Contacts of the strand formed by residues 183 - 191 (chain A) in PDB entry 1BO1
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 183 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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103A PHE* 3.7 23.0 - - + -
106A LEU* 3.7 23.2 - - - +
110A PHE* 3.7 4.3 - - - -
150A LYS* 6.1 3.4 - - - -
160A MET* 3.9 24.7 - - - -
163A ILE* 4.9 0.9 - - + -
167A TYR* 3.0 45.1 + + + +
181A PRO* 3.7 17.0 - - + -
182A GLN* 1.3 70.5 - - - +
184A LEU* 1.3 61.1 + - - +
185A GLY 4.8 0.4 - - - +
199A VAL* 3.6 21.5 - - + -
200A VAL 4.6 0.7 - - - +
201A THR* 3.3 20.6 - - + -
370A ILE* 3.3 49.6 - - + -
371A LEU* 5.0 7.6 - - + -
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Residues in contact with LEU 184 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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103A PHE* 3.5 11.6 - - - +
107A ARG* 3.0 45.3 + - + +
110A PHE* 3.8 22.0 - - + -
112A ILE* 3.3 28.7 - - + -
117A TYR* 4.0 20.8 + - + -
147A PHE* 3.4 35.4 - - + -
182A GLN* 3.5 19.7 - - + +
183A PHE* 1.3 73.0 - - - +
185A GLY* 1.3 59.2 + - - +
200A VAL 3.0 7.9 + - - +
201A THR* 4.1 3.6 - - - +
202A ARG* 3.6 13.2 - - + +
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Residues in contact with GLY 185 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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97A GLU* 5.8 1.6 - - - -
103A PHE* 3.7 15.8 - - - -
107A ARG* 5.4 0.9 - - - -
117A TYR* 4.3 10.2 + - - -
183A PHE* 3.6 1.8 - - - +
184A LEU* 1.3 83.0 - - - +
186A MET* 1.3 59.8 + - - +
187A TYR* 4.1 13.9 - - - -
199A VAL* 3.5 4.7 - - - +
200A VAL 2.8 30.6 + - - +
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Residues in contact with MET 186 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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97A GLU* 3.9 2.0 - - - +
98A TYR* 3.1 54.4 + - + -
103A PHE* 4.0 22.5 - - + -
152A VAL* 4.5 0.2 - - + -
156A ASP 4.5 0.7 - - - +
157A VAL* 3.4 41.3 - - + +
160A MET* 3.4 39.0 - - + -
161A HIS* 4.6 2.9 - - - -
185A GLY* 1.3 74.8 - - - +
187A TYR* 1.3 69.4 + - - +
198A MET 3.3 8.3 - - - +
199A VAL* 3.4 23.8 - - + -
371A LEU* 5.3 0.2 - - + -
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Residues in contact with TYR 187 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46A LEU* 4.5 8.1 - - + -
50A VAL* 3.6 17.0 - - + +
53A THR* 4.1 9.4 - - - -
54A ILE* 4.4 4.2 - - - +
95A PHE* 3.3 41.1 - + + -
96A LYS 3.3 7.4 - - - +
97A GLU* 4.0 28.1 + - + -
98A TYR* 4.1 7.0 - - - -
107A ARG* 5.3 1.4 + - - -
117A TYR* 3.0 29.2 + - - -
184A LEU 5.0 0.2 + - - -
185A GLY* 4.1 14.1 - - - -
186A MET* 1.3 78.8 - - - +
188A ARG* 1.3 59.9 + - - +
189A LEU* 4.2 7.0 - - + -
197A TYR* 3.4 4.5 - - - +
198A MET* 2.8 44.2 + - + +
200A VAL* 3.4 31.9 - - + -
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Residues in contact with ARG 188 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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76A LYS* 4.0 18.8 - - - +
94A LYS* 4.2 10.8 - - - +
95A PHE* 3.9 2.4 - - - -
96A LYS* 2.9 64.3 + - + +
98A TYR* 3.6 18.5 + - + +
187A TYR* 1.3 75.0 - - - +
189A LEU* 1.3 61.5 + - - +
190A THR* 4.1 6.8 - - - +
195A GLU* 3.1 48.4 + - + -
196A THR 3.0 15.0 - - - +
197A TYR* 3.6 27.9 + - + -
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Residues in contact with LEU 189 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42A ILE* 3.4 21.5 - - + +
45A VAL* 3.5 16.8 - - + -
46A LEU* 3.2 41.1 - - + +
94A LYS 3.6 5.6 - - - -
95A PHE* 3.6 16.8 - - + -
187A TYR* 4.8 2.2 - - + -
188A ARG* 1.3 77.9 - - - +
190A THR* 1.3 61.8 + - - +
191A VAL* 5.2 2.2 - - + -
194A VAL 3.6 0.3 - - - +
196A THR* 2.7 47.5 + - - +
198A MET* 3.6 39.3 - - + -
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Residues in contact with THR 190 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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93A PHE* 3.5 9.0 - - - +
94A LYS* 2.9 61.1 + - + +
188A ARG* 4.1 10.8 - - - +
189A LEU* 1.3 79.9 - - - +
191A VAL* 1.3 64.9 + - - +
193A GLY* 4.8 5.8 - - - -
194A VAL 3.2 13.5 - - - -
195A GLU* 3.3 39.0 - - + +
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Residues in contact with VAL 191 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41A PRO* 4.3 10.3 - - + +
42A ILE* 4.5 27.1 - - + +
45A VAL* 4.0 24.2 - - + -
90A PRO* 3.8 30.3 - - + -
92A ARG 4.7 4.7 - - - +
93A PHE* 5.0 1.3 - - - -
189A LEU* 5.2 1.3 - - + -
190A THR* 1.3 81.0 - - - +
192A ASP* 1.3 91.4 + - - +
193A GLY 3.1 0.7 - - - +
194A VAL* 3.0 21.2 + - - +
196A THR* 6.1 0.7 - - - +
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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