Contacts of the strand formed by residues 96 - 101 (chain B) in PDB entry 1M6B
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 96 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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67B TYR* 3.7 3.5 - - - +
91B VAL* 3.6 8.4 - - - +
92B TYR* 2.9 41.4 + - - +
93B ASP* 4.2 5.4 - - + -
95B LYS* 1.3 114.0 - - + +
97B ALA* 1.3 60.9 + - - +
98B ILE 3.6 16.5 - - - +
99B PHE* 3.6 26.0 - + + -
127B GLY 3.5 2.0 - - - +
128B VAL 3.7 22.0 - - - -
129B TYR* 3.5 39.3 - + + -
154B GLU* 4.0 24.5 - - + -
156B VAL* 4.5 9.4 - - + -
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Residues in contact with ALA 97 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67B TYR* 3.2 8.9 - - - +
68B VAL 2.7 32.1 + - - -
86B VAL* 3.8 16.6 - - + +
88B GLY* 4.6 4.9 - - - -
91B VAL* 4.5 1.3 - - - -
96B PHE* 1.3 74.1 - - - +
98B ILE* 1.3 61.0 + - + +
123B ILE* 3.5 21.8 - - + -
125B SER 3.1 26.0 - - - +
126B GLY 4.1 0.2 - - - -
127B GLY 2.7 9.5 + - - +
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Residues in contact with ILE 98 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68B VAL* 3.4 19.1 - - + +
83B LEU* 5.9 1.1 - - + -
86B VAL* 4.5 12.3 - - + -
96B PHE* 3.6 6.2 - - - +
97B ALA* 1.3 84.3 - - - +
99B PHE* 1.3 63.6 + - - +
100B VAL* 3.7 21.3 - - + -
115B LEU* 5.3 1.6 - - + -
117B LEU* 4.1 15.5 - - + -
120B LEU* 3.9 28.7 - - + -
123B ILE* 4.0 19.1 - - + -
127B GLY 3.2 4.0 + - - -
128B VAL* 4.2 18.2 - - + -
129B TYR 2.9 25.3 + - - -
130B ILE* 4.8 3.1 - - + -
144B TRP* 4.4 7.6 - - + -
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Residues in contact with PHE 99 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68B VAL 2.7 12.9 + - - +
69B LEU* 3.3 20.0 - - + -
70B VAL 2.7 33.1 + - - +
71B ALA* 5.5 0.4 - - + -
92B TYR* 3.3 44.9 - + + -
93B ASP* 4.5 7.6 - - + -
96B PHE* 3.6 28.9 - + + -
98B ILE* 1.3 77.0 - - - +
100B VAL* 1.3 56.4 + - - +
101B MET* 3.6 41.1 - - + -
129B TYR* 3.3 36.3 - + + -
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Residues in contact with VAL 100 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70B VAL* 3.2 21.3 - - + +
78B LEU* 5.8 0.2 - - + -
98B ILE* 3.7 23.6 - - + -
99B PHE* 1.3 81.0 - - - +
101B MET* 1.3 64.0 + - - +
103B ASN* 3.6 15.3 - - - +
112B LEU* 4.0 16.4 - - + -
115B LEU* 4.3 17.3 - - + -
129B TYR* 2.8 12.4 + - - +
130B ILE* 3.3 14.6 - - + -
131B GLU 3.0 25.1 + - - -
133B ASN* 3.2 13.0 + - - +
136B LEU* 4.3 2.7 - - + -
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Residues in contact with MET 101 (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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70B VAL 2.9 10.5 + - - -
71B ALA* 3.2 26.1 - - + +
72B MET* 3.3 24.8 + - + -
92B TYR* 6.1 0.9 - - - +
99B PHE* 3.6 38.1 - - + -
100B VAL* 1.3 75.0 - - - +
102B LEU* 1.3 90.2 + - + +
103B ASN* 3.2 7.5 + - - +
129B TYR* 4.2 15.7 - - + +
131B GLU 3.4 11.7 - - - +
132B LYS* 5.2 1.8 - - + -
133B ASN* 3.7 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