Contacts of the helix formed by residues 245 - 253 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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239A VAL* 3.8 2.5 - - - -
244A GLU* 1.3 82.7 + - - +
246A PHE* 1.3 67.9 + - - +
247A GLN* 3.4 15.7 + - - +
248A ILE* 3.0 44.6 + - + +
249A MET* 3.0 22.5 + - - +
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Residues in contact with PHE 246 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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104A VAL* 5.5 0.9 - - + -
106A THR* 4.0 3.6 - - + -
182A LEU 5.0 0.4 - - - -
183A ALA 4.8 1.3 - - - -
185A ALA* 3.5 30.7 - - + -
186A GLU* 3.4 31.0 - - + -
235A LEU* 3.9 25.1 - - + -
236A GLY* 4.0 19.3 - - - +
239A VAL* 3.5 35.4 - - + +
240A GLY 5.6 0.2 - - - +
244A GLU 4.3 0.2 + - - -
245A ASP* 1.3 75.5 + - - +
247A GLN* 1.3 65.3 + - + +
249A MET* 3.8 2.9 - - - +
250A ALA* 2.9 41.6 + - + +
320A ILE* 3.4 22.2 - - + -
322A PHE* 4.8 2.2 - + - -
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Residues in contact with GLN 247 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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178A ASN* 5.6 1.4 + - - +
179A PRO* 5.0 2.6 - - - +
180A PRO* 3.8 32.6 - - + +
183A ALA* 3.2 43.0 + - - +
186A GLU* 3.7 20.0 - - + +
245A ASP* 3.2 13.9 + - - +
246A PHE* 1.3 84.6 - - + +
248A ILE* 1.3 64.4 + - + +
250A ALA* 4.1 1.9 + - - -
251A VAL* 4.1 4.2 + - - +
403A NAG 4.0 10.5 - - + +
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Residues in contact with ILE 248 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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244A GLU* 5.0 8.3 - - - +
245A ASP* 3.0 51.5 + - + +
247A GLN* 1.3 76.3 - - + +
249A MET* 1.3 60.1 + - + +
251A VAL* 2.7 31.0 - - - +
281A ARG* 5.8 2.7 - - - +
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Residues in contact with MET 249 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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239A VAL* 3.6 26.2 - - + -
244A GLU* 3.7 15.7 - - + -
245A ASP 3.0 12.2 + - - +
246A PHE* 3.8 4.0 - - - +
248A ILE* 1.3 77.1 - - + +
250A ALA* 1.3 52.3 + - - +
251A VAL* 2.5 18.6 + - - +
252A ARG* 3.0 4.0 + - - +
253A GLY* 2.9 34.0 + - - +
254A GLY* 4.4 3.6 - - - -
256A MET* 4.0 11.0 - - - -
281A ARG* 3.2 53.2 - - - +
320A ILE* 3.9 33.9 - - + -
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Residues in contact with ALA 250 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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106A THR* 3.0 42.1 + - + -
107A ASN* 3.6 9.0 - - - +
180A PRO* 3.6 17.6 - - + +
182A LEU 5.6 0.7 - - - +
183A ALA* 5.9 0.7 - - - -
246A PHE* 2.9 41.1 + - + +
247A GLN* 4.6 0.7 - - - +
248A ILE 3.5 0.2 - - - -
249A MET* 1.3 70.8 - - - +
251A VAL* 1.3 60.0 + - - +
253A GLY 4.2 2.9 + - - +
320A ILE* 4.4 8.0 - - + +
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Residues in contact with VAL 251 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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107A ASN* 2.9 29.8 + - - +
176A PRO* 3.9 11.4 - - + +
177A PRO 3.5 23.1 - - - +
178A ASN* 3.8 27.1 - - + +
180A PRO* 3.9 11.3 - - + +
247A GLN 4.1 4.0 + - - +
248A ILE* 2.7 31.4 - - - +
249A MET 2.5 8.7 + - - -
250A ALA* 1.3 75.0 - - - +
252A ARG* 1.3 74.4 + - + +
318A TYR* 3.8 6.1 - - - +
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Residues in contact with ARG 252 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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175A ASP* 4.3 14.3 + - - +
176A PRO* 3.2 35.4 - - - +
249A MET 3.0 3.1 + - - +
251A VAL* 1.3 88.9 - - + +
253A GLY* 1.3 61.8 + - - +
293A PRO* 4.3 25.0 - - - +
294A GLY* 3.7 2.6 - - - -
295A TYR 3.2 15.9 + - - +
318A TYR* 3.4 28.9 - - + -
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Residues in contact with GLY 253 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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249A MET* 2.9 24.7 + - - +
250A ALA* 4.2 2.5 - - - -
251A VAL 3.6 1.6 - - - +
252A ARG* 1.3 78.9 - - - +
254A GLY* 1.3 57.4 + - - -
281A ARG* 4.5 2.6 + - - -
283A ASP* 4.0 1.2 - - - +
294A GLY* 3.0 16.5 - - - -
295A TYR 3.4 10.8 - - - -
318A TYR* 4.4 0.6 - - - +
319A GLY* 3.1 23.8 - - - -
320A 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