Contacts of the helix formed by residues 342 - 352 (chain A) in PDB entry 6MOL
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 HIS 342 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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308A GLY* 3.7 26.3 + - - -
310A LEU* 4.0 10.6 - - + +
337A ALA* 3.2 6.8 + - - +
340A ILE* 4.0 17.0 - - + -
341A GLY* 1.3 73.4 - - - +
343A LEU* 1.3 66.7 + - - +
344A GLU* 3.5 26.2 + - + -
345A ILE* 3.1 51.1 + - + +
346A VAL* 3.1 26.0 + - - +
378A ILE* 4.3 0.6 - - - +
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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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341A GLY 3.7 4.9 + - - -
342A HIS* 1.3 73.1 + - - +
344A GLU* 1.3 77.7 + - - +
346A VAL* 3.4 2.6 + - + +
347A GLU* 3.0 35.7 + - + +
377A GLU* 3.9 42.8 - - + +
378A ILE* 4.0 17.4 - - + +
381A VAL* 3.9 18.4 - - + -
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Residues in contact with GLU 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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310A LEU* 3.7 24.0 - - + -
342A HIS* 3.3 20.2 + - + -
343A LEU* 1.3 96.4 + - - +
345A ILE* 1.3 57.0 + - - +
347A GLU* 3.2 13.6 + - - +
348A VAL* 3.0 32.0 + - + +
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Residues in contact with ILE 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 ALA* 3.8 30.1 - - + +
308A GLY* 3.8 23.6 - - - -
310A LEU* 3.7 23.1 - - + -
313A VAL* 4.0 14.1 - - + -
337A ALA* 3.8 19.3 - - + -
342A HIS* 3.1 43.2 + - + +
344A GLU* 1.3 75.7 - - - +
346A VAL* 1.3 57.5 + - - +
348A VAL* 3.1 3.5 + - - +
349A LEU* 2.8 36.0 + - + +
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Residues in contact with VAL 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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334A LEU* 4.2 14.1 - - + -
337A ALA* 3.7 32.8 - - + +
338A ALA* 3.8 10.1 - - + +
342A HIS 3.1 19.2 + - - +
343A LEU* 3.7 4.7 - - + +
344A GLU 3.3 0.2 - - - -
345A ILE* 1.3 77.2 - - - +
347A GLU* 1.3 61.3 + - - +
349A LEU* 4.0 0.9 - - - +
350A LEU* 3.1 43.5 + - + +
378A ILE* 4.0 26.2 - - + -
381A VAL* 4.6 9.4 - - + -
382A LEU* 4.3 4.9 - - + -
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Residues in contact with GLU 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* 3.0 39.2 + - - +
344A GLU* 3.6 15.5 - - - +
346A VAL* 1.3 76.8 - - - +
348A VAL* 1.3 63.2 + - + +
350A LEU* 4.3 1.9 - - - +
351A LYS* 3.2 50.8 + - + +
381A VAL* 4.1 29.4 - - + +
385A TYR* 5.7 2.0 - - + +
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Residues in contact with VAL 348 (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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310A LEU* 4.0 17.7 - - + -
313A VAL* 4.8 5.4 - - + -
314A GLU* 4.1 28.5 - - + +
317A LEU* 3.9 15.0 - - + -
344A GLU* 3.0 20.4 + - + +
345A ILE* 3.1 7.6 + - - +
347A GLU* 1.3 76.8 - - + +
349A LEU* 1.3 64.5 + - - +
351A LYS* 3.4 5.7 + - + -
352A ASN* 2.6 45.3 + - - +
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Residues in contact with LEU 349 (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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301A LEU* 4.3 15.5 - - + -
305A ALA* 4.6 2.0 - - + -
313A VAL* 4.3 7.9 - - + -
317A LEU* 3.8 22.9 - - + -
323A VAL* 3.5 18.8 - - + +
333A PRO* 3.5 38.6 - - + +
334A LEU* 3.7 20.9 - - + +
337A ALA* 3.9 15.3 - - + -
345A ILE* 2.8 23.5 + - + +
346A VAL 4.1 0.2 - - - +
348A VAL* 1.3 76.8 - - - +
350A LEU* 1.3 61.9 + - - +
352A ASN 3.2 7.1 + - - -
353A GLY 3.3 1.6 + - - -
354A ALA* 3.1 25.8 + - + +
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Residues in contact with LEU 350 (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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334A LEU* 3.8 28.7 - - + -
346A VAL* 3.1 24.2 + - + +
347A GLU 4.3 1.3 - - - +
349A LEU* 1.3 77.8 - - - +
351A LYS* 1.3 60.8 + - - +
353A GLY* 3.3 11.8 + - - -
354A ALA* 4.0 17.8 + - - +
356A VAL* 4.2 15.0 - - + -
381A VAL* 3.9 17.0 - - + +
382A LEU* 3.8 22.7 - - + -
385A TYR* 3.7 53.3 - - + -
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Residues in contact with LYS 351 (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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347A GLU* 3.2 39.5 + - - +
348A VAL* 3.9 6.3 - - + +
349A LEU 3.3 0.2 - - - -
350A LEU* 1.3 75.5 - - - +
352A ASN* 1.3 63.4 + - - +
353A GLY 3.3 0.4 + - - -
385A TYR* 3.3 24.9 - - - +
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Residues in contact with ASN 352 (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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317A LEU* 3.8 36.5 - - + +
318A LYS* 5.9 1.4 - - - +
323A VAL* 3.9 14.4 - - + +
348A VAL* 2.6 44.3 + - - +
349A LEU 3.2 4.5 + - - +
350A LEU 3.2 0.4 - - - -
351A LYS* 1.3 81.8 - - - +
353A GLY* 1.3 58.2 + - - +
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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