Contacts of the strand formed by residues 147 - 150 (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 THR 147 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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82D VAL* 4.3 8.3 - - + -
86D LYS* 4.4 24.4 + - - +
87D LEU 3.1 12.6 - - - +
88D GLU* 3.7 25.8 - - + +
118D TYR 3.7 0.3 - - - +
119D LYS* 3.5 4.9 - - - +
120D ASN* 2.9 47.6 + - - +
145D GLY 4.1 2.9 - - - +
146D ASP* 1.3 80.0 - - - +
148D ILE* 1.3 67.3 + - - +
149D ASP* 4.3 2.2 + - - +
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Residues in contact with ILE 148 (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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86D LYS* 3.3 2.3 - - - +
87D LEU* 2.8 33.1 + - + +
89D ILE* 4.3 12.3 - - + -
97D ILE* 3.8 17.9 - - + -
117D LEU* 3.6 23.1 - - + -
118D TYR 3.4 9.2 - - - +
119D LYS* 4.1 18.4 - - + -
124D ILE* 4.6 1.3 - - + -
140D TYR* 6.5 0.2 - - + -
142D LEU* 3.9 32.1 - - + -
146D ASP* 4.4 0.4 + - + -
147D THR* 1.3 81.1 - - - +
149D ASP* 1.3 67.0 + - - +
165D TRP* 3.3 34.5 - - + -
167D ILE* 4.5 2.0 - - + -
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Residues in contact with ASP 149 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84D ASP 4.6 1.0 - - - +
85D TRP* 3.2 12.9 - - - +
86D LYS* 2.8 42.2 + - + +
116D ARG 4.0 0.5 - - - +
117D LEU* 3.7 5.3 - - - +
118D TYR* 2.9 41.6 + - + +
120D ASN 5.7 1.8 - - - +
147D THR* 5.3 2.5 - - - +
148D ILE* 1.3 79.4 - - - +
150D LEU* 1.3 74.2 + - - +
151D ILE* 3.9 24.7 + - + +
165D TRP* 4.7 0.7 - - - -
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Residues in contact with LEU 150 (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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85D TRP* 2.9 36.9 + - + +
101D VAL* 4.1 16.6 - - + -
115D VAL* 3.7 16.2 - - + -
116D ARG 3.4 20.9 - - - +
117D LEU* 4.0 18.4 - - + +
136D VAL* 4.6 12.1 - - + -
149D ASP* 1.3 74.2 + - - +
151D ILE* 1.3 66.9 + - - +
152D PHE* 4.0 30.8 + - + -
163D THR* 4.3 5.6 - - + -
164D TYR 5.3 0.9 - - - -
165D TRP* 3.6 37.5 - - + +
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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