Contacts of the helix formed by residues 238 - 243 (chain A) in PDB entry 5B76
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 HIS 238 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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209A CYS* 3.4 19.2 - - + +
212A CYS* 3.3 9.4 - - - -
214A GLY 3.9 3.4 - - - -
215A THR 2.7 25.6 + - - -
218A GLN 3.3 19.4 + - - -
219A ASN* 3.6 17.4 - - + -
225A GLU* 3.3 38.3 + - + +
227A LEU* 3.5 9.5 - - + +
237A GLY* 1.3 73.0 - - - -
239A PRO* 1.3 70.7 - - - +
240A SER* 3.6 8.1 - - - +
241A CYS* 2.9 4.6 + - - +
242A LEU* 2.8 20.7 + - - +
403A ZN 2.1 38.1 - - - -
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Residues in contact with PRO 239 (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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225A GLU* 3.2 16.6 - - + +
226A GLU 3.1 23.3 - - - +
228A ILE* 3.7 13.0 - - + -
237A GLY 3.6 5.1 - - - +
238A HIS* 1.3 82.4 - - - +
240A SER* 1.3 54.6 + - - +
242A LEU* 3.2 11.0 + - + -
243A LYS 2.9 23.4 + - - -
244A PHE* 3.0 18.3 + - + +
249A THR* 3.4 41.5 - - + +
253A LYS* 4.8 3.6 - - - +
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Residues in contact with SER 240 (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 ASN* 4.0 11.3 + - - +
220A ARG* 5.2 1.9 + - - +
221A GLU* 6.0 2.2 - - - -
225A GLU* 2.7 33.0 + - - -
238A HIS* 3.6 4.9 - - - +
239A PRO* 1.3 75.3 - - - +
241A CYS* 1.3 65.4 + - - +
243A LYS* 3.4 22.2 + - - +
244A PHE 5.3 2.2 - - - -
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Residues in contact with CYS 241 (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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209A CYS* 3.8 3.6 - - - -
211A PHE* 3.9 22.2 - - + -
212A CYS* 3.9 7.0 - - - -
220A ARG* 3.8 37.2 + - - +
238A HIS* 2.9 11.5 + - - +
240A SER* 1.3 84.9 + - - +
242A LEU* 1.3 61.8 + - - +
243A LYS* 3.2 12.2 + - - +
403A ZN 2.3 38.1 - - - -
11B THR* 3.4 17.8 - - - +
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Residues in contact with LEU 242 (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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211A PHE* 3.6 31.6 - - + -
228A ILE* 4.4 9.2 - - + -
237A GLY* 3.8 18.6 - - - +
238A HIS 2.8 20.2 + - - +
239A PRO* 3.7 5.8 - - + +
241A CYS* 1.3 75.4 - - - +
243A LYS* 1.3 70.9 + - - +
244A PHE* 3.4 43.5 - - + -
257A TRP* 4.2 19.3 - - + -
260A ILE* 5.6 7.0 - - + -
11B THR* 4.1 16.1 + - + -
14B KCR 4.1 13.0 - - + +
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Residues in contact with LYS 243 (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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220A ARG* 4.9 8.5 - - - +
239A PRO 2.9 5.1 + - - -
240A SER* 3.4 16.6 + - - +
241A CYS* 3.2 11.7 - - - +
242A LEU* 1.3 82.1 - - - +
244A PHE* 1.3 62.9 + - - +
245A SER 3.9 1.2 + - - -
10B SER* 3.5 13.8 + - - +
11B THR* 3.3 34.3 + - - +
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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