Contacts of the strand formed by residues 158 - 163 (chain A) in PDB entry 6BM0
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 ARG 158 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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127A GLU 4.0 14.1 + - - -
128A LEU* 3.5 47.6 + - + +
130A ASP* 4.9 3.8 + - - +
153A LEU* 3.4 3.6 - - - +
154A VAL* 2.5 58.1 + - + +
155A TYR* 5.3 0.7 - - + -
157A THR* 1.3 99.6 + - - +
159A LEU* 1.3 58.8 + - - +
160A VAL* 4.1 0.4 - - + -
190A ILE* 3.8 25.3 - - + +
191A ILE 3.6 7.6 - - - -
192A ASP* 2.8 38.1 + - - +
194A ARG* 3.2 24.2 - - - +
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Residues in contact with LEU 159 (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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151A ALA* 4.9 6.5 - - + -
152A MET 3.4 10.5 - - - +
153A LEU* 3.7 28.0 - - + +
157A THR 3.6 0.2 + - - -
158A ARG* 1.3 71.0 - - - +
160A VAL* 1.3 64.4 + - - +
161A VAL* 3.9 2.8 + - + -
189A TYR 3.7 0.9 - - - +
190A ILE* 3.3 2.6 - - - -
191A ILE* 2.6 62.2 + - + +
193A VAL* 3.7 24.5 - - + -
196A LEU* 5.4 3.4 - - + -
206A LEU* 4.3 10.5 - - + -
217A LEU* 3.9 30.7 - - + -
219A ILE* 4.1 11.9 - - + -
243A ILE* 5.6 3.1 - - + -
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Residues in contact with VAL 160 (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 LEU* 6.1 0.7 - - + -
123A PHE* 3.5 42.2 - - + -
150A ALA 3.8 0.2 - - - +
151A ALA* 3.2 6.8 - - - +
152A MET* 2.7 43.5 + - + +
154A VAL* 3.7 20.6 - - + -
158A ARG* 5.4 0.2 - - + -
159A LEU* 1.3 73.9 - - - +
161A VAL* 1.3 65.5 + - - +
162A LEU* 4.0 9.2 + - + +
188A SER* 3.9 17.7 - - - +
189A TYR 3.8 3.8 - - - +
190A ILE* 3.8 23.1 - - + -
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Residues in contact with VAL 161 (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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149A CYS* 4.5 2.9 - - - -
150A ALA 3.5 7.0 - - - +
151A ALA* 5.2 5.2 - - + -
159A LEU* 4.7 3.8 - - + +
160A VAL* 1.3 75.9 - - - +
162A LEU* 1.3 66.5 + - - +
163A PRO* 3.3 9.5 - - - +
188A SER* 3.3 19.5 - - - -
189A TYR* 3.1 43.3 + - + +
191A ILE* 3.7 29.6 - - + -
217A LEU* 6.5 0.7 - - + -
245A LEU* 3.8 26.9 - - + -
247A ILE* 4.2 12.3 - - + -
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Residues in contact with LEU 162 (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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95A LEU* 4.7 4.3 - - + -
103A LEU* 3.8 41.3 - - + -
105A VAL* 5.1 4.3 - - + -
121A HIS* 4.0 25.1 - - + +
123A PHE* 5.7 0.7 - - + -
149A CYS* 3.3 6.2 - - - +
150A ALA* 2.7 51.6 + - + +
151A ALA* 6.1 1.1 - - - -
152A MET* 6.3 0.2 - - + -
160A VAL* 4.7 9.4 - - + +
161A VAL* 1.3 72.8 - - - +
163A PRO* 1.3 64.8 - - - +
164A PHE* 4.0 13.2 - - + -
185A PHE* 5.9 6.3 - - + -
186A LEU 4.7 7.4 - - - +
188A SER* 3.7 23.6 - - - -
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Residues in contact with PRO 163 (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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149A CYS* 4.3 8.1 - - + -
161A VAL* 3.3 11.2 - - + +
162A LEU* 1.3 86.7 - - - +
164A PHE* 1.3 68.1 - - - +
185A PHE* 4.4 1.0 - - - +
186A LEU* 3.4 41.2 + - + +
187A PRO 3.8 22.2 - - - +
188A SER* 4.2 0.4 - - - -
189A TYR* 4.1 17.0 - - + -
247A ILE* 3.7 35.4 - - + -
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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