Contacts of the helix formed by residues 344 - 356 (chain A) in PDB entry 2A79
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 344 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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341A PRO 4.6 1.5 + - - -
342A LYS 2.7 12.5 + - - -
343A LEU* 1.3 76.4 - - - +
345A SER* 1.3 65.6 + - - +
346A SER* 2.9 25.0 + - - -
347A ILE* 3.1 15.5 + - - +
348A VAL* 3.1 19.8 + - - +
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Residues in contact with SER 345 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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344A SER* 1.3 72.7 - - - +
346A SER* 1.3 59.2 + - - +
348A VAL* 3.4 9.2 + - - +
349A HIS* 2.9 28.4 + - - +
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Residues in contact with SER 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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344A SER* 2.9 14.0 + - - -
345A SER* 1.3 79.3 + - - +
347A ILE* 1.3 70.0 + - - +
349A HIS* 2.9 8.8 + - - +
350A GLU* 2.8 37.7 + - - +
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Residues in contact with ILE 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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295A ILE* 4.1 14.4 - - + -
298A ARG* 4.4 8.1 - - - +
299A LEU* 3.7 42.0 - - + -
342A LYS 3.9 12.3 - - - +
343A LEU* 4.1 11.4 - - + -
344A SER* 3.1 26.1 + - - +
346A SER* 1.3 84.7 + - - +
348A VAL* 1.3 62.3 + - - +
350A GLU* 3.4 16.4 + - - +
351A ILE* 3.1 45.4 + - + +
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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 TRP* 4.8 7.8 + - + +
313A ARG* 4.0 35.9 - - + +
343A LEU* 4.1 20.9 - - + +
344A SER 3.1 15.7 + - - +
345A SER* 3.5 10.3 - - - +
346A SER 3.0 0.6 - - - -
347A ILE* 1.3 75.2 - - + +
349A HIS* 1.3 67.2 + - - +
351A ILE* 3.1 10.5 + - - +
352A ASP* 2.8 35.3 + - - +
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Residues in contact with HIS 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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345A SER 2.9 13.9 + - - +
346A SER* 2.9 10.7 + - - +
348A VAL* 1.3 76.0 - - - +
350A GLU* 1.3 64.2 + - - +
352A ASP* 3.2 13.9 + - + +
353A SER* 3.0 42.8 + - - -
358A LYS* 6.0 4.0 - - - -
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Residues in contact with GLU 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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295A ILE* 3.2 19.8 - - + +
298A ARG* 2.7 46.9 + - - -
346A SER* 2.8 12.7 + - - +
347A ILE* 3.4 19.6 - - - +
349A HIS* 1.3 78.6 + - - +
351A ILE* 1.3 59.0 + - - +
353A SER* 3.1 18.7 + - - -
354A ILE* 2.9 23.5 - - + +
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Residues in contact with ILE 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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219A MET* 3.9 14.4 - - + -
292A LEU* 3.5 20.0 - - + -
295A ILE* 3.8 17.3 - - + -
306A LEU* 4.4 20.9 - - + -
310A TRP* 4.3 24.5 - - + +
343A LEU* 4.9 2.9 - - + -
347A ILE* 3.1 31.6 - - + +
348A VAL* 3.1 8.2 + - - +
350A GLU* 1.3 71.8 - - - +
352A ASP* 1.3 67.1 + - - +
354A ILE* 3.3 8.8 + - - +
355A LEU* 2.9 46.1 + - + +
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Residues in contact with ASP 352 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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222A ARG* 2.7 38.2 + - - +
310A TRP* 6.1 1.3 - - - -
348A VAL* 2.8 31.5 + - - +
349A HIS* 3.2 17.3 + - + +
351A ILE* 1.3 77.3 - - - +
353A SER* 1.3 51.9 + - - +
355A LEU* 3.5 4.2 - - - +
356A GLY* 2.6 35.7 + - - -
357A ASN 4.2 1.6 + - - -
358A LYS* 3.4 33.5 + - + +
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Residues in contact with SER 353 (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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349A HIS* 3.0 32.5 + - - -
350A GLU* 3.1 11.6 - - - -
352A ASP* 1.3 72.9 - - - +
354A ILE* 1.3 68.1 + - - +
356A GLY* 3.1 14.5 + - - -
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Residues in contact with ILE 354 (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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288A LYS* 2.9 68.0 - - + +
291A GLU* 3.8 31.8 - - + +
292A LEU* 3.4 28.7 - - + +
295A ILE* 4.4 10.3 - - + -
350A GLU* 2.9 24.7 - - + +
351A ILE* 3.8 5.4 - - - +
353A SER* 1.3 75.9 - - - +
355A LEU* 1.3 61.8 + - - +
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Residues in contact with LEU 355 (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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219A MET* 3.7 27.6 - - + +
220A PHE* 3.5 33.0 - - + -
222A ARG* 4.2 9.0 - - - +
288A LYS* 3.2 24.5 + - + +
292A LEU* 3.9 19.7 - - + -
310A TRP* 4.8 4.3 - - + -
351A ILE* 2.9 39.7 + - + +
352A ASP 3.7 2.5 - - - +
354A ILE* 1.3 84.0 - - + +
356A GLY* 1.3 63.7 + - - +
357A ASN* 3.1 26.5 + - - +
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Residues in contact with GLY 356 (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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288A LYS* 5.3 0.7 - - - -
352A ASP 2.6 20.1 + - - -
353A SER* 3.1 9.8 + - - -
355A LEU* 1.3 73.0 - - - +
357A ASN* 1.3 54.7 + - - +
358A LYS 3.7 3.1 + - - -
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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