Contacts of the helix formed by residues 338 - 347 (chain A) in PDB entry 4B18
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 338 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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299A ARG* 5.4 1.4 + - - -
302A VAL* 4.2 2.8 - - - +
335A LEU 2.8 12.6 + - - -
336A ASN 3.3 5.3 + - - -
337A CYS* 1.4 82.1 + - - +
339A ALA* 1.3 66.4 + - - +
340A LEU 3.3 3.1 + - - +
341A GLN* 3.5 32.9 + - - +
342A SER* 4.1 2.9 + - - -
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Residues in contact with ALA 339 (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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302A VAL* 3.4 26.9 - - + -
305A LEU* 4.8 4.0 - - + -
320A VAL* 4.9 0.9 - - + -
334A ILE* 3.7 33.9 + - + +
335A LEU* 4.1 4.2 + - + -
337A CYS 3.3 1.4 - - - -
338A SER* 1.3 76.3 - - - +
340A LEU* 1.3 67.3 + - + +
342A SER* 2.8 16.0 + - - -
343A LEU* 2.9 25.7 + - + +
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Residues in contact with LEU 340 (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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335A LEU* 4.2 17.0 - - + -
338A SER* 3.3 2.7 - - - +
339A ALA* 1.3 77.0 - - - +
341A GLN* 1.3 57.8 + - - +
343A LEU* 3.6 10.5 - - + -
344A LEU* 2.8 32.6 + - - +
362A ILE* 4.7 4.9 - - + -
365A ILE* 3.9 26.2 - - + -
375A THR* 3.2 47.3 - - - +
376A VAL* 3.9 21.3 - - + +
379A ALA* 3.8 15.9 - - + -
381A ILE* 3.7 14.8 - - + +
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Residues in contact with GLN 341 (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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306A MET* 4.3 3.0 - - + +
338A SER* 3.5 29.7 + - - +
339A ALA 3.0 1.0 - - - -
340A LEU* 1.3 80.7 - - - +
342A SER* 1.3 64.5 + - - +
344A LEU* 3.6 10.3 - - - +
345A HIS* 3.3 18.9 + - - +
379A ALA* 4.8 7.3 - - + +
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Residues in contact with SER 342 (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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302A VAL* 4.2 8.9 + - - +
305A LEU* 4.1 21.3 - - - -
306A MET* 2.5 38.4 - - - +
338A SER 4.1 2.5 + - - -
339A ALA* 2.8 13.4 + - - -
341A GLN* 1.3 82.6 + - - +
343A LEU* 1.3 60.2 + - - -
345A HIS* 3.3 3.8 + - - +
346A LEU* 2.9 33.6 + - - +
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Residues in contact with LEU 343 (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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305A LEU* 4.2 14.6 - - + -
317A LEU* 3.9 28.0 - - + -
320A VAL* 5.3 2.5 - - + -
339A ALA* 2.9 23.9 + - + +
340A LEU* 3.7 18.4 - - + +
342A SER* 1.3 72.2 - - - +
344A LEU* 1.3 67.1 + - - +
346A LEU* 2.9 17.5 + - + +
347A LEU* 2.9 17.3 + - - +
358A ALA* 4.3 10.8 - - + +
361A THR* 4.0 28.9 - - + -
362A ILE* 4.3 18.4 - - + -
365A ILE* 4.0 19.7 - - + -
381A ILE* 4.5 0.4 - - + -
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Residues in contact with LEU 344 (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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340A LEU 2.8 19.8 + - - +
341A GLN* 3.6 10.1 - - - +
343A LEU* 1.3 71.6 - - - +
345A HIS* 1.3 63.9 - - - +
347A LEU* 3.2 15.7 + - + +
348A SER* 4.0 5.0 + - - -
379A ALA 3.7 19.1 - - - +
380A ASN* 4.2 16.8 - - + +
381A ILE* 3.6 19.5 - - + +
384A ALA* 3.9 27.1 - - + -
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Residues in contact with HIS 345 (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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305A LEU 5.0 0.7 - - - -
306A MET* 3.4 37.9 + - + -
341A GLN 3.3 7.1 + - - +
342A SER 3.3 8.0 + - - +
343A LEU 3.2 0.4 - - - -
344A LEU* 1.3 80.3 - - - +
346A LEU* 1.3 78.9 + - + +
348A SER* 3.0 24.2 + - - -
349A SER 4.1 1.0 + - - -
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Residues in contact with LEU 346 (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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305A LEU* 3.7 46.4 - - + +
310A TYR* 6.2 1.3 - - + -
313A VAL* 4.1 18.8 - - + -
317A LEU* 4.3 18.8 - - + -
342A SER 2.9 16.9 + - - +
343A LEU* 2.9 11.4 + - + +
345A HIS* 1.3 89.0 - - + +
347A LEU* 1.3 53.4 + - - +
348A SER 3.0 0.2 - - - -
349A SER* 2.8 36.6 + - - +
354A ILE* 4.1 16.1 - - + +
355A LYS* 4.0 7.6 - - - +
358A ALA* 4.1 12.3 - - + -
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Residues in contact with LEU 347 (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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343A LEU 2.9 15.2 + - - +
344A LEU* 3.3 16.8 - - + +
345A HIS 3.1 0.6 + - - -
346A LEU* 1.3 75.2 - - - +
348A SER* 1.3 55.4 - - - +
349A SER 3.4 0.4 - - - -
355A LYS* 3.5 29.8 - - - +
358A ALA* 4.2 8.7 - - + -
359A CYS* 3.6 33.4 - - - +
362A ILE* 4.0 22.2 - - + -
381A ILE* 4.2 10.1 - - + +
384A ALA* 3.5 33.3 - - + +
385A LEU* 4.3 8.1 - - + +
388A ILE* 3.7 17.3 - - + +
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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