Contacts of the helix formed by residues 139 - 147 (chain D) in PDB entry 4OBZ
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 139 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37C SER* 2.6 22.2 + - - -
138D ALA* 1.3 74.2 - - - +
140D PRO* 1.4 71.9 - - + +
141D ARG 3.1 3.8 + - - +
142D ILE* 3.4 6.8 + - - +
200D VAL* 4.0 5.9 - - + +
203D LYS* 3.4 44.8 - - + +
204D ALA* 2.9 16.6 + - - +
205D TYR 3.6 26.0 - - - -
206D TRP* 3.4 38.6 - + - -
335D ARG* 3.4 35.0 - - - +
338D ASN* 2.7 35.2 + - - +
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Residues in contact with PRO 140 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
139D TYR* 1.4 87.4 - - + +
141D ARG* 1.4 61.2 + - - +
142D ILE 3.4 0.2 - - - -
143D SER* 3.3 17.5 + - - -
146D ASN* 3.6 18.7 - - - +
147D VAL 5.2 1.6 - - - +
148D LEU* 4.8 9.2 - - + -
149D PRO* 4.0 21.1 - - + -
152D ASP* 3.3 35.0 - - + +
335D ARG* 3.9 7.9 - - - +
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Residues in contact with ARG 141 (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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139D TYR* 3.1 1.4 + - - +
140D PRO* 1.4 78.8 - - - +
142D ILE* 1.4 59.4 + - + +
143D SER 3.3 5.8 + - - +
146D ASN* 4.3 9.3 - - - +
202D ARG* 3.6 29.6 - - - +
203D LYS* 3.6 34.8 + - - +
204D ALA* 4.2 15.3 - - + -
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Residues in contact with ILE 142 (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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35C GLY 3.6 24.5 - - - +
36C SER* 3.9 6.5 - - - -
37C SER* 3.4 16.6 + - - +
38C ASN* 3.8 5.5 - - - +
138D ALA* 3.6 17.9 - - + -
139D TYR 3.4 1.0 + - - +
141D ARG* 1.4 77.6 - - + +
143D SER* 1.3 58.5 + - - +
144D VAL* 3.8 5.4 + - - +
204D ALA* 3.4 39.5 - - + +
205D TYR* 3.6 29.4 - - + +
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Residues in contact with SER 143 (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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37C SER* 3.6 19.3 + - - -
38C ASN* 3.5 14.5 + - - -
140D PRO* 3.3 17.9 - - - -
141D ARG 3.3 5.2 - - - +
142D ILE* 1.3 75.7 - - - +
144D VAL* 1.3 63.4 + - - +
145D ASN 3.5 0.3 + - - -
146D ASN* 3.2 16.1 + - - +
147D VAL* 2.6 37.5 + - - +
149D PRO* 4.5 0.2 - - - -
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Residues in contact with VAL 144 (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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38C ASN* 2.8 38.5 + - - +
74C PHE* 4.3 7.2 - - + -
75C ASP 3.5 35.7 - - - +
76C ILE* 4.2 20.6 - - + -
77C HIS 5.5 0.7 - - - +
87C LEU* 5.5 1.0 - - - +
142D ILE 3.8 4.5 + - - +
143D SER* 1.3 69.6 - - - +
145D ASN* 1.3 82.4 + - - +
146D ASN 3.4 0.7 + - - -
147D VAL* 3.4 9.9 - - - +
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Residues in contact with ASN 145 (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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72C THR* 4.0 14.5 - - + +
73C SER 3.6 23.5 + - - +
74C PHE* 3.8 7.9 - - - +
75C ASP 4.8 0.2 + - - -
87C LEU* 4.5 10.7 - - + +
143D SER 3.5 0.8 + - - -
144D VAL* 1.3 90.8 - - - +
146D ASN* 1.3 65.6 + - - +
147D VAL* 3.1 13.5 + - + +
1E NAG 5.5 0.9 - - - +
2E NAG 3.1 30.5 + - + +
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Residues in contact with ASN 146 (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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140D PRO* 3.6 21.7 + - - +
141D ARG* 4.3 7.6 - - - +
143D SER* 3.2 16.8 + - - +
145D ASN* 1.3 76.5 - - - +
147D VAL* 1.3 63.1 + - - +
148D LEU* 3.6 1.9 + - - -
2E NAG 3.9 33.3 + - + +
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Residues in contact with VAL 147 (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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37C SER 4.6 1.1 - - - +
38C ASN* 4.5 7.0 - - - +
39C LEU 6.2 1.6 - - - +
87C LEU* 4.0 31.2 - - + -
113D GLN* 4.6 0.7 - - - +
114D VAL* 3.4 43.3 - - + +
115D PHE* 5.3 1.3 - - - -
140D PRO* 5.0 1.1 - - - +
143D SER* 2.6 34.0 + - - +
144D VAL 3.4 16.2 - - - +
145D ASN 3.8 8.5 - - - +
146D ASN* 1.3 75.0 - - - +
148D LEU* 1.3 70.4 + - - +
149D PRO* 3.3 5.6 - - + +
1E NAG 4.8 10.3 - - - -
2E NAG 6.1 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