Contacts of the helix formed by residues 374 - 379 (chain A) in PDB entry 1H41
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 374 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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337A PHE* 5.9 1.6 - - + -
341A TYR* 3.6 28.2 - - + -
363A PRO* 5.4 2.6 - - - +
372A PHE* 3.2 6.4 + - - -
373A SER* 1.3 71.2 - - - +
375A LEU* 1.3 63.6 + - - +
377A ALA* 3.0 14.8 + - - +
378A GLY 3.2 8.5 + - - -
570A GLN* 3.7 25.0 - - + +
571A TYR* 3.9 29.3 + - + -
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Residues in contact with LEU 375 (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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326A ALA* 4.2 21.8 - - + -
340A ALA* 3.7 26.5 - - + -
341A TYR* 3.8 28.1 - - - +
344A PHE* 3.8 16.8 - - + -
345A MET* 4.2 8.7 - - + -
357A LEU* 5.7 1.1 - - + -
359A ILE* 4.0 29.2 - - + -
373A SER* 3.1 2.7 + - - -
374A ALA* 1.3 79.2 - - - +
376A PHE* 1.3 61.7 + - - +
378A GLY 4.4 0.7 - - - +
379A MET* 3.0 56.1 + - + +
384A MET* 3.6 3.4 - - - +
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Residues in contact with PHE 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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359A ILE* 3.5 42.8 - - + -
360A LYS 3.6 17.3 - - - -
361A ASN 4.1 4.0 - - - -
373A SER* 3.0 29.4 + - - +
375A LEU* 1.3 78.1 - - - +
377A ALA* 1.3 57.7 + - - +
384A MET* 3.4 34.6 - - + +
385A MET 4.0 6.3 - - - -
386A MET* 3.6 27.1 - - + -
425A ILE* 3.6 30.7 - - + -
428A ILE* 3.5 15.0 - - + +
429A LEU* 4.0 26.0 - - + -
434A PHE* 3.5 11.3 - - - -
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Residues in contact with ALA 377 (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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372A PHE* 3.9 6.7 - - + -
373A SER 4.3 0.4 + - - -
374A ALA* 3.0 8.2 + - - +
376A PHE* 1.3 78.1 - - - +
378A GLY* 1.3 58.5 + - - +
416A THR* 3.9 15.9 - - - +
418A ALA* 3.6 29.7 - - + +
428A ILE* 4.4 1.1 - - - -
434A PHE* 3.6 9.6 - - - -
570A GLN 6.0 0.2 - - - +
572A PRO* 3.8 34.7 - - + +
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Residues in contact with GLY 378 (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 TYR* 4.5 5.6 - - - -
345A MET* 3.5 32.7 - - - +
348A ASP* 3.9 2.8 - - - +
374A ALA 3.2 8.0 + - - -
375A LEU 3.1 3.9 + - - -
377A ALA* 1.3 81.0 - - - +
379A MET* 1.3 60.2 + - - +
380A SER* 3.2 12.9 + - - -
570A GLN 5.8 0.2 - - - -
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Residues in contact with MET 379 (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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344A PHE* 3.4 26.5 - - + +
345A MET* 3.5 22.2 - - - +
348A ASP* 3.6 17.7 - - - +
351A PHE* 4.4 3.1 - - + -
357A LEU* 3.5 30.1 - - + -
359A ILE* 5.5 0.2 - - + -
375A LEU* 3.0 36.0 + - + +
378A GLY* 1.3 71.8 - - - +
380A SER* 1.3 60.2 + - - +
381A ARG 3.5 2.1 + - - -
382A THR* 3.6 27.1 - - + +
384A MET* 3.2 34.5 - - + +
434A PHE* 3.5 7.7 - - - +
1727A EDO 5.2 0.2 + - - -
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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