Contacts of the helix formed by residues 383 - 393 (chain B) in PDB entry 1H3F
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 SER 383 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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376B THR* 3.1 19.2 + - - -
381B THR* 3.3 6.2 + - - -
382B PRO* 1.3 84.6 - - - +
384B ASN* 1.3 62.7 + - - +
385B ALA* 3.6 9.6 + - - +
386B GLU* 3.3 20.3 + - - +
387B ALA 3.4 15.1 + - - -
389B ARG* 4.7 2.4 + - - -
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Residues in contact with ASN 384 (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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370B TRP* 3.7 31.6 - - + -
372B ALA* 3.7 7.0 - - + +
373B ARG* 3.0 40.9 - - - +
376B THR* 3.0 19.6 + - - +
383B SER* 1.3 72.7 - - - +
385B ALA* 1.3 65.9 + - - +
387B ALA* 3.3 3.4 + - - +
388B ARG* 3.1 29.6 + - - +
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Residues in contact with ALA 385 (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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383B SER* 3.2 9.5 + - - +
384B ASN* 1.3 79.6 - - - +
386B GLU* 1.3 62.6 + - - +
388B ARG* 3.2 30.3 + - - +
389B ARG* 3.2 39.6 + - - +
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Residues in contact with GLU 386 (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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381B THR* 4.6 0.9 - - + -
382B PRO* 3.6 32.8 - - + +
383B SER* 3.3 18.5 + - - +
384B ASN 3.3 0.2 - - - -
385B ALA* 1.3 75.8 - - - +
387B ALA* 1.3 67.1 + - - +
389B ARG* 3.0 34.3 + - - +
390B LEU* 2.9 38.3 + - + +
420B ARG* 3.3 22.7 + - - -
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Residues in contact with ALA 387 (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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372B ALA* 3.8 30.7 - - - +
375B PHE* 4.5 5.6 - - + -
381B THR* 3.9 21.9 - - + +
383B SER 3.4 9.5 + - - +
384B ASN 3.3 9.8 + - - +
385B ALA 3.3 0.2 - - - -
386B GLU* 1.3 79.2 - - - +
388B ARG* 1.3 63.7 + - - +
390B LEU* 3.4 2.9 + - - +
391B ILE* 3.1 29.8 + - + +
396B LEU* 3.7 6.5 - - + +
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Residues in contact with ARG 388 (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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370B TRP* 3.3 38.9 - - + -
372B ALA* 4.2 5.4 - - + -
384B ASN* 3.1 19.0 + - - +
385B ALA* 3.4 28.5 - - - +
386B GLU 3.1 0.2 - - - -
387B ALA* 1.3 73.9 - - - +
389B ARG* 1.3 66.2 + - + +
391B ILE* 3.3 7.0 + - - +
392B GLN* 3.1 31.4 + - - +
406B PRO* 4.3 20.6 - - + +
407B MET* 4.0 15.3 - - - +
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Residues in contact with ARG 389 (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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383B SER* 4.7 2.2 + - - -
385B ALA* 3.4 19.7 + - - +
386B GLU* 3.0 56.2 + - - +
388B ARG* 1.3 77.3 - - + +
390B LEU* 1.3 64.4 + - + +
392B GLN* 3.1 21.2 + - - +
393B ASN* 3.1 29.7 + - - +
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Residues in contact with LEU 390 (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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381B THR* 3.8 23.3 - - + -
386B GLU* 2.9 22.4 + - + +
387B ALA* 3.6 6.7 - - - +
389B ARG* 1.3 77.9 - - + +
391B ILE* 1.3 61.3 + - - +
393B ASN* 3.0 9.4 + - + +
394B ARG 3.0 4.2 + - - -
395B GLY* 2.8 35.5 + - - -
396B LEU* 3.8 19.5 - - + -
420B ARG* 3.5 42.8 - - + +
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Residues in contact with ILE 391 (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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371B VAL* 3.7 30.3 - - + -
372B ALA* 5.2 2.5 - - - +
375B PHE* 5.8 0.2 - - + -
387B ALA* 3.1 18.9 + - + +
388B ARG* 3.6 8.5 - - + +
389B ARG 3.3 0.2 - - - -
390B LEU* 1.3 74.8 - - - +
392B GLN* 1.3 64.4 + - - +
394B ARG* 3.0 16.7 + - - +
395B GLY 4.7 1.8 - - - +
396B LEU* 3.8 18.6 - - + -
403B LEU* 3.3 49.9 - - + +
404B THR 3.9 2.0 - - - -
405B ASP 3.8 22.4 - - - +
406B PRO* 3.9 16.2 - - + +
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Residues in contact with GLN 392 (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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388B ARG* 3.1 14.8 + - - +
389B ARG* 3.1 26.2 + - - +
391B ILE* 1.3 76.7 - - - +
393B ASN* 1.3 65.8 + - - +
394B ARG* 3.2 13.5 + - - +
404B THR 6.0 0.9 - - - -
406B PRO* 4.8 22.2 - - + +
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Residues in contact with ASN 393 (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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389B ARG* 3.1 16.8 + - - +
390B LEU* 3.0 12.1 + - + +
392B GLN* 1.3 85.0 + - - +
394B ARG* 1.3 73.6 + - - +
395B GLY* 3.2 3.0 + - - +
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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