Contacts of the strand formed by residues 151 - 157 (chain A) in PDB entry 1BQ5
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 SER 151 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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64A PHE* 4.0 3.2 - - - -
69A PRO* 3.4 8.3 - - - +
70A GLY* 2.7 29.0 + - - -
133A VAL* 4.8 1.8 - - - -
134A TYR* 3.2 21.1 - - - -
135A HIS* 4.0 2.0 - - - +
146A VAL* 5.0 2.8 + - - -
149A GLY 3.1 5.3 + - - +
150A MET* 1.3 75.3 - - - +
152A GLY* 1.3 54.4 + - - +
181A PHE* 3.4 23.6 - - - -
246A SER* 5.4 3.5 + - - -
248A ALA* 3.7 31.8 + - - +
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Residues in contact with GLY 152 (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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69A PRO* 4.1 8.1 - - - -
70A GLY 4.0 10.8 - - - -
133A VAL* 3.4 7.8 - - - +
134A TYR* 2.9 46.2 + - - +
151A SER* 1.3 77.2 + - - +
153A THR* 1.3 64.6 + - - -
246A SER* 4.6 6.0 + - - -
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Residues in contact with THR 153 (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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70A GLY 4.8 0.6 + - - -
71A PRO 4.4 2.6 + - - -
72A THR* 3.2 23.3 + - + +
73A LEU 3.1 21.5 + - - -
131A THR* 3.9 15.7 - - + -
132A PHE 3.3 10.8 - - - +
134A TYR* 3.5 11.3 - - - -
152A GLY* 1.3 73.8 - - - -
154A LEU* 1.3 73.2 + - - +
155A MET* 4.3 1.3 - - + +
177A THR* 4.6 2.5 + - - -
244A ILE* 3.9 25.2 - - + +
246A SER* 3.2 30.1 + - - -
288A ALA* 4.0 3.8 - - + +
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Residues in contact with LEU 154 (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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73A LEU* 3.5 35.0 - - + +
75A VAL* 4.4 11.4 - - + -
81A VAL* 4.3 20.0 - - + -
99A PHE* 4.2 20.4 - - + -
101A GLY* 4.3 16.6 - - - -
124A PHE* 4.0 26.9 - - + -
126A ALA* 5.2 0.2 - - + -
130A GLY 3.6 2.4 - - - +
131A THR* 3.4 0.7 - - - -
132A PHE* 2.7 45.9 + - + +
133A VAL 5.8 0.2 - - - -
134A TYR* 4.1 2.0 - - + -
153A THR* 1.3 74.3 - - - +
155A MET* 1.3 58.8 + - - +
156A VAL* 3.9 20.2 - - + -
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Residues in contact with MET 155 (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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28A HIS* 5.8 0.9 - - - -
72A THR* 4.5 10.3 - - + +
73A LEU 2.8 10.8 + - - +
74A VAL* 3.2 18.9 - - + +
75A VAL* 3.0 26.9 + - - +
130A GLY 3.5 1.8 - - - -
131A THR* 3.3 24.0 - - + +
153A THR* 4.1 1.4 - - + +
154A LEU* 1.3 73.8 - - - +
156A VAL* 1.3 63.9 + - - +
157A LEU* 3.9 18.6 - - + -
162A LEU* 5.5 0.7 - - + -
172A TYR* 4.7 3.6 - - - -
242A LEU* 3.3 35.9 - - + -
244A ILE* 4.1 12.1 - - + -
270A PHE* 3.1 39.7 - - + -
290A ALA* 4.6 1.3 - - + -
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Residues in contact with VAL 156 (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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75A VAL* 3.4 7.2 - - + -
76A HIS 3.8 4.5 - - - +
77A GLU* 3.6 32.1 - - - +
101A GLY* 5.9 0.9 - - - +
126A ALA* 3.9 21.3 - - + +
128A ARG 3.3 29.4 - - - +
129A SER* 3.5 4.4 + - - -
130A GLY 2.8 34.2 + - - +
132A PHE* 4.2 4.7 - - + -
154A LEU* 3.9 27.4 - - + -
155A MET* 1.3 73.9 - - - +
157A LEU* 1.3 60.9 + - - +
270A PHE* 3.6 4.2 - - - -
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Residues in contact with LEU 157 (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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28A HIS* 3.7 18.6 - - + +
29A GLU 3.7 22.9 - - - +
30A GLN* 4.0 11.0 - - + +
74A VAL* 4.1 9.4 - - + -
75A VAL 2.9 9.1 + - - +
76A HIS* 3.3 18.3 - - + +
77A GLU 2.7 31.2 + - - -
129A SER* 4.2 1.3 - - - -
155A MET* 4.3 15.0 - - + -
156A VAL* 1.3 74.2 - - - +
158A PRO* 1.3 76.0 - - + +
161A GLY* 5.6 1.1 - - - -
162A LEU* 4.2 22.7 - - + +
172A TYR* 3.7 18.2 - - + +
270A PHE* 4.2 9.9 - - + -
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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