Contacts of the helix formed by residues 245 - 253 (chain B) 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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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186B GLU* 5.3 2.9 - - - +
239B VAL* 3.8 3.1 - - - -
244B GLU* 1.3 82.0 + - - +
246B PHE* 1.3 70.1 + - - +
247B GLN* 3.5 15.4 + - - +
248B ILE* 3.0 44.6 + - + +
249B MET* 3.0 22.2 + - - +
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Residues in contact with PHE 246 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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104B VAL* 5.5 0.7 - - + -
106B THR* 4.0 3.8 - - + -
182B LEU 5.0 0.4 - - - -
183B ALA 4.8 1.1 - - - -
185B ALA* 3.5 31.0 - - + -
186B GLU* 3.5 42.6 - - + +
235B LEU* 3.9 24.7 - - + -
236B GLY* 4.0 15.5 - - - +
239B VAL* 3.5 34.8 - - + +
244B GLU 4.3 0.2 + - - -
245B ASP* 1.3 74.7 + - - +
247B GLN* 1.3 65.0 + - - +
249B MET* 3.8 2.6 - - - +
250B ALA* 2.8 51.7 + - + +
320B ILE* 3.4 22.7 - - + -
322B PHE* 4.8 2.2 - + - -
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Residues in contact with GLN 247 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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178B ASN* 5.6 1.4 + - - +
179B PRO* 5.0 2.9 - - - +
180B PRO* 3.8 33.1 - - + +
183B ALA* 3.2 42.9 + - - +
186B GLU* 3.3 34.0 + - - +
245B ASP* 3.2 13.2 + - - +
246B PHE* 1.3 85.5 - - - +
248B ILE* 1.3 61.7 + - + +
250B ALA* 4.0 2.0 + - - -
251B VAL* 4.1 4.7 + - - +
403B NAG 4.4 4.7 - - - +
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Residues in contact with ILE 248 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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244B GLU* 5.0 8.5 - - - +
245B ASP* 3.0 49.7 + - + +
247B GLN* 1.3 75.5 - - + +
249B MET* 1.3 60.5 + - + +
251B VAL* 2.7 30.8 - - - +
281B ARG* 5.8 2.9 - - - +
285B LYS* 6.4 1.6 - - + -
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Residues in contact with MET 249 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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239B VAL* 3.6 28.0 - - + -
244B GLU* 3.7 14.6 - - + -
245B ASP 3.0 13.1 + - - +
246B PHE* 3.8 4.3 - - - +
248B ILE* 1.3 75.5 - - + +
250B ALA* 1.3 53.4 + - - +
251B VAL 2.6 18.2 + - - -
252B ARG* 3.0 4.0 + - - +
253B GLY* 2.9 33.5 + - - +
254B GLY* 4.4 4.0 - - - +
256B MET* 4.0 10.3 - - - -
281B ARG* 3.2 52.7 - - - +
320B ILE* 4.0 33.7 - - + -
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Residues in contact with ALA 250 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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106B THR* 3.1 40.9 + - + -
107B ASN* 3.4 10.4 - - - +
180B PRO* 3.6 16.8 - - + +
182B LEU 5.6 0.4 - - - +
183B ALA* 5.9 0.7 - - - -
246B PHE* 2.8 41.6 + - + +
247B GLN* 4.0 1.1 + - - +
248B ILE 3.5 0.4 - - - -
249B MET* 1.3 71.0 - - - +
251B VAL* 1.3 60.4 + - - +
252B ARG 3.6 0.2 - - - -
253B GLY 4.2 2.4 + - - +
320B ILE* 4.5 7.4 - - + +
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Residues in contact with VAL 251 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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107B ASN* 2.9 29.1 + - - +
176B PRO* 3.9 12.1 - - + +
177B PRO 3.5 22.9 - - - +
178B ASN* 3.8 27.4 - - + +
180B PRO* 4.0 11.3 - - + +
247B GLN 4.1 4.0 + - - +
248B ILE* 2.7 31.4 - - - +
249B MET 2.6 8.1 + - - -
250B ALA* 1.3 76.1 - - - +
252B ARG* 1.3 68.6 + - + +
318B TYR* 3.8 6.6 - - - +
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Residues in contact with ARG 252 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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175B ASP* 4.1 10.3 - - - +
176B PRO* 3.2 35.9 - - - +
249B MET 3.0 3.5 + - - +
251B VAL* 1.3 87.9 - - + +
253B GLY* 1.3 61.2 + - - +
293B PRO* 4.3 25.6 - - - +
294B GLY* 3.7 2.6 - - - -
295B TYR 3.2 15.8 + - - +
318B TYR* 3.4 29.4 - - + -
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Residues in contact with GLY 253 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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249B MET* 2.9 23.8 + - - +
250B ALA* 4.2 2.2 - - - -
251B VAL 3.6 1.6 - - - +
252B ARG* 1.3 77.6 - - - +
254B GLY* 1.3 58.5 + - - -
281B ARG* 4.4 2.8 + - - -
283B ASP* 4.0 1.4 - - - +
294B GLY* 3.0 15.9 - - - -
295B TYR 3.4 11.2 - - - -
318B TYR* 4.4 0.4 - - - +
319B GLY* 3.1 24.2 - - - -
320B 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