Contacts of the helix formed by residues 348 - 359 (chain A) in PDB entry 1HKC
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 348 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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341A ALA 3.8 3.8 - - - -
342A ILE* 3.0 34.2 - - - +
344A LYS 3.2 18.7 + - - -
345A ASN 4.5 0.4 + - - -
346A LYS 3.4 4.2 + - - -
347A GLU* 1.3 77.5 - - - +
349A LEU* 1.3 57.5 + - - +
351A ASN* 3.2 3.3 + - - +
352A ALA* 3.0 24.3 + - - +
372A GLN* 4.0 4.0 - - - -
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Residues in contact with LEU 349 (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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346A LYS 5.1 0.8 + - - -
347A GLU 3.5 0.2 - - - -
348A GLY* 1.3 72.2 - - - +
350A HIS* 1.3 63.2 + - - +
352A ALA* 3.5 5.9 - - + +
353A LYS* 3.2 21.0 + - - +
368A CYS* 3.6 36.7 - - + +
369A VAL* 3.7 26.7 - - + +
372A GLN* 3.6 30.2 - - + +
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Residues in contact with HIS 350 (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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347A GLU* 3.4 18.7 + - + +
348A GLY 3.2 0.6 - - - -
349A LEU* 1.3 76.2 - - - +
351A ASN* 1.3 79.9 + - - +
353A LYS* 3.4 7.9 + - - +
354A GLU* 3.1 54.5 + - + +
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Residues in contact with ASN 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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341A ALA* 2.6 43.2 + - - +
344A LYS* 4.2 4.8 - - - +
347A GLU* 2.9 47.1 + - - +
348A GLY 3.4 4.5 - - - +
350A HIS* 1.3 87.4 - - - +
352A ALA* 1.3 59.2 + - - +
354A GLU* 3.3 8.3 + - - +
355A ILE* 2.8 43.1 + - + +
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Residues in contact with ALA 352 (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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342A ILE* 3.8 30.7 - - + +
348A GLY 3.0 13.1 + - - +
349A LEU* 3.5 15.0 - - + +
351A ASN* 1.3 75.6 - - - +
353A LYS* 1.3 64.2 + - - +
355A ILE* 3.1 2.1 + - - +
356A LEU* 2.8 34.0 + - + +
368A CYS* 4.1 22.9 - - + +
371A VAL* 5.1 0.9 - - + -
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Residues in contact with LYS 353 (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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349A LEU 3.2 8.6 + - - +
350A HIS* 3.4 11.6 + - - +
352A ALA* 1.3 77.4 - - - +
354A GLU* 1.3 63.2 + - + +
357A THR* 2.6 41.3 + - - +
363A PRO* 3.4 31.3 + - + +
364A SER* 4.8 0.4 - - - +
365A ASP* 3.5 23.1 + - - +
368A CYS* 3.7 25.4 - - - -
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Residues in contact with GLU 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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350A HIS* 3.1 46.4 + - + +
351A ASN* 3.6 11.0 - - - +
352A ALA 3.2 0.2 - - - -
353A LYS* 1.3 79.7 - - + +
355A ILE* 1.3 64.5 + - + +
357A THR* 3.5 4.9 - - - -
358A ARG* 2.8 59.0 + - - +
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Residues in contact with ILE 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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333A LYS 6.1 0.4 - - - +
334A PHE* 3.8 30.5 - - + -
338A ASP* 3.8 34.5 - - + +
341A ALA* 4.2 13.5 - - + -
342A ILE* 3.6 24.2 - - + -
351A ASN* 2.8 29.4 + - + +
352A ALA* 3.6 2.9 - - - +
354A GLU* 1.3 73.0 - - + +
356A LEU* 1.3 66.5 + - + +
358A ARG* 2.9 33.4 + - - +
359A LEU* 3.2 13.5 + - + +
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Residues in contact with LEU 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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310A LEU* 4.3 10.8 - - + -
320A PHE* 4.1 24.7 - - + -
334A PHE* 4.4 13.7 - - + -
342A ILE* 5.6 0.2 - - + -
352A ALA* 2.8 27.4 + - - +
355A ILE* 1.3 75.8 - - + +
357A THR* 1.3 54.2 + - - +
359A LEU* 2.8 41.8 + - + +
361A VAL* 3.6 16.4 + - + +
363A PRO* 3.9 28.0 - - + -
367A ASP 4.7 0.7 - - - +
368A CYS* 4.6 9.6 - - - -
371A VAL* 3.7 36.6 - - + -
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Residues in contact with THR 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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353A LYS* 2.6 32.0 + - - +
354A GLU* 3.5 6.1 - - - +
356A LEU* 1.3 75.3 - - - +
358A ARG* 1.3 60.0 + - + +
360A GLY* 2.9 20.6 + - - -
361A VAL 3.5 13.9 - - - +
362A GLU* 4.9 10.9 + - - +
363A PRO* 3.4 17.3 - - - +
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Residues in contact with ARG 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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327A GLU* 5.0 6.1 - - - +
338A ASP* 5.7 0.8 + - - -
354A GLU* 2.8 58.4 + - - +
355A ILE* 2.9 32.6 + - - +
357A THR* 1.3 77.6 - - + +
359A LEU* 1.3 58.5 + - + +
360A GLY 3.1 4.4 + - - -
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Residues in contact with LEU 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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307A ARG* 5.9 1.1 - - + -
325A THR* 2.9 23.0 + - - -
327A GLU* 3.4 27.4 - - + +
328A LEU* 3.8 28.5 - - + +
333A LYS* 4.1 34.1 - - + +
334A PHE* 4.1 25.8 - - + -
355A ILE* 3.2 13.9 + - + +
356A LEU* 2.8 24.3 + - + +
358A ARG* 1.3 81.3 - - + +
360A GLY* 1.3 54.9 + - - +
361A VAL* 3.1 11.3 + - + +
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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