Contacts of the helix formed by residues 348 - 358 (chain B) in PDB entry 1HKB
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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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341B ALA 4.2 3.1 - - - -
342B ILE* 3.8 12.8 - - - +
344B LYS 3.1 24.1 + - - -
345B ASN 4.6 0.9 - - - -
346B LYS 2.9 14.5 + - - -
347B GLU* 1.3 76.4 - - - +
349B LEU* 1.3 62.1 + - - +
351B ASN* 3.1 9.5 + - - +
352B ALA* 3.1 8.8 + - - +
372B GLN* 3.8 12.8 - - - -
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Residues in contact with LEU 349 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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348B GLY* 1.3 71.0 - - - +
350B HIS* 1.3 67.2 + - - +
352B ALA* 3.1 9.0 + - - +
353B LYS* 3.0 22.5 + - - +
368B CYS* 3.2 34.8 - - + +
369B VAL* 3.5 31.4 - - + -
372B GLN* 3.5 26.8 - - - +
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Residues in contact with HIS 350 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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347B GLU* 4.1 30.7 - - + -
348B GLY 3.2 0.8 - - - -
349B LEU* 1.3 78.3 - - - +
351B ASN* 1.3 66.9 + - - +
353B LYS* 3.3 22.5 - - + +
354B GLU* 3.2 38.2 + - + +
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Residues in contact with ASN 351 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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341B ALA* 3.3 38.4 + - - +
344B LYS* 4.3 7.3 - - - +
347B GLU* 3.1 44.6 + - - +
348B GLY 3.1 5.0 + - - +
350B HIS* 1.3 82.2 - - - +
352B ALA* 1.3 67.2 + - - +
353B LYS 3.0 2.0 + - - -
354B GLU* 3.0 14.3 + - - +
355B ILE* 3.0 32.5 + - + +
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Residues in contact with ALA 352 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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342B ILE* 3.5 36.0 - - + +
348B GLY 3.1 3.7 + - - +
349B LEU* 3.1 15.8 + - - +
351B ASN* 1.3 77.0 - - - +
353B LYS* 1.3 58.4 + - - +
355B ILE* 3.4 0.7 + - - +
356B LEU* 2.9 38.8 + - + +
368B CYS* 3.8 27.8 - - + +
371B VAL* 5.1 0.9 - - + -
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Residues in contact with LYS 353 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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349B LEU 3.0 8.3 + - - +
350B HIS* 3.3 18.6 - - + +
351B ASN 3.0 0.2 + - - -
352B ALA* 1.3 77.4 - - - +
354B GLU* 1.3 62.2 + - + +
355B ILE 3.1 0.2 + - - -
357B THR* 2.7 39.1 + - - +
363B PRO* 3.7 14.2 + - + +
365B ASP* 2.8 37.7 + - - +
368B CYS* 3.3 24.0 - - - -
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Residues in contact with GLU 354 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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350B HIS* 3.2 43.9 + - + +
351B ASN* 3.0 14.8 + - - +
353B LYS* 1.3 78.6 - - + +
355B ILE* 1.3 60.4 + - + +
357B THR* 3.5 6.8 - - - -
358B ARG* 3.0 49.2 + - - +
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Residues in contact with ILE 355 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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334B PHE* 3.9 22.7 - - + -
338B ASP* 3.9 38.8 - - + +
341B ALA* 4.7 7.0 - - + -
342B ILE* 3.5 26.9 - - + -
351B ASN* 3.0 28.7 + - + +
352B ALA* 3.7 5.6 - - - +
354B GLU* 1.3 74.1 - - + +
356B LEU* 1.3 63.9 + - + +
357B THR 3.0 5.3 + - - -
358B ARG* 3.2 17.0 + - - +
359B LEU* 3.2 15.7 + - + +
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Residues in contact with LEU 356 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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310B LEU* 4.4 8.1 - - + -
320B PHE* 3.4 33.0 - - + -
334B PHE* 5.3 2.9 - - + -
342B ILE* 5.3 0.7 - - + -
352B ALA* 2.9 26.0 + - + +
355B ILE* 1.3 74.6 - - + +
357B THR* 1.3 59.6 + - - +
359B LEU* 3.3 27.9 + - + +
361B VAL* 3.1 19.4 + - + +
363B PRO* 3.4 16.4 - - + -
367B ASP* 4.4 3.8 - - + -
368B CYS* 3.8 35.9 - - - +
371B VAL* 3.5 28.7 - - + -
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Residues in contact with THR 357 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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353B LYS* 2.7 31.0 + - - +
354B GLU* 3.5 9.1 - - - +
355B ILE 3.0 0.2 - - - -
356B LEU* 1.3 75.0 - - - +
358B ARG* 1.3 60.4 + - + +
359B LEU 2.9 4.5 - - - -
360B GLY* 2.9 24.8 + - - +
361B VAL 3.8 0.6 - - - +
363B PRO* 2.9 25.0 - - + +
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Residues in contact with ARG 358 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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327B GLU* 4.8 9.2 - - - +
354B GLU* 3.0 33.7 + - - +
355B ILE* 3.2 8.4 + - - +
357B THR* 1.3 75.1 - - + +
359B LEU* 1.3 58.9 + - + +
360B GLY* 2.9 11.7 + - - -
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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