Contacts of the helix formed by residues 248 - 254 (chain A) in PDB entry 2H31
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 248 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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211A ASN* 3.7 0.9 - - - +
246A LYS 3.5 3.3 + - - +
247A LYS* 1.3 73.4 - - - +
249A PHE* 1.3 63.7 - - + +
250A GLU* 2.6 58.2 + - - +
251A TRP* 2.8 29.1 + - - +
252A VAL* 3.2 8.4 + - - -
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Residues in contact with PHE 249 (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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53A LYS* 3.4 53.2 - - + +
56A ILE* 3.6 25.7 - - + +
60A ILE* 4.9 0.3 - - - +
211A ASN* 3.0 36.5 - - + +
248A ASN* 1.3 75.2 - - + +
250A GLU* 1.3 83.6 + - + +
252A VAL* 4.1 2.8 - - - +
253A ALA* 3.1 28.9 + - - +
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Residues in contact with GLU 250 (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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56A ILE* 5.5 3.4 - - + -
248A ASN* 2.6 25.0 + - - +
249A PHE* 1.3 99.9 - - + +
251A TRP* 1.3 63.8 + - - +
253A ALA* 3.2 19.1 - - - +
254A GLU* 3.4 20.2 + - - +
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Residues in contact with TRP 251 (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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180A TRP* 4.9 4.0 - + - -
183A GLN* 3.8 10.8 - - + -
184A ASN 5.2 0.2 - - - -
185A CYS* 3.3 35.4 - - - -
216A LEU* 5.6 0.7 - - + -
247A LYS* 3.4 46.2 - - + -
248A ASN* 2.8 24.7 + - - +
250A GLU* 1.3 72.5 - - - +
252A VAL* 1.3 71.7 + - + +
253A ALA 3.3 0.2 + - - -
254A GLU* 3.4 9.7 + - + +
255A ARG* 3.1 75.6 - - + +
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Residues in contact with VAL 252 (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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60A ILE* 3.9 14.6 - - + -
180A TRP* 4.2 6.7 - - + -
211A ASN* 3.4 26.5 - - + +
214A TRP* 3.8 28.9 - - + -
216A LEU* 4.4 8.5 - - + -
247A LYS* 3.5 27.4 - - + +
248A ASN 3.2 9.1 + - - +
249A PHE* 4.1 5.8 - - - +
251A TRP* 1.3 80.7 - - + +
253A ALA* 1.3 65.0 + - - +
255A ARG* 3.1 14.7 + - - +
256A VAL* 3.2 17.2 + - + +
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Residues in contact with ALA 253 (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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56A ILE* 3.5 33.4 - - + -
59A LYS* 2.9 27.9 - - + -
60A ILE* 3.3 13.2 - - + +
249A PHE 3.1 18.7 + - - +
250A GLU* 3.2 9.0 - - - +
252A VAL* 1.3 79.2 - - - +
254A GLU* 1.3 60.8 + - + +
255A ARG 3.1 0.3 + - - -
256A VAL* 3.0 13.5 - - - +
257A GLU* 4.8 0.3 + - - +
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Residues in contact with GLU 254 (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 LYS* 4.7 7.0 - - - +
250A GLU* 3.4 17.2 + - - +
251A TRP* 3.4 7.1 + - + +
252A VAL 3.3 1.0 + - - -
253A ALA* 1.3 78.0 - - + +
255A ARG* 1.3 68.8 + - + +
257A GLU* 5.4 4.5 - - - -
258A LEU* 4.8 5.6 - - - +
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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