Contacts of the helix formed by residues 115 - 120 (chain D) in PDB entry 3L73
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 TYR 115 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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64C PHE* 4.8 11.7 - + - -
68C ALA* 3.3 25.5 + - + +
71C CYS* 5.1 3.9 - - + +
72C ARG* 2.8 42.4 + - - +
257C PHE* 3.6 43.5 - + + +
2011C GOL 3.8 15.6 + - - -
45D TYR* 3.9 21.8 - + - -
112D ASP* 4.5 2.0 + - - -
114D SER* 1.3 84.2 - - - +
116D ILE* 1.3 64.8 + - - +
117D VAL 3.4 2.2 - - - -
118D ASN* 3.1 7.0 + - - -
119D ALA* 3.0 20.5 + - - +
194D ALA* 3.7 22.4 - - - -
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Residues in contact with ILE 116 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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111D PRO* 4.7 9.2 - - + -
112D ASP 4.6 5.5 + - - +
113D LEU* 3.4 33.1 + - + +
114D SER 3.6 0.2 - - - -
115D TYR* 1.3 76.3 - - - +
117D VAL* 1.3 72.6 + - + +
119D ALA* 2.8 21.7 + - + +
120D ARG* 3.3 51.4 + - + +
127D VAL* 4.6 4.7 - - + -
190D LEU* 3.5 34.5 - - + +
194D ALA* 5.2 0.2 - - - +
501D HEC 3.9 25.4 - - + -
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Residues in contact with VAL 117 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116D ILE* 1.3 85.3 - - + +
118D ASN* 1.3 60.6 + - - +
119D ALA 3.5 0.2 - - - -
120D ARG* 3.7 4.5 - - - +
123D GLY* 3.2 25.1 - - - -
124D GLU* 3.9 25.4 - - - +
127D VAL* 4.4 6.3 - - + -
187D CYS* 4.6 2.2 - - - +
190D LEU* 3.7 35.4 - - + +
191D ARG* 3.4 38.0 + - - +
194D ALA* 3.5 24.9 - - + -
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Residues in contact with ASN 118 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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249C ASN* 4.2 16.1 + - - +
254C PRO* 3.1 27.4 - - - +
257C PHE* 3.5 42.0 - - + -
115D TYR* 3.1 4.8 + - - +
116D ILE 2.9 1.2 - - - -
117D VAL* 1.3 82.6 - - - +
119D ALA* 1.3 58.0 + - - +
120D ARG 3.2 5.6 - - - -
191D ARG* 3.2 31.6 + - - +
194D ALA* 3.9 19.6 + - - +
195D GLU* 4.0 8.5 + - - +
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Residues in contact with ALA 119 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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254C PRO* 3.5 20.6 - - - +
255C GLU* 4.9 3.3 + - - +
257C PHE* 3.9 14.8 - - + +
258C THR* 4.0 13.4 + - - +
115D TYR 3.0 14.7 + - - +
116D ILE* 2.8 10.9 + - + +
118D ASN* 1.3 80.9 - - - +
120D ARG* 1.3 83.3 + - - +
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Residues in contact with ARG 120 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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254C PRO* 4.5 5.6 - - - +
258C THR* 4.6 6.5 + - - -
111D PRO* 4.4 12.7 - - - +
116D ILE* 3.3 33.6 + - + +
117D VAL* 3.7 8.8 - - - +
118D ASN* 3.2 1.9 - - - -
119D ALA* 1.3 109.1 + - - +
121D HIS* 1.3 64.6 + - - +
122D GLY 3.3 0.3 + - - -
123D GLY* 3.2 14.3 + - - +
126D TYR* 4.0 29.8 - - + -
127D VAL* 5.7 1.1 - - + -
501D HEC 3.0 48.1 + - + +
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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