Contacts of the strand formed by residues 110 - 118 (chain B) in PDB entry 3MB8
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 110 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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105B LEU* 4.5 2.4 - - - +
108B GLY 4.4 1.8 - - - +
109B ASP* 1.3 79.0 - - - +
111B CYS* 1.3 63.4 + - - +
152B ILE* 5.5 0.2 - - + -
153B GLU* 4.2 14.5 + - - +
154B ALA* 3.6 9.0 - - + -
155B ALA* 2.9 27.0 + - - +
206B ILE* 3.6 34.8 - - + -
207B LEU 3.4 5.6 - - - +
208B ALA* 4.5 0.9 - - + -
231B GLY* 3.4 30.1 - - - +
234B ASN* 4.3 9.4 - - + +
235B MET* 4.0 13.5 - - + +
238B ILE* 4.4 10.5 - - + -
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Residues in contact with CYS 111 (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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97B CYS* 5.5 0.9 - - - -
105B LEU* 4.6 9.9 - - + -
109B ASP 4.3 0.2 - - - -
110B VAL* 1.3 75.1 - - - +
112B VAL* 1.3 68.3 + - - +
113B THR* 3.5 13.2 + - + +
155B ALA* 3.5 16.4 - - + -
157B GLY* 3.8 31.2 - - - -
183B ASP* 4.9 0.9 - - - -
184B VAL* 4.2 27.8 - - + -
206B ILE* 3.4 1.9 - - - -
207B LEU* 2.8 44.1 + - + +
209B VAL* 5.6 1.6 - - + -
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Residues in contact with VAL 112 (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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111B CYS* 1.3 70.7 - - - +
113B THR* 1.3 60.2 - - - +
114B TYR 3.6 1.6 + - - -
140B TYR* 3.6 29.4 - - + -
143B LEU* 4.3 19.5 - - + +
144B MET* 3.7 25.1 - - - -
154B ALA* 4.2 9.6 - - + -
155B ALA 2.8 14.2 + - - +
156B SER* 3.5 3.8 - - - -
157B GLY 3.0 22.5 + - - -
204B CYS* 3.9 8.7 - - - -
205B GLY 3.5 14.6 - - - +
206B ILE* 3.9 26.0 - - + -
238B ILE* 5.5 0.2 - - + -
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Residues in contact with THR 113 (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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111B CYS* 4.1 11.9 - - - +
112B VAL* 1.3 71.9 - - - +
114B TYR* 1.3 62.6 + - - +
115B ALA 3.6 12.9 + - - -
135B ALA* 4.1 1.7 - - - +
157B GLY 3.3 7.0 - - - +
159B GLY* 4.5 4.5 - - - +
184B VAL* 3.8 18.4 - - + -
189B MET* 3.5 23.0 - - + +
193B LEU* 4.3 3.5 - - - +
204B CYS* 3.7 4.3 - - - -
205B GLY 2.9 33.8 + - - +
207B LEU* 3.6 27.4 - - + -
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Residues in contact with TYR 114 (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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112B VAL 3.6 1.0 + - - -
113B THR* 1.3 73.6 - - - +
115B ALA* 1.3 68.2 + - + +
134B VAL* 3.4 11.5 - - + +
135B ALA* 2.8 36.5 + - + -
140B TYR* 3.7 26.2 - + + -
156B SER* 3.5 27.1 - - - -
157B GLY* 3.1 30.6 + - - -
158B ILE* 3.7 30.1 - - + +
193B LEU* 4.5 0.4 - - - -
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Residues in contact with ALA 115 (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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113B THR* 3.2 8.1 - - - -
114B TYR* 1.3 93.0 - - + +
116B ALA* 1.3 65.5 + - - +
133B CYS 3.2 14.1 - - - +
134B VAL* 4.4 7.9 - - + -
157B GLY 4.0 0.8 + - - -
158B ILE* 3.5 20.8 - - + -
159B GLY* 2.9 20.8 + - - -
193B LEU* 3.9 6.1 - - - -
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Residues in contact with ALA 116 (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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115B ALA* 1.3 78.7 - - - +
117B VAL* 1.3 62.9 + - - +
118B ASN 3.4 2.4 + - - -
133B CYS* 2.9 26.4 + - - +
158B ILE* 4.3 2.5 - - - -
159B GLY* 3.2 14.1 - - - +
161B THR* 3.9 11.0 - - - +
189B MET* 4.2 14.1 - - + -
190B SER* 3.8 29.2 - - - +
193B LEU* 4.5 0.4 - - + -
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Residues in contact with VAL 117 (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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116B ALA* 1.3 70.3 - - - +
118B ASN* 1.3 69.8 + - - +
119B GLU 3.6 0.2 + - - -
158B ILE* 4.4 8.5 - - + +
159B GLY 2.7 18.6 + - - +
160B VAL* 3.8 9.1 - - + +
161B THR* 2.9 29.1 + - - -
178B TYR* 3.7 29.2 - - + +
181B CYS* 5.1 8.3 - - - +
182B CYS* 3.7 19.1 - - + -
190B SER* 4.3 0.4 - - - -
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Residues in contact with ASN 118 (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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116B ALA 3.4 3.0 + - - -
117B VAL* 1.3 79.9 - - - +
119B GLU* 1.3 59.1 + - - +
120B THR* 2.6 46.6 + - - +
123B ILE* 3.4 20.8 - - + +
124B SER* 3.6 13.7 + - - +
131B PHE 5.7 1.6 - - - +
133B CYS* 4.1 11.4 - - - -
178B TYR* 5.4 0.5 + - - -
190B SER* 2.7 25.7 + - - +
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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