Contacts of the helix formed by residues 249 - 257 (chain C) in PDB entry 2CMH
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 PRO 249 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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202B LEU* 3.7 24.5 - - + -
236B TYR* 3.2 40.8 - - + +
241B ILE* 3.7 8.7 - - + -
175C LEU* 5.2 3.6 - - + -
248C LEU* 1.3 88.1 - - - +
250C LYS* 1.3 67.5 + - - +
251C ASN* 3.6 11.2 - - - +
252C LEU* 3.2 36.6 + - + -
253C GLN* 3.1 17.8 + - - +
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Residues in contact with LYS 250 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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231B LEU 3.7 7.5 + - - -
232B THR* 3.3 23.0 + - - +
234B VAL* 2.7 48.5 + - - +
235B ARG* 3.6 10.8 - - - +
236B TYR 2.9 16.6 + - - +
237B TYR 4.0 7.0 - - - +
238B ASN* 3.6 16.7 + - + +
249C PRO* 1.3 73.2 - - - +
251C ASN* 1.3 65.1 + - - +
253C GLN* 3.2 16.1 + - - +
254C GLU* 3.3 29.3 + - + +
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Residues in contact with ASN 251 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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56B HIS* 5.7 5.8 + - - -
235B ARG* 2.9 46.8 + - - +
236B TYR* 4.6 1.7 - - - +
175C LEU* 5.2 5.9 - - - +
249C PRO* 3.6 19.1 - - - +
250C LYS* 1.3 71.5 - - - +
252C LEU* 1.3 86.7 + - - +
254C GLU* 2.8 34.9 + - - +
255C VAL* 2.9 19.8 + - + +
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Residues in contact with LEU 252 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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202B LEU* 4.5 4.3 - - + -
174C PRO 4.1 22.2 - - - +
175C LEU* 3.9 30.5 - - + -
178C HIS* 4.8 11.0 - - + -
248C LEU* 3.9 19.1 - - + -
249C PRO* 3.2 35.0 - - + +
250C LYS 3.4 0.4 - - - -
251C ASN* 1.3 96.9 + - - +
253C GLN* 1.3 66.7 + - - +
255C VAL* 3.1 11.1 + - + +
256C PHE* 2.9 39.1 + - + -
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Residues in contact with GLN 253 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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238B ASN* 3.4 13.0 + - - +
240B ASP* 3.8 17.0 - - - +
248C LEU* 3.2 38.0 + - + +
249C PRO 3.1 17.3 + - - +
250C LYS* 3.2 10.6 + - - +
252C LEU* 1.3 75.3 - - - +
254C GLU* 1.3 59.8 + - + +
256C PHE* 3.8 1.2 - - - -
257C LYS* 2.8 34.1 + - + +
260C ILE* 5.4 1.4 - - - +
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Residues in contact with GLU 254 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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178A HIS* 3.3 22.3 - - + -
235B ARG* 6.2 0.5 - - - -
250C LYS* 3.5 30.2 + - + +
251C ASN* 2.8 15.5 + - - +
253C GLN* 1.3 79.8 - - + +
255C VAL* 1.3 62.8 + - + +
257C LYS* 3.4 15.0 - - - +
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Residues in contact with VAL 255 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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178A HIS* 3.2 15.9 + - - +
179A VAL* 4.1 1.4 - - - +
182A GLN* 5.7 0.2 - - - +
255A VAL* 4.7 21.1 - - + -
178C HIS* 4.6 21.3 - - + +
182C GLN* 2.8 39.6 + - + +
251C ASN* 2.9 23.8 + - + +
252C LEU* 3.1 17.9 + - + +
254C GLU* 1.3 78.8 - - + +
256C PHE* 1.3 66.5 + - + +
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Residues in contact with PHE 256 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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179A VAL* 4.9 0.2 - - - -
174C PRO* 3.7 35.9 - - + -
178C HIS* 3.4 26.9 - - + -
181C MET* 3.5 22.9 - - + -
182C GLN* 3.4 33.4 - - + -
185C LEU* 4.1 10.5 - - + -
197C PRO* 4.8 2.9 - - + -
248C LEU* 4.5 15.7 - - + -
252C LEU* 2.9 32.8 + - + +
253C GLN 3.8 0.9 - - - +
255C VAL* 1.3 80.2 - - + +
257C LYS* 1.3 66.2 + - - +
258C ASP 3.4 2.2 - - - -
259C ASN* 2.8 16.4 + - - -
260C ILE* 2.9 35.2 + - + +
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Residues in contact with LYS 257 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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178A HIS* 5.1 4.3 - - + -
253C GLN* 2.8 18.3 + - + +
254C GLU* 3.4 17.9 - - - +
255C VAL 3.4 1.0 + - - -
256C PHE* 1.3 77.1 - - - +
258C ASP* 1.3 77.0 + - - +
260C ILE* 3.3 24.1 + - - +
262C SER* 6.3 1.6 - - - -
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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