Contacts of the strand formed by residues 9 - 17 (chain C) in PDB entry 2BME
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 PHE 9 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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139A SER* 4.9 5.6 - - - -
143A GLN* 3.7 40.2 - - + -
148A MET* 4.9 1.3 - - - -
149A PHE 5.6 1.8 - - - +
1183A BME 4.1 13.2 - - - -
7C TYR* 3.2 9.7 - - - -
8C ASP* 1.3 98.9 - - + +
10C LEU* 1.3 60.8 + - - +
11C PHE* 3.8 24.0 - + + -
57C LYS* 3.9 22.4 - - + -
58C TYR 3.0 8.8 + - - +
59C VAL* 3.5 8.6 - - + -
60C LYS 2.9 25.1 + - - -
172C LEU* 3.7 32.5 - - + -
175C ILE* 4.4 11.0 - - + -
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Residues in contact with LEU 10 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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135A PHE* 3.9 8.7 - - - -
148A MET* 5.4 0.2 - - - +
149A PHE 4.5 9.1 + - - +
150A LEU* 3.5 28.5 - - + -
162A GLU* 4.5 1.6 - - - +
1181A TRS 3.2 29.4 + - - +
7C TYR* 3.7 15.0 - - + +
9C PHE* 1.3 75.7 - - - +
11C PHE* 1.3 73.6 + - - +
60C LYS* 3.5 41.7 - - + +
62C GLN* 2.7 43.3 - - + +
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Residues in contact with PHE 11 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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135A PHE* 4.2 15.7 - + - -
139A SER* 5.6 0.2 - - - -
1181A TRS 4.1 1.1 - - - -
9C PHE* 3.8 19.1 - + + -
10C LEU* 1.3 92.1 - - - +
12C LYS* 1.3 60.3 + - - +
13C PHE* 3.8 20.5 + + + -
59C VAL* 3.6 22.7 - - + -
60C LYS 3.0 7.1 + - - -
61C LEU* 3.5 9.5 - - + +
62C GLN* 3.0 24.1 + - - +
84C ALA* 4.5 6.3 - - + -
168C ALA* 3.9 14.8 - - - -
171C ILE* 3.6 42.0 - - + -
172C LEU* 3.8 18.6 - - + -
175C ILE* 3.8 24.9 - - + -
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Residues in contact with LYS 12 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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125A LYS* 5.5 0.8 - - - +
158A GLU* 4.8 8.5 + - - +
1181A TRS 3.6 39.2 + - - +
11C PHE* 1.3 71.2 - - - +
13C PHE* 1.3 68.8 + - - +
14C LEU* 4.1 5.4 - - - -
62C GLN* 3.4 9.2 - - - +
64C TRP* 3.7 33.3 - - + +
78C SER 5.3 0.2 + - - -
79C TYR* 2.7 37.0 + - - +
81C ARG 2.9 20.7 + - - +
82C GLY 4.2 3.4 - - - +
83C ALA* 3.6 20.3 - - + +
84C ALA* 2.9 31.0 + - - +
85C GLY 3.4 0.3 + - - -
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Residues in contact with PHE 13 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11C PHE* 3.8 16.8 + - + -
12C LYS* 1.3 82.2 - - - +
14C LEU* 1.3 67.6 + - - +
61C LEU* 3.6 29.6 - - + -
62C GLN 2.9 11.3 + - - +
63C ILE* 4.2 13.7 - - + -
64C TRP* 2.9 30.4 + - - -
85C GLY* 3.2 13.5 - - - +
87C LEU* 4.5 5.4 - - + -
164C PHE* 3.7 32.5 - + + -
167C CYS* 3.5 34.8 - - + -
168C ALA* 3.7 11.4 - - - -
171C ILE* 3.5 24.5 - - + -
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Residues in contact with LEU 14 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12C LYS* 4.1 3.4 - - - -
13C PHE* 1.3 82.5 - - - +
15C VAL* 1.3 65.4 + - - +
16C ILE* 3.8 20.2 - - + -
64C TRP* 3.5 19.3 - - + +
66C THR* 4.8 2.7 - - + -
79C TYR* 3.5 26.7 - - + +
80C TYR* 3.9 36.8 - - + +
83C ALA* 3.8 23.6 - - + -
85C GLY 3.1 7.1 + - - -
86C ALA* 3.2 14.1 - - + -
87C LEU* 2.9 25.5 + - - +
108C ALA* 5.7 1.3 - - + -
112C ALA* 4.9 0.7 - - + -
116C ILE* 4.6 5.8 - - + -
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Residues in contact with VAL 15 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13C PHE* 5.9 0.2 - - + -
14C LEU* 1.3 76.8 - - - +
16C ILE* 1.3 56.6 + - - +
23C LYS* 3.6 38.2 - - + +
26C LEU* 5.4 2.9 - - + -
27C LEU* 5.2 3.1 - - + -
63C ILE* 3.7 25.8 - - + -
64C TRP 2.9 9.3 + - - +
65C ASP* 4.3 12.3 - - + +
66C THR* 2.6 35.2 + - - -
87C LEU* 3.4 11.7 - - + +
89C VAL* 3.9 16.2 - - + -
164C PHE* 4.5 17.3 - - + -
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Residues in contact with ILE 16 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14C LEU* 3.8 19.5 - - + -
15C VAL* 1.3 78.9 - - - +
17C GLY* 1.3 58.2 + - - +
23C LYS* 3.3 10.4 - - - +
66C THR* 3.6 13.0 - - + +
80C TYR* 3.7 32.3 - - + +
86C ALA* 4.6 10.8 - - + -
87C LEU 3.0 14.9 + - - +
88C LEU* 3.9 21.8 - - + -
89C VAL* 2.8 26.5 + - - +
104C TRP* 4.2 15.0 - - + +
108C ALA* 3.9 28.0 - - + -
118C ILE* 5.9 0.7 - - + -
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Residues in contact with GLY 17 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16C ILE* 1.3 77.5 - - - +
18C ASN* 1.3 70.8 + - - +
23C LYS* 3.0 14.8 + - - +
66C THR* 4.8 0.2 + - - -
68C GLY* 3.3 11.8 - - - -
88C LEU* 4.5 1.1 - - - -
89C VAL 3.5 13.2 - - - -
104C TRP* 3.4 30.0 - - - -
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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