Contacts of the helix formed by residues 248 - 252 (chain E) 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 LYS 248 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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109E ASP* 5.4 1.2 - - - +
206E GLU* 4.9 9.4 + - - +
246E LYS 4.4 5.6 - - - +
247E VAL* 1.3 76.5 - - - +
249E SER* 1.3 59.7 + - - +
250E LEU* 2.8 13.9 + - - +
251E SER* 4.2 3.8 + - - -
284E PRO* 4.8 10.1 - - - +
285E LYS 5.2 1.4 - - - +
286E THR* 4.9 9.6 + - - -
287E HIS* 3.9 48.7 + - + +
290E LYS* 3.2 28.0 - - - +
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Residues in contact with SER 249 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
109E ASP* 5.2 2.5 - - - -
110E PRO* 3.9 28.9 - - - -
201E PHE* 3.6 27.1 - - - -
206E GLU 5.2 6.7 - - - -
247E VAL* 3.6 4.4 - - - +
248E LYS* 1.3 77.0 - - - +
250E LEU* 1.3 54.1 + - - +
251E SER* 2.7 19.5 + - - -
252E VAL* 3.0 22.8 + - - +
253E TYR* 4.0 4.9 - - - -
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Residues in contact with LEU 250 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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244E LEU 3.6 21.8 - - - +
245E HIS* 3.5 26.5 - - + +
247E VAL 3.6 14.3 + - - +
248E LYS* 2.8 2.2 + - - +
249E SER* 1.3 76.2 + - - +
251E SER* 1.3 64.0 + - - +
252E VAL 2.7 2.9 + - - -
253E TYR* 3.1 33.3 + - + -
254E HIS* 3.1 34.6 + - + +
257E LEU* 4.2 11.4 - - + -
290E LYS* 3.5 32.8 - - + -
293E MSE 4.4 2.7 - - - -
294E PHE* 3.9 11.0 - - + -
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Residues in contact with SER 251 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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109E ASP* 4.0 13.1 + - - -
111E GLU* 3.5 28.6 - - - +
248E LYS 4.2 3.5 + - - -
249E SER* 2.7 11.2 + - - -
250E LEU* 1.3 73.6 - - - +
252E VAL* 1.3 60.7 + - - +
254E HIS 4.2 2.3 + - - -
255E PRO* 4.4 4.9 - - - +
287E HIS* 5.8 6.9 - - - -
289E PRO* 6.4 1.3 - - - -
290E LYS* 5.6 0.6 - - - +
293E MSE 3.6 32.5 - - - +
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Residues in contact with VAL 252 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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110E PRO* 4.2 21.5 - - + +
111E GLU* 3.6 31.4 - - + +
209E ASN 5.8 3.8 - - - +
212E ALA* 4.1 15.3 - - + +
249E SER* 3.2 17.7 - - - +
250E LEU 2.7 5.5 + - - -
251E SER* 1.3 75.7 - - - +
253E TYR* 1.3 61.9 + - + +
254E HIS 3.6 0.4 - - - -
255E PRO* 4.5 1.3 - - - +
256E GLN* 3.9 13.9 + - - -
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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