contact with SER 374 (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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370A GLU* 2.8 27.6 + - - +
371A ILE* 3.8 2.6 + - - -
372A SER 3.1 0.8 - - - -
373A LYS* 1.3 77.7 - - - +
375A SER* 1.3 56.7 + - - +
376A VAL* 2.6 22.1 + - - +
377A ILE* 3.1 19.2 + - - +
378A ASP* 5.3 0.7 - - - -
398A HIS* 3.9 18.4 + - - -
400A ILE* 3.0 20.2 + - - +
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Residues in contact with SER 375 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
371A ILE* 3.4 18.6 + - - -
372A SER* 3.6 10.9 + - - -
374A SER* 1.3 76.6 - - - +
376A VAL* 1.3 53.6 + - - +
377A ILE 2.7 13.6 + - - -
378A ASP* 2.8 38.0 + - - +
379A ASP 4.5 0.5 + - - -
489A LYS 4.6 4.2 + - - -
490A ALA* 4.7 7.3 - - - +
491A PRO* 5.7 0.3 - - - +
499A PRO* 6.4 2.0 - - - -
501A ASN* 3.3 8.9 + - - +
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Residues in contact with VAL 376 (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 LYS* 4.8 7.0 - - - -
326A THR* 3.8 28.0 - - + +
329A LYS* 4.2 10.5 - - + -
330A SER* 4.1 21.6 - - - -
372A SER 4.1 6.9 + - - +
373A LYS 3.7 15.3 - - - +
374A SER 2.6 12.5 + - - +
375A SER* 1.3 75.1 + - - +
377A ILE* 1.3 67.9 + - + +
379A ASP* 3.5 4.6 - - - +
380A ILE* 4.2 5.9 - - - +
489A LYS 4.4 7.4 - - - +
501A ASN* 2.9 40.1 - - + +
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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