Contacts of the helix formed by residues 377 - 386 (chain A) in PDB entry 1B3U
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 PRO 377 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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338A GLN* 5.6 0.7 - - - +
375A GLU 3.2 10.5 - - - +
376A CYS* 1.3 86.5 - - + +
378A GLU* 1.3 57.6 + - - +
380A ARG* 3.6 28.1 + - - +
381A LEU* 3.0 32.3 + - - +
421A ALA* 6.0 2.7 - - + -
425A TYR* 4.4 1.1 + - - +
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Residues in contact with GLU 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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339A HIS* 5.9 3.1 - - - -
342A SER* 3.5 26.3 + - - +
376A CYS* 3.2 14.8 - - - -
377A PRO* 1.3 79.6 - - - +
379A VAL* 1.3 62.3 + - - +
381A LEU* 3.5 10.1 + - + +
382A ASN* 3.1 40.8 + - - +
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Residues in contact with VAL 379 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
338A GLN 4.4 1.3 - - - +
341A LYS* 3.8 22.4 - - + -
342A SER* 3.7 19.7 - - - +
345A ALA* 3.6 9.9 - - + +
371A GLN* 3.5 44.2 - - + +
374A ASP* 3.7 16.6 - - + +
376A CYS* 3.0 27.7 + - + +
378A GLU* 1.3 79.8 - - - +
380A ARG* 1.3 63.3 + - - +
382A ASN* 3.2 10.7 + - - +
383A ILE* 3.3 9.7 + - - +
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Residues in contact with ARG 380 (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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371A GLN 4.0 9.4 - - - +
372A LEU* 3.5 26.3 + - + +
374A ASP 3.3 23.5 + - - +
375A GLU* 3.5 18.4 + - - +
376A CYS 3.3 5.1 + - - +
377A PRO* 3.7 25.4 - - - +
379A VAL* 1.3 79.6 - - - +
381A LEU* 1.3 63.6 + - - +
383A ILE* 3.2 6.7 + - - +
384A ILE* 3.0 26.3 + - - +
410A LEU* 4.2 17.5 - - - +
418A VAL* 4.6 27.9 - - - +
421A ALA* 4.1 17.6 - - - +
422A ILE* 4.6 1.1 - - - +
425A TYR* 2.7 45.1 + - + +
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Residues in contact with LEU 381 (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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377A PRO 3.0 19.7 + - - +
378A GLU* 3.8 10.8 - - + +
379A VAL 3.3 0.2 - - - -
380A ARG* 1.3 78.8 - - - +
382A ASN* 1.3 63.3 + - - +
384A ILE* 3.3 3.4 + - + +
385A SER* 2.9 48.2 + - - +
425A TYR* 4.1 24.7 - - + +
428A LEU* 4.2 14.6 - - + -
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Residues in contact with ASN 382 (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 SER* 3.1 34.4 + - - +
345A ALA* 3.7 19.9 - - + +
346A SER* 3.8 14.0 - - - +
378A GLU* 3.1 30.5 + - - +
379A VAL 3.2 7.8 + - - +
381A LEU* 1.3 82.9 - - - +
383A ILE* 1.3 61.9 + - - +
385A SER* 3.6 6.1 + - - -
386A ASN* 2.9 29.2 + - - +
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Residues in contact with ILE 383 (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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345A ALA* 3.9 14.1 - - + +
348A ILE* 4.2 10.1 - - + -
349A MET* 5.1 5.6 - - + +
368A PHE* 3.3 43.9 - - + +
371A GLN* 3.6 42.2 - - + +
372A LEU* 4.1 24.2 - - + +
379A VAL 3.3 12.3 + - - +
380A ARG 3.2 8.4 + - - +
382A ASN* 1.3 77.5 - - - +
384A ILE* 1.3 64.5 + - - +
386A ASN* 3.0 16.7 + - - +
387A LEU* 3.6 10.0 - - + +
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Residues in contact with ILE 384 (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 LEU* 3.8 20.6 - - + -
380A ARG 3.0 16.5 + - - +
381A LEU* 3.7 9.4 - - - +
383A ILE* 1.3 78.1 - - - +
385A SER* 1.3 57.5 + - - +
386A ASN 3.1 3.5 + - - -
387A LEU* 3.2 18.1 - - + +
403A LEU* 4.8 9.9 - - + -
407A ILE* 5.2 6.3 - - + -
425A TYR* 3.7 52.5 - - + +
428A LEU* 4.3 19.7 - - + -
429A LEU* 4.5 20.6 - - + -
432A GLN* 2.9 19.6 - - - +
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Residues in contact with SER 385 (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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381A LEU* 2.9 34.5 + - - +
382A ASN* 4.0 7.2 - - - -
383A ILE 3.2 0.4 - - - -
384A ILE* 1.3 75.0 - - - +
386A ASN* 1.3 68.1 + - - +
388A ASP* 4.4 2.8 - - - +
428A LEU* 3.7 16.0 - - - +
432A GLN* 3.3 16.1 + - - -
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Residues in contact with ASN 386 (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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345A ALA 4.5 2.0 + - - +
346A SER* 3.8 26.7 + - - +
349A MET* 4.1 23.9 - - + +
382A ASN* 2.9 25.8 + - - +
383A ILE* 3.0 10.2 + - - +
385A SER* 1.3 89.8 + - - +
387A LEU* 1.3 62.1 + - - +
388A ASP* 3.3 7.2 + - - +
389A CYS* 4.3 6.6 + - + +
390A VAL* 4.3 2.3 - - - +
432A GLN* 3.7 1.3 - - - +
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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