Contacts of the helix formed by residues 337 - 343 (chain A) in PDB entry 2Y01
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 ALA 337 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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51A VAL* 5.3 2.2 - - + +
54A LEU* 4.4 28.2 - - + +
55A ILE* 3.7 25.1 - - + +
58A GLY* 6.0 0.2 - - - -
59A ASN* 5.0 0.2 - - - +
334A ALA* 3.1 13.2 + - - +
335A ASN 3.0 0.8 - - - -
336A SER* 1.3 77.9 - - - +
338A MET* 1.3 64.3 + - + +
339A ASN 3.6 0.9 - - - -
340A PRO* 3.7 11.5 - - - +
341A ILE* 3.6 17.6 - - + +
504A 2CV 5.9 2.9 - - - +
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Residues in contact with MET 338 (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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298A VAL* 3.6 27.4 - - + -
302A CYS* 3.7 22.7 - - - -
331A LEU* 4.8 2.5 - - + -
334A ALA* 3.6 28.3 - - + +
335A ASN* 3.0 10.0 + - - +
337A ALA* 1.3 81.3 - - + +
339A ASN* 1.3 67.6 + - - +
341A ILE* 3.1 13.4 + - + +
342A ILE* 3.1 35.6 + - + +
504A 2CV 3.6 38.4 - - - +
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Residues in contact with ASN 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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59A ASN* 5.1 2.5 - - - +
83A LEU* 3.8 23.0 - - - +
87A ASP* 4.0 18.1 + - - +
295A ILE* 3.2 36.7 - - + +
298A VAL* 5.7 0.5 - - - +
335A ASN* 4.0 19.8 + - - +
336A SER 5.8 0.2 - - - +
338A MET* 1.3 77.3 - - - +
340A PRO* 1.4 70.2 - - + +
342A ILE* 3.3 4.9 + - - +
343A TYR* 3.0 52.3 + - + +
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Residues in contact with PRO 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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54A LEU 5.6 0.2 - - - +
58A GLY* 3.3 45.5 - - - +
59A ASN* 3.7 20.6 - - - +
62A VAL* 3.9 16.6 - - + -
336A SER 4.5 1.6 - - - +
337A ALA* 3.7 13.9 - - - +
338A MET 3.6 3.6 - - - -
339A ASN* 1.4 94.3 - - + +
341A ILE* 1.3 63.9 + - + +
343A TYR* 3.4 11.8 + - + +
344A CYS* 3.5 12.8 - - - -
353A PHE* 3.8 9.1 - - + -
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Residues in contact with ILE 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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54A LEU* 5.0 20.2 - - + -
337A ALA* 3.6 20.9 - - + +
338A MET* 3.1 12.0 + - + +
340A PRO* 1.3 78.4 - - + +
342A ILE* 1.3 57.3 + - + +
344A CYS* 2.8 40.7 + - + +
345A ARG 4.4 0.2 + - - -
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Residues in contact with ILE 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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291A THR* 4.0 13.0 - - + +
294A ILE* 3.9 31.9 - - + +
295A ILE* 3.6 32.8 - - + -
298A VAL* 4.2 19.7 - - + -
338A MET* 3.1 26.7 + - + +
339A ASN* 3.6 9.9 - - - +
341A ILE* 1.3 78.2 - - + +
343A TYR* 1.3 60.6 + - - +
344A CYS 3.2 1.6 + - - -
345A ARG* 3.3 29.0 + - - +
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Residues in contact with TYR 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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59A ASN* 6.1 0.2 - - - -
62A VAL* 3.7 30.3 - - + -
80A ILE* 3.3 47.9 + - + +
83A LEU* 4.5 4.7 - - - +
84A ALA* 6.2 0.4 - - + -
291A THR* 4.3 16.4 - - + -
292A LEU* 5.6 2.0 - - + -
295A ILE* 3.7 24.2 - - + +
339A ASN* 3.0 47.1 + - + +
340A PRO* 3.7 6.1 - - + +
341A ILE 3.0 1.2 + - - -
342A ILE* 1.3 72.5 - - - +
344A CYS* 1.3 56.6 + - - +
345A ARG 3.0 6.1 - - - -
346A SER* 3.1 19.8 + - - -
349A PHE* 3.4 44.9 - + + +
353A PHE* 4.7 1.8 - - + -
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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