Contacts of the helix formed by residues 247 - 252 (chain C) in PDB entry 3ECS
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 247 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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238C LEU* 4.0 22.9 - - + -
240C PRO* 6.2 0.7 - - + -
245C ASP 3.3 8.0 - - - +
246C VAL* 1.4 88.9 - - + +
248C ASP* 1.3 67.0 + - - +
249C LYS* 3.9 15.3 - - + +
250C PHE* 2.9 49.9 + - + +
251C LYS* 3.4 8.0 + - - +
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Residues in contact with ASP 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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246C VAL 4.1 6.4 - - - +
247C PRO* 1.3 73.1 - - - +
249C LYS* 1.3 62.6 + - - +
250C PHE 3.0 1.4 + - - -
251C LYS* 3.1 21.2 + - - +
252C TYR* 3.1 41.3 + - + +
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Residues in contact with LYS 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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55C THR* 5.5 10.3 - - - +
58C GLY* 6.3 3.4 - - - -
61C SER* 3.4 27.0 + - - -
66C SER* 4.6 8.5 + - - -
247C PRO* 3.1 12.7 - - + +
248C ASP* 1.3 78.4 - - - +
250C PHE* 1.3 98.6 + - + +
252C TYR 4.2 1.5 - - - +
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Residues in contact with PHE 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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58C GLY* 6.6 0.2 - - - -
61C SER* 3.5 30.9 - - - +
62C SER 4.8 1.8 - - - -
63C VAL* 3.7 39.6 - - + +
66C SER* 4.1 21.5 - - - -
207C ILE* 5.3 1.1 - - + -
236C VAL* 5.4 2.2 - - + -
238C LEU* 3.5 29.4 - - + -
246C VAL* 4.3 9.9 - - + -
247C PRO* 2.9 38.7 + - + +
249C LYS* 1.3 113.3 - - + +
251C LYS* 1.3 59.5 + - - +
252C TYR 3.6 0.7 - - - -
272C TRP* 5.2 1.7 - - - +
273C VAL* 3.8 17.0 - - + +
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Residues in contact with LYS 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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185A TYR* 3.5 28.1 + - - +
243C GLN 3.2 25.3 + - - -
244C GLN* 4.7 3.6 + - - +
246C VAL* 3.4 34.5 + - + -
247C PRO 3.4 1.0 + - - -
248C ASP* 3.1 13.9 + - - +
250C PHE* 1.3 79.8 - - - +
252C TYR* 1.3 96.0 + - + +
270C HIS 3.9 0.5 - - - +
271C PRO* 3.3 16.5 - - + +
272C TRP* 2.8 29.8 + - - +
273C VAL* 3.9 20.2 - - + +
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Residues in contact with TYR 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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185A TYR* 3.8 10.7 + - - -
61C SER* 2.7 20.4 + - - -
248C ASP* 3.1 35.7 + - + +
249C LYS* 4.2 4.7 - - - +
250C PHE 3.6 0.6 - - - -
251C LYS* 1.3 116.0 + - + +
253C LYS* 1.3 68.1 + - + +
269C GLU* 3.9 16.9 + - + +
270C HIS 3.6 37.2 - - - -
271C PRO* 3.9 4.0 - - + +
272C TRP* 4.7 0.7 - - - -
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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