Contacts of the strand formed by residues 164 - 171 (chain D) in PDB entry 3B94
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 164 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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61D LYS* 3.8 27.4 - - + -
62D PHE 3.4 16.4 - - - +
63D GLY 3.7 12.8 - - - -
64D PRO* 4.1 17.3 - - + -
85D TRP* 4.0 5.6 - - - -
98D TYR* 4.1 20.8 - + - -
99D GLY* 3.0 9.1 - - - -
100D GLN* 2.9 67.1 + - + +
136D VAL* 4.7 0.9 - - - +
150D LEU* 5.3 1.2 - - - +
162D ASN* 4.5 2.9 - - - -
163D THR* 1.3 84.7 - - - +
165D TRP* 1.3 67.7 + - - +
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Residues in contact with TRP 165 (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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61D LYS* 3.4 6.6 - - - +
62D PHE* 2.7 40.8 + - + +
69D TRP* 3.6 17.8 - + - -
85D TRP* 3.0 42.1 + + - +
87D LEU* 3.7 22.0 - - + -
97D ILE* 3.8 15.9 - - + -
98D TYR* 3.3 10.8 - - - +
99D GLY* 3.9 0.7 - - - -
117D LEU* 4.8 3.4 - - + -
136D VAL* 4.4 14.1 - - + -
148D ILE* 3.3 52.9 - - + -
150D LEU* 3.6 27.0 - - + +
164D TYR* 1.3 78.8 - - - +
166D GLY* 1.3 84.8 + - - +
167D ILE* 4.1 11.4 - - + -
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Residues in contact with GLY 166 (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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60D ALA 2.9 16.4 - - - -
61D LYS* 4.0 0.7 - - - -
62D PHE 4.7 0.2 - - - -
69D TRP* 5.2 0.7 - - - -
97D ILE* 3.4 6.6 - - - +
98D TYR* 2.9 47.1 + - - +
165D TRP* 1.3 82.3 - - - +
167D ILE* 1.3 64.1 + - - +
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Residues in contact with ILE 167 (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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59D MET* 3.0 8.3 - - - +
60D ALA* 3.0 39.6 + - + +
69D TRP* 5.6 0.2 - - + -
78D CYS* 6.2 0.7 - - - -
79D VAL* 4.4 7.2 - - + -
87D LEU* 3.5 28.5 - - + -
89D ILE* 4.0 22.0 - - + -
95D TYR* 3.7 32.5 - - + -
96D LEU 3.2 12.6 - - - +
97D ILE* 3.9 12.6 - - + -
98D TYR* 3.6 5.2 - - - -
142D LEU* 4.0 12.6 - - + -
148D ILE* 4.5 5.4 - - + -
165D TRP* 4.1 6.1 - - + -
166D GLY* 1.3 77.6 - - - +
168D ILE* 1.3 64.2 + - - +
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Residues in contact with ILE 168 (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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57D PRO* 3.5 35.2 - - + -
58D CYS 3.5 10.1 - - - +
59D MET* 3.8 24.5 - - + -
95D TYR* 3.3 8.9 - - - -
96D LEU* 2.9 53.8 + - + +
98D TYR* 5.0 9.4 - - + -
167D ILE* 1.3 77.3 - - - +
169D LEU* 1.3 69.6 + - - +
170D LEU* 3.4 12.6 + - + +
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Residues in contact with LEU 169 (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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57D PRO* 4.2 9.5 - - - +
58D CYS* 3.0 37.9 + - + +
78D CYS* 4.1 12.6 - - + -
91D GLN* 5.4 5.4 - - + -
92D ASN 4.3 1.1 - - - +
93D GLY* 3.9 1.8 - - - -
94D LEU 3.8 3.1 - - - +
95D TYR* 3.5 39.7 - - + +
168D ILE* 1.3 76.8 - - - +
170D LEU* 1.3 66.4 + - - +
171D ALA* 3.5 19.1 - - - +
172D ASN* 3.5 28.9 - - - +
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Residues in contact with LEU 170 (chain D).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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94D LEU* 2.6 43.0 + - + +
96D LEU* 4.2 35.0 - - + +
139D THR* 3.8 18.4 - - + -
168D ILE* 3.4 14.5 + - + +
169D LEU* 1.3 79.6 - - - +
171D ALA* 1.3 63.0 + - + +
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Residues in contact with ALA 171 (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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93D GLY* 3.1 4.2 - - - -
94D LEU* 2.6 37.6 + - + +
169D LEU* 3.4 5.3 - - - +
170D LEU* 1.3 87.5 - - + +
172D ASN* 1.3 66.2 + - - +
173D PRO* 4.0 9.6 - - + +
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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