Contacts of the strand formed by residues 147 - 152 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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82B VAL* 4.7 4.5 - - + -
86B LYS* 4.6 19.7 + - + +
87B LEU 3.3 8.5 - - - -
88B GLU* 3.0 36.8 - - + +
118B TYR* 3.5 1.2 - - - +
119B LYS* 3.4 4.7 - - - -
120B ASN* 2.9 41.2 + - - +
145B GLY 4.1 2.7 - - - +
146B ASP* 1.3 73.0 - - - +
148B ILE* 1.3 64.8 + - - +
149B ASP* 4.0 1.0 + - - -
88D GLU* 4.4 6.7 - - - +
145D GLY* 5.2 4.0 - - - -
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Residues in contact with ILE 148 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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86B LYS* 3.4 2.2 - - - +
87B LEU* 3.0 37.5 + - + -
89B ILE* 4.4 11.9 - - + -
97B ILE* 3.8 17.9 - - + -
117B LEU* 3.7 20.2 - - + -
118B TYR 3.1 6.7 - - - +
119B LYS* 3.9 25.8 - - + -
124B ILE* 5.6 0.4 - - + -
142B LEU* 4.1 24.5 - - + -
146B ASP* 5.0 0.4 - - + -
147B THR* 1.3 80.6 - - - +
149B ASP* 1.3 70.7 + - - +
165B TRP* 3.5 33.3 - - + -
167B ILE* 5.2 1.6 - - + -
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Residues in contact with ASP 149 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84B ASP 5.1 0.9 - - - +
85B TRP* 3.3 12.9 - - - +
86B LYS* 3.1 40.5 + - + +
116B ARG 3.7 0.7 - - - +
117B LEU* 3.0 10.2 - - - +
118B TYR* 2.5 48.4 + - - +
120B ASN 5.6 0.2 - - - +
147B THR* 4.0 1.5 + - - -
148B ILE* 1.3 79.3 - - - +
150B LEU* 1.3 63.0 + - - +
151B ILE* 3.3 28.7 - - - +
165B TRP* 4.5 0.2 - - - -
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Residues in contact with LEU 150 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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85B TRP* 3.6 30.1 + - + +
101B VAL* 4.2 15.0 - - + -
115B VAL* 3.6 20.2 - - + -
116B ARG 3.3 19.3 - - - +
117B LEU* 4.0 16.8 - - + -
127B LEU* 4.9 1.8 - - + -
136B VAL* 4.3 20.4 - - + -
149B ASP* 1.3 76.9 - - - +
151B ILE* 1.3 63.3 + - - +
152B PHE* 4.1 31.1 - - + -
163B THR* 4.8 3.6 - - + -
164B TYR 5.0 0.9 - - - +
165B TRP* 3.7 35.2 - - + +
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Residues in contact with ILE 151 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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114B GLU 3.8 0.2 - - - +
115B VAL* 3.0 8.6 - - - -
116B ARG* 2.7 42.2 + - - +
118B TYR* 3.3 39.9 - - + -
149B ASP* 3.3 28.7 - - - +
150B LEU* 1.3 76.7 - - - +
152B PHE* 1.3 79.2 + - - +
153B ASN* 4.7 2.0 - - - +
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Residues in contact with PHE 152 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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85B TRP* 3.6 63.9 - + - -
101B VAL* 5.2 0.4 - - + -
114B GLU 3.8 3.8 - - - -
115B VAL* 4.2 7.9 - - + -
150B LEU* 4.1 24.5 - - + -
151B ILE* 1.3 88.3 - - - +
153B ASN* 1.3 62.8 + - - +
154B SER* 3.2 24.1 + - - +
155B GLU* 4.9 8.3 - - + -
159B LEU* 3.5 45.5 - - + -
163B THR* 4.5 2.9 - - + -
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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