Contacts of the strand formed by residues 97 - 108 (chain B) in PDB entry 2Y1Z
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 VAL 97 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1153A MPD 4.2 23.3 - - + -
93B VAL* 3.6 1.7 - - - -
94B LEU* 2.7 48.6 + - + +
95B GLY 3.4 0.6 - - - -
96B ASP* 1.3 95.4 - - - +
98B ILE* 1.3 75.2 + - - +
121B LYS* 4.2 22.7 - - + -
122B TYR 3.4 10.8 - - - +
123B ARG* 4.6 6.1 - - + -
124B ILE* 4.0 2.1 - - - +
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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
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75B PHE* 4.5 15.7 - - + -
77B VAL* 5.1 2.0 - - + -
91B VAL* 4.5 4.9 - - + -
92B LYS 3.6 6.3 - - - +
93B VAL* 4.7 10.5 - - + +
97B VAL* 1.3 76.5 - - - +
99B GLU* 1.3 71.2 + - - +
100B VAL* 4.0 8.7 - - + -
121B LYS* 3.0 6.1 - - - -
122B TYR* 2.8 64.7 + - + +
124B ILE* 3.7 29.6 - - + -
133B ILE* 4.4 10.3 - - + -
145B VAL* 3.8 32.8 - - + +
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Residues in contact with GLU 99 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90B LYS 3.9 0.6 - - - +
91B VAL* 3.7 0.2 - - - -
92B LYS* 2.8 52.2 + - + +
94B LEU* 3.9 25.4 - - + +
97B VAL* 4.0 0.6 + - + -
98B ILE* 1.3 76.4 - - - +
100B VAL* 1.3 68.8 + - - +
101B HIS* 6.0 2.5 - - - -
119B HIS* 3.2 27.7 + - + -
120B GLY 3.4 2.0 - - - -
121B LYS* 3.6 29.2 + - + -
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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
----------------------------------------------------------
114A ILE* 5.4 0.7 - - + -
79B LEU* 4.1 12.8 - - + -
90B LYS 3.4 4.3 - - - +
91B VAL* 4.2 19.1 - - + -
98B ILE* 4.0 9.0 - - + -
99B GLU* 1.3 81.8 - - - +
101B HIS* 1.3 64.6 + - - +
118B PHE* 4.1 14.6 - - + -
119B HIS* 3.4 7.3 + - - -
120B GLY* 2.8 45.9 + - - +
122B TYR* 3.1 38.8 - - + +
143B LEU* 4.6 3.4 - - + -
145B VAL* 4.4 8.1 - - + -
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Residues in contact with HIS 101 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88B GLU 3.8 1.3 + - - +
89B LEU* 3.5 1.9 - - - -
90B LYS* 2.8 52.2 + - + +
99B GLU* 5.9 3.1 - - + -
100B VAL* 1.3 77.4 - - - +
102B GLY* 1.3 64.1 + - - +
103B LYS* 3.8 29.4 + - + -
117B GLU* 3.2 24.0 + - - +
118B PHE* 3.2 31.3 - - - -
119B HIS* 4.2 17.7 - + + +
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Residues in contact with GLY 102 (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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84B PHE* 3.4 9.4 - - - -
88B GLU 3.4 10.1 - - - -
89B LEU* 4.0 3.1 - - - -
101B HIS* 1.3 77.6 + - - +
103B LYS* 1.3 61.2 + - - +
117B GLU* 3.3 5.9 - - - +
118B PHE* 3.1 52.6 + - - +
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Residues in contact with LYS 103 (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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84B PHE* 3.4 2.3 - - - -
88B GLU* 3.3 29.8 + - - +
101B HIS* 3.8 19.2 - - + +
102B GLY* 1.3 75.0 - - - +
104B HIS* 1.3 62.6 + - - +
105B GLU* 3.4 33.7 + - + -
115B SER* 5.2 3.8 - - - +
116B ARG 3.3 9.0 - - - +
117B GLU* 4.5 21.8 - - + +
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Residues in contact with HIS 104 (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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83B HIS* 3.9 19.8 + - + +
84B PHE* 3.7 16.2 - - + -
88B GLU* 3.1 37.9 - - - +
103B LYS* 1.3 75.0 - - - +
105B GLU* 1.3 66.5 + - - +
106B GLU* 3.5 41.6 + - + +
114B ILE* 3.9 6.5 + - + +
115B SER* 3.4 2.8 - - - -
116B ARG* 2.7 59.5 + - + +
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Residues in contact with GLU 105 (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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88B GLU* 4.7 3.0 + - - +
103B LYS* 3.4 33.4 + - + -
104B HIS* 1.3 83.4 - - - +
106B GLU* 1.3 67.2 + - - +
107B ARG* 4.2 1.5 + - + -
113B PHE* 4.6 17.7 - - + -
114B ILE 3.4 3.6 - - - +
115B SER* 3.8 22.6 + - - +
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Residues in contact with GLU 106 (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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104B HIS* 3.5 33.2 + - + +
105B GLU* 1.3 73.9 - - - +
107B ARG* 1.3 61.2 + - - +
112B GLY 3.9 1.4 - - - +
113B PHE* 3.4 7.3 - - - -
114B ILE* 2.9 52.4 + - + +
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Residues in contact with ARG 107 (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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105B GLU* 4.2 1.9 + - + -
106B GLU* 1.3 73.9 - - - +
108B GLN* 1.3 62.8 + - - +
109B ASP* 4.1 32.0 + - - +
112B GLY 3.7 4.0 - - - +
113B PHE* 4.3 20.6 - - + -
1152B MRD 4.3 25.6 + - - +
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Residues in contact with GLN 108 (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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68A MET* 6.0 1.6 - - - +
106B GLU 4.2 0.2 - - - -
107B ARG* 1.3 75.0 - - - +
109B ASP* 1.3 60.7 + - - +
111B HIS* 2.7 45.9 + - + +
112B GLY* 2.8 30.7 + - - +
1152B MRD 4.3 1.3 - - - +
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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