Contacts of the helix formed by residues 338 - 346 (chain A) in PDB entry 2NYM
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 ASN 338 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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296A ALA* 3.5 22.7 - - + +
297A GLU* 5.7 1.0 + - - -
299A ARG* 4.3 6.1 - - - +
300A ALA* 5.2 0.4 - - - +
336A ASP* 2.7 16.4 + - - +
337A ALA* 1.3 69.9 - - - +
339A GLN* 1.3 56.1 + - - +
340A HIS* 3.7 29.0 + - - +
341A VAL* 2.7 58.8 + - + +
342A LYS* 3.3 5.9 + - - +
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Residues in contact with GLN 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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337A ALA 3.5 7.5 + - - +
338A ASN* 1.3 71.1 + - - +
340A HIS* 1.3 71.7 + - + +
341A VAL 2.9 0.7 + - - -
342A LYS* 2.9 17.3 + - - +
343A SER* 2.5 38.4 + - - -
376A GLU* 6.1 0.8 - - - +
377A CYS* 3.8 40.3 - - + +
378A PRO* 5.6 1.4 - - - +
380A VAL* 4.0 0.3 - - - +
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Residues in contact with HIS 340 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
297A GLU* 5.8 5.6 - - - +
300A ALA* 3.7 8.3 - - + +
338A ASN* 3.0 22.4 + - - +
339A GLN* 1.3 92.5 - - + +
341A VAL* 1.3 55.8 + - - +
343A SER* 4.0 7.3 - - - -
344A ALA* 3.1 27.6 + - - +
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Residues in contact with VAL 341 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
296A ALA 3.5 12.1 - - - +
299A ARG* 4.1 11.2 - - + +
300A ALA* 3.3 26.5 - - + +
303A SER* 3.7 18.5 + - - +
333A LEU* 4.4 17.4 - - + +
336A ASP* 4.1 19.5 - - + +
338A ASN* 2.7 40.2 + - + +
340A HIS* 1.3 69.9 - - - +
342A LYS* 1.3 64.9 + - - +
344A ALA* 3.9 0.7 - - - +
345A LEU* 3.1 23.6 + - - +
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Residues in contact with LYS 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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333A LEU 4.1 11.0 - - - +
334A VAL* 3.8 21.5 - - - +
335A SER* 5.1 0.4 - - - -
336A ASP* 3.6 30.2 + - + +
337A ALA* 4.6 5.5 + - - +
338A ASN 3.3 2.6 + - - +
339A GLN* 2.9 25.4 + - - +
341A VAL* 1.3 79.3 - - - +
343A SER* 1.3 58.4 + - - +
345A LEU* 4.1 5.7 - - - +
346A ALA* 2.9 35.3 + - - +
372A GLN* 4.7 0.8 + - + +
375A ASP* 2.9 39.1 + - - +
376A GLU* 4.0 8.7 + - - -
377A CYS* 5.0 2.6 - - - +
380A VAL* 3.6 17.5 - - + -
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Residues in contact with SER 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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339A GLN 2.5 24.9 + - - -
340A HIS* 4.0 6.7 - - - -
342A LYS* 1.3 74.7 - - - +
344A ALA* 1.3 60.4 + - - +
347A SER 3.8 1.7 + - - -
377A CYS* 4.6 0.9 - - - -
379A GLU* 2.8 31.7 - - - +
380A VAL* 3.1 20.2 + - - +
383A ASN* 2.8 35.2 + - - +
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Residues in contact with ALA 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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300A ALA* 4.2 16.8 - - + +
303A SER* 4.4 0.9 - - - -
304A HIS* 3.7 38.7 - - + +
340A HIS 3.1 20.8 + - - +
341A VAL 3.9 3.4 - - - +
342A LYS 3.2 0.4 - - - -
343A SER* 1.3 74.1 - - - +
345A LEU* 1.3 66.9 + - - +
347A SER* 2.6 25.6 + - - -
348A VAL* 3.9 6.1 + - - +
383A ASN* 4.9 0.7 - - - +
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Residues in contact with LEU 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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303A SER* 3.7 24.8 - - - +
306A VAL* 5.2 8.3 - - + -
330A ILE* 4.1 25.4 - - + +
333A LEU* 3.7 35.7 - - + -
334A VAL* 4.5 13.7 - - - -
341A VAL 3.1 13.7 + - - +
342A LYS* 4.1 5.4 - - - +
344A ALA* 1.3 79.1 - - - +
346A ALA* 1.3 57.3 + - - +
347A SER 3.1 0.3 + - - -
348A VAL* 3.2 4.1 + - + +
349A ILE* 2.8 40.5 + - + +
372A GLN* 3.0 32.3 - - - +
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Residues in contact with ALA 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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342A LYS 2.9 20.1 + - - +
343A SER 4.2 4.0 - - - +
344A ALA 3.1 0.2 - - - -
345A LEU* 1.3 76.3 - - - +
347A SER* 1.3 58.3 + - - +
348A VAL 3.4 0.6 + - - -
349A ILE* 4.0 6.5 - - - +
350A MSE 5.3 0.5 - - - +
372A GLN* 3.3 29.4 - - + +
380A VAL* 3.5 28.5 - - + +
383A ASN* 3.3 13.4 - - + +
384A ILE* 3.6 15.5 - - + +
387A ASN* 5.1 0.9 + - - -
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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