Contacts of the helix formed by residues 242 - 249 (chain C) in PDB entry 3Q37
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 GLU 242 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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216C THR* 3.5 11.8 - - - +
217C ALA* 2.6 43.9 + - + +
218C LYS 4.5 0.2 + - - -
237C ALA* 3.7 17.4 - - + +
240C LYS* 3.7 33.9 + - + +
241C PRO* 1.3 79.2 - - + +
243C PHE* 1.3 61.0 + - - +
244C VAL 3.1 0.4 - - - -
245C GLU* 3.1 19.8 + - - +
246C ILE* 3.3 10.3 + - + +
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Residues in contact with PHE 243 (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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9C ALA* 3.7 31.6 - - + -
10C ALA 3.9 2.0 - - - -
11C ALA* 3.7 27.4 - - + -
29C PHE* 3.8 23.8 - + + -
40C CYS* 5.4 0.4 - - + -
41C VAL 4.7 0.4 - - - -
61C PHE* 4.5 11.9 - + - -
234C VAL* 3.9 22.0 - - + -
237C ALA 3.8 8.8 + - - +
238C SER* 3.8 20.9 - - - +
240C LYS 3.0 15.4 + - - +
242C GLU* 1.3 78.5 - - - +
244C VAL* 1.3 56.9 + - - +
246C ILE* 3.1 21.9 + - + +
247C ILE* 2.9 50.5 + - + +
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Residues in contact with VAL 244 (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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28C LEU* 4.1 19.7 - - + -
29C PHE* 4.8 12.3 - - + -
32C THR* 3.7 39.5 - - + +
241C PRO 3.5 13.9 - - - +
242C GLU 3.1 0.4 - - - -
243C PHE* 1.3 77.6 - - - +
245C GLU* 1.3 69.4 + - + +
247C ILE* 3.3 15.3 + - + +
248C GLU* 3.0 39.1 + - + +
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Residues in contact with GLU 245 (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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217C ALA* 4.2 20.6 - - + +
241C PRO 5.3 0.9 - - - +
242C GLU* 3.1 14.9 + - - +
244C VAL* 1.3 85.9 - - + +
246C ILE* 1.3 63.1 + - - +
248C GLU* 3.2 24.3 + - - +
249C ALA* 3.2 12.6 + - - +
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Residues in contact with ILE 246 (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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9C ALA* 5.2 1.8 - - + -
215C VAL* 4.1 7.9 - - + +
216C THR 4.0 15.5 - - - +
217C ALA* 4.0 15.5 - - - +
220C ALA* 4.2 7.9 - - + -
232C PHE* 3.7 34.0 - - + -
234C VAL* 4.1 25.6 - - + -
237C ALA* 3.8 29.8 - - + -
242C GLU* 3.3 13.0 + - + +
243C PHE* 3.1 20.3 + - + +
245C GLU* 1.3 74.9 - - - +
247C ILE* 1.3 65.2 + - - +
249C ALA* 3.1 16.1 + - - +
250C THR* 3.9 1.6 + - - +
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Residues in contact with ILE 247 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9C ALA* 4.3 12.8 - - + -
29C PHE* 5.6 1.3 - - + -
32C THR* 5.8 2.0 - - + -
34C ILE* 4.1 28.9 - - + -
36C HIS* 3.5 5.3 - - + -
38C VAL* 4.3 5.8 - - + -
40C CYS* 3.8 31.6 - - - -
61C PHE* 3.9 12.6 - - + -
243C PHE* 2.9 48.5 + - + +
244C VAL* 3.5 17.5 - - + +
246C ILE* 1.3 76.6 - - - +
248C GLU* 1.3 62.3 + - + +
250C THR* 2.7 26.3 + - - +
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Residues in contact with GLU 248 (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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32C THR* 5.0 3.5 - - - +
33C SER 4.9 8.3 - - - +
34C ILE* 5.8 4.3 - - - +
35C ASN 5.8 1.2 + - - -
36C HIS* 4.5 6.7 - - - -
221C ARG* 4.7 1.4 + - - -
244C VAL* 3.0 31.5 + - + +
245C GLU* 3.6 19.7 - - - +
246C ILE 3.2 0.4 - - - -
247C ILE* 1.3 80.1 - - - +
249C ALA* 1.3 56.4 + - - +
250C THR 3.1 0.9 - - - -
251C LYS* 3.2 60.1 + - + +
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Residues in contact with ALA 249 (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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220C ALA* 3.6 28.3 - - + -
221C ARG* 2.8 47.0 + - + +
224C TYR* 3.4 13.9 - - - +
232C PHE* 4.6 1.3 - - + -
245C GLU 3.2 9.3 + - - +
246C ILE 3.1 12.9 + - - +
247C ILE 3.1 1.6 - - - -
248C GLU* 1.3 77.1 - - - +
250C THR* 1.3 55.7 + - - +
251C LYS 3.2 2.2 - - - -
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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