Contacts of the strand formed by residues 132 - 140 (chain B) in PDB entry 5BOU
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 VAL 132 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28B ILE* 3.6 6.7 - - - +
76B VAL* 4.3 5.8 - - + -
77B ALA 3.7 4.3 - - - +
79B LEU 3.5 22.9 - - - +
82B ASP* 3.5 18.8 - - + +
83B ALA* 3.5 13.9 - - + +
86B LEU* 4.5 9.4 - - + -
118B LYS* 3.4 15.6 + - - -
130B PHE* 3.0 7.9 + - + +
131B GLY* 1.3 82.8 - - - +
133B SER* 1.3 69.0 + - - +
134B PHE* 3.6 38.6 - - + -
152B PRO* 3.4 15.9 - - - +
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Residues in contact with SER 133 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25B LEU* 4.6 2.6 - - - +
28B ILE* 3.5 25.3 - - - +
75B ALA 3.8 1.6 - - - +
76B VAL* 3.9 1.7 - - - -
77B ALA* 2.9 38.6 + - - +
132B VAL* 1.3 72.4 - - - +
134B PHE* 1.3 62.4 + - - +
150B SER 3.2 8.3 - - - -
151B ASN* 3.5 23.6 - - - +
164B VAL* 4.4 22.0 - - - +
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Residues in contact with PHE 134 (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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74B VAL* 4.1 12.6 - - + -
75B ALA 3.4 10.5 - - - -
76B VAL* 3.8 23.6 - - + -
83B ALA* 4.0 9.9 - - + -
86B LEU* 3.8 40.4 - - + -
87B ILE* 4.1 14.8 - - + -
114B LEU* 4.1 11.0 - - + -
118B LYS* 3.4 17.9 - - - -
132B VAL* 3.6 19.7 - - + -
133B SER* 1.3 73.5 - - - +
135B ILE* 1.3 63.2 + - - +
136B TYR* 3.4 39.0 - + + -
149B THR* 3.2 10.8 - - - +
150B SER* 3.0 27.8 + - - +
164B VAL* 4.6 2.1 - - - +
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Residues in contact with ILE 135 (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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34B ALA* 3.5 35.7 - - + +
35B ILE 4.0 1.3 - - - +
36B GLY* 3.9 13.7 - - - +
45B LEU* 3.9 12.0 - - + +
74B VAL* 3.2 6.5 - - - -
75B ALA* 2.9 40.2 + - + +
134B PHE* 1.3 73.9 - - - +
136B TYR* 1.3 62.7 + - - +
137B ALA 3.9 0.3 + - - -
147B LEU* 3.8 24.9 - - + -
148B TYR 3.3 9.4 - - - +
149B THR* 3.8 12.1 - - + -
162B ILE* 4.0 16.6 - - + +
164B VAL* 3.7 23.1 - - + +
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Residues in contact with TYR 136 (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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68B LEU* 4.5 1.3 - - + -
72B ILE* 5.1 3.8 - - + -
73B ALA 3.6 4.0 - - - +
74B VAL* 3.4 25.4 - - + -
107B VAL* 5.0 5.2 - - + -
110B LEU* 4.4 14.1 - - + -
111B VAL* 3.6 43.7 + - + -
114B LEU* 3.5 32.6 - - + +
118B LYS* 4.6 0.3 + - - -
134B PHE* 3.4 21.9 - - + -
135B ILE* 1.3 72.6 - - - +
137B ALA* 1.3 61.5 + - - +
138B GLY 4.1 0.2 - - - -
146B GLN 3.6 0.9 - - - +
147B LEU* 3.3 11.2 - - - +
148B TYR* 2.7 50.2 + - + +
149B THR* 4.3 0.2 - - - -
150B SER* 2.8 40.0 + - - -
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Residues in contact with ALA 137 (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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43B ILE* 3.7 22.2 - - + -
45B LEU* 3.7 35.4 - - + -
72B ILE* 3.4 3.1 - - - +
73B ALA 2.8 37.2 + - - -
107B VAL* 5.3 0.2 - - - -
135B ILE 3.9 1.4 + - - -
136B TYR* 1.3 73.2 - - - +
138B GLY* 1.3 59.2 + - - +
146B GLN 3.7 4.5 - - - -
147B LEU* 4.1 1.8 - - + -
215B ILE* 3.2 15.3 - - + +
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Residues in contact with GLY 138 (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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43B ILE* 3.4 10.7 - - - +
71B LYS 3.2 12.1 - - - -
72B ILE* 4.1 4.3 - - - -
107B VAL* 3.7 20.3 - - - +
136B TYR 4.1 0.6 - - - -
137B ALA* 1.3 75.0 - - - +
139B TYR* 1.3 59.8 + - - -
144B GLY 3.8 0.3 - - - +
145B TYR* 3.6 0.9 - - - -
146B GLN* 3.0 33.7 + - - +
215B ILE* 4.3 2.7 - - - -
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Residues in contact with TYR 139 (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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71B LYS* 3.2 41.1 + - + +
72B ILE* 5.0 0.5 - - - +
105B ILE 5.5 1.4 - - - +
107B VAL* 3.6 7.8 - - - +
138B GLY* 1.3 74.3 - - - +
140B ASP* 1.3 78.6 + - - +
141B ASP* 4.2 10.7 - - + +
144B GLY* 3.5 31.4 - - - -
145B TYR* 3.6 29.4 - + + -
215B ILE* 4.8 0.9 - - + -
217B LYS* 2.9 37.9 + - - -
224B VAL* 3.6 30.5 - - + -
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Residues in contact with ASP 140 (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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71B LYS* 5.9 2.5 - - - +
104B ASP 5.8 1.3 - - - +
105B ILE 5.0 2.0 - - - +
106B PRO* 3.6 22.9 - - + +
107B VAL* 3.0 21.9 + - + +
108B GLU 4.7 0.2 + - - -
139B TYR* 1.3 86.1 - - - +
141B ASP* 1.3 60.5 + - - +
142B ARG* 3.0 19.2 + - - +
143B TYR* 3.0 15.1 + - - +
144B GLY* 2.9 31.0 + - - -
146B GLN* 2.8 21.5 + - - +
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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