Contacts of the helix formed by residues 245 - 253 (chain C) in PDB entry 3I5D
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 ASP 245 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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186C GLU* 5.3 3.1 - - - +
239C VAL* 3.7 3.4 - - - -
244C GLU* 1.3 82.6 + - - +
246C PHE* 1.3 69.0 + - - +
247C GLN* 3.4 15.6 + - - +
248C ILE* 3.0 47.1 + - + +
249C MET* 3.0 22.6 + - - +
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Residues in contact with PHE 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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104C VAL* 5.5 0.9 - - + -
106C THR* 4.0 4.3 - - + -
182C LEU 5.0 0.4 - - - -
183C ALA* 4.7 1.3 - - - -
185C ALA* 3.5 30.7 - - + -
186C GLU* 3.5 42.8 - - + +
235C LEU* 3.8 25.6 - - + -
236C GLY* 4.0 15.0 + - - +
239C VAL* 3.4 35.2 - - + +
245C ASP* 1.3 74.6 + - - +
247C GLN* 1.3 64.6 + - - +
249C MET* 3.8 3.1 - - - +
250C ALA* 2.8 51.6 + - + +
320C ILE* 3.4 22.4 - - + -
322C PHE* 4.8 1.1 - + - -
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Residues in contact with GLN 247 (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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178C ASN* 5.6 1.6 + - - +
179C PRO* 5.0 2.9 - - - +
180C PRO* 3.8 33.5 - - + +
183C ALA* 3.2 44.2 + - - +
186C GLU* 3.3 34.5 + - - +
245C ASP* 3.2 13.6 + - - +
246C PHE* 1.3 83.0 - - - +
248C ILE* 1.3 65.0 + - + +
250C ALA* 4.0 1.6 + - - -
251C VAL* 4.1 4.3 + - - +
403C NAG 4.3 6.1 - - - +
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Residues in contact with ILE 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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244C GLU* 5.0 8.1 - - - +
245C ASP* 3.0 51.3 + - + +
247C GLN* 1.3 76.3 - - + +
249C MET* 1.3 61.2 + - + +
251C VAL* 2.6 31.9 - - - +
252C ARG* 5.5 0.2 - - - +
281C ARG* 5.8 2.9 - - - +
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Residues in contact with MET 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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239C VAL* 3.6 26.5 - - + -
244C GLU* 3.7 15.5 - - + +
245C ASP 3.0 13.4 + - - +
246C PHE* 3.8 4.5 - - - +
248C ILE* 1.3 76.5 - - + +
250C ALA* 1.3 53.5 + - - +
251C VAL 2.6 18.0 + - - -
252C ARG* 3.0 4.9 + - - +
253C GLY* 2.9 34.0 + - - +
254C GLY* 4.4 3.6 - - - -
256C MET* 4.0 11.2 - - - -
281C ARG* 3.2 52.0 - - - +
320C ILE* 3.9 33.4 - - + -
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Residues in contact with ALA 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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106C THR* 3.1 41.0 + - + -
107C ASN* 3.5 10.4 - - - +
180C PRO* 3.5 17.1 - - + +
182C LEU 5.5 0.9 - - - +
183C ALA* 5.9 0.4 - - - -
246C PHE* 2.8 41.1 + - + +
247C GLN* 4.7 1.3 - - - +
248C ILE 3.5 0.4 - - - -
249C MET* 1.3 70.8 - - - +
251C VAL* 1.3 59.6 + - - +
252C ARG 3.6 0.2 - - - -
253C GLY 4.2 2.2 + - - +
320C ILE* 4.5 7.4 - - + +
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Residues in contact with VAL 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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107C ASN* 2.9 28.4 + - - +
176C PRO* 3.9 13.2 - - + +
177C PRO 3.4 23.6 - - - +
178C ASN* 3.8 27.1 - - + +
180C PRO* 3.9 10.6 - - + +
247C GLN 4.1 4.0 + - - +
248C ILE* 2.6 31.8 + - - +
249C MET 2.6 7.9 + - - -
250C ALA* 1.3 75.4 - - - +
252C ARG* 1.3 69.1 + - + +
318C TYR* 3.8 7.3 - - - +
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Residues in contact with ARG 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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176C PRO* 5.3 4.0 - - + -
248C ILE 5.5 0.4 - - - +
249C MET 3.0 3.4 + - - +
251C VAL* 1.3 84.8 - - + +
253C GLY* 1.3 62.1 + - - +
293C PRO* 4.2 6.3 - - + +
294C GLY* 3.6 6.8 - - - +
295C TYR 3.1 20.8 + - - +
318C TYR* 3.6 22.6 - - + -
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Residues in contact with GLY 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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249C MET* 2.9 23.7 + - - +
250C ALA* 4.2 2.8 - - - -
251C VAL 3.6 2.0 - - - +
252C ARG* 1.3 81.3 - - - +
254C GLY* 1.3 57.0 + - - -
281C ARG* 4.4 3.1 + - - -
283C ASP* 4.0 1.0 - - - +
294C GLY* 3.0 16.8 - - - -
295C TYR 3.4 9.2 - - - -
318C TYR* 4.4 0.6 - - - +
319C GLY* 3.1 24.2 - - - -
320C ILE* 5.1 0.2 - - - -
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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