Contacts of the strand formed by residues 122 - 129 (chain B) in PDB entry 2O6F
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 GLY 122 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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85A GLY 3.0 19.8 + - - -
86A TYR 5.3 0.2 - - - -
87A GLY 5.3 1.8 - - - -
118B ASN* 4.0 1.1 - - - -
119B ALA 2.9 28.9 + - - -
120B GLY 3.3 1.8 + - - -
121B ASP* 1.3 79.8 - - - +
123B PRO* 1.3 72.1 - - - +
124B HIS* 2.9 12.7 - - - -
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Residues in contact with PRO 123 (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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85A GLY 4.2 3.6 - - - +
86A TYR* 5.1 6.5 - - + -
87A GLY 5.0 8.5 - - - +
90A ASP* 6.0 0.9 - - - +
93A PRO* 6.1 1.3 - - + -
152A TYR* 3.7 9.9 - - - +
74B ASP* 4.0 2.4 - - - +
76B HIS* 5.5 5.1 + - - +
91B PHE* 3.8 46.6 - - + -
117B MET 3.3 7.6 - - - +
118B ASN* 3.3 16.3 - - - +
122B GLY* 1.3 83.8 - - - +
124B HIS* 1.3 71.5 + - - +
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Residues in contact with HIS 124 (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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155A HIS* 5.0 2.0 - - - -
72B GLU* 3.3 41.5 + - + -
73B ALA 4.3 0.7 - - - -
74B ASP* 2.6 33.4 + - - +
91B PHE* 4.4 8.9 - - - -
115B ALA 3.7 0.2 - - - +
116B PRO* 3.5 3.8 - - - +
117B MET* 2.8 36.7 + - + +
119B ALA* 3.9 10.3 - - + -
121B ASP* 2.7 39.3 + - - -
122B GLY 2.9 24.5 + - - -
123B PRO* 1.3 77.6 + - - +
125B TYR* 1.3 74.6 + - - +
126B GLY 3.9 0.6 + - - +
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Residues in contact with TYR 125 (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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94A TYR* 3.9 11.2 - - - -
72B GLU* 3.4 2.4 - - - -
73B ALA* 2.8 50.1 + - + +
75B ILE* 3.8 29.6 - - + -
91B PHE* 3.4 21.1 - + - -
92B VAL 2.6 30.1 + - - -
93B PRO* 3.2 8.3 - - - +
94B TYR 3.3 0.2 + - - -
95B LEU* 3.1 42.2 + - + +
97B VAL* 3.8 15.0 - - + -
114B PHE* 3.9 16.9 - - + -
115B ALA* 3.4 4.7 - - - -
116B PRO* 4.2 21.1 - - + -
124B HIS* 1.3 72.3 - - - +
126B GLY* 1.3 58.5 + - - +
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Residues in contact with GLY 126 (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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61B GLN* 3.3 5.2 + - - -
70B HIS* 3.9 11.4 - - - -
71B ILE 3.3 9.4 - - - -
72B GLU* 4.4 2.5 - - - -
114B PHE* 3.3 4.8 - - - +
115B ALA 2.8 30.9 + - - -
117B MET* 3.4 16.2 - - - +
124B HIS 3.9 1.6 - - - -
125B TYR* 1.3 75.5 - - - +
127B ALA* 1.3 63.5 + - - +
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Residues in contact with ALA 127 (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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61B GLN* 3.2 21.3 - - + +
70B HIS* 3.3 9.3 - - - -
71B ILE 2.8 37.7 + - - +
112B VAL* 3.6 31.2 - - + -
113B MET 4.3 0.2 - - - +
114B PHE* 3.6 11.0 - - + -
126B GLY* 1.3 76.4 - - - +
128B ASN* 1.3 65.1 - - - +
129B VAL* 3.6 3.0 - - + +
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Residues in contact with ASN 128 (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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51B PRO* 3.8 0.7 - - - +
52B VAL* 2.8 38.4 + - - +
54B MET* 3.5 15.4 - - + +
61B GLN* 2.9 12.8 + - - +
62B PRO* 3.1 44.0 + - + +
63B SER* 3.6 2.4 + - - +
64B LYS* 3.6 13.9 - - - +
67B ALA* 3.9 11.0 - - + -
69B CYS 3.4 3.4 - - - -
70B HIS* 2.8 22.8 + - - +
112B VAL* 5.0 1.4 - - - +
127B ALA* 1.3 77.9 - - - +
129B VAL* 1.3 59.9 + - - +
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Residues in contact with VAL 129 (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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62B PRO* 4.0 5.3 - - - +
67B ALA* 4.2 0.2 - - - +
68B ASP* 2.9 23.7 + - - +
69B CYS* 2.7 28.0 + - - +
71B ILE* 3.7 25.6 - - + -
101B LEU* 4.0 24.2 - - + -
110B GLN* 4.2 5.8 - - - +
112B VAL* 4.0 23.3 - - + -
127B ALA 3.6 11.9 - - - +
128B ASN* 1.3 78.8 - - - +
130B LYS* 1.3 74.1 + - - +
131B PHE* 4.2 9.2 - - + +
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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