Contacts of the helix formed by residues 91 - 102 (chain B) in PDB entry 4YET
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 91 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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90B THR* 1.3 74.5 - - - +
92B PRO* 1.3 77.6 - - - +
94B ARG* 3.0 20.3 + - - +
95B LYS* 3.6 3.5 + - - +
189B ASN* 4.1 2.7 - - - -
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Residues in contact with PRO 92 (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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91B GLY* 1.3 82.4 - - - +
93B ILE* 1.3 60.3 + - - +
95B LYS* 3.2 10.4 + - + +
96B LYS* 3.1 24.7 + - + +
189B ASN* 3.5 21.5 - - + +
192B LEU* 3.8 17.3 - - + -
193B GLU* 6.6 0.2 - - + -
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Residues in contact with ILE 93 (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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89B PRO* 4.1 3.8 - - + -
90B THR 3.3 13.5 - - - +
92B PRO* 1.3 72.5 - - - +
94B ARG* 1.3 65.8 + - - +
96B LYS* 3.4 8.7 + - + -
97B ILE* 3.0 37.4 + - + +
126B LEU* 3.8 15.3 - - + -
134B ALA* 5.7 0.9 - - + -
154B LEU* 3.8 29.2 - - + -
185B TRP* 3.9 26.5 - - + +
188B ALA* 3.9 17.5 - - + -
189B ASN* 2.8 29.9 + - - +
192B LEU* 3.6 12.5 - - + +
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Residues in contact with ARG 94 (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* 3.0 32.3 + - - +
89B PRO* 3.3 51.4 + - + +
90B THR* 4.1 4.5 - - - +
91B GLY 3.0 12.8 + - - +
93B ILE* 1.3 82.1 - - - +
95B LYS* 1.3 56.9 + - - +
97B ILE* 3.3 3.0 + - - +
98B GLU* 2.9 56.3 + - + +
104B PHE* 5.3 2.1 - - - +
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Residues in contact with LYS 95 (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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91B GLY 3.6 3.8 + - - +
92B PRO* 3.2 12.9 + - + +
94B ARG* 1.3 80.0 - - - +
96B LYS* 1.3 59.0 + - + +
98B GLU* 3.3 8.5 + - - +
99B GLU* 2.9 44.9 + - + +
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Residues in contact with LYS 96 (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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92B PRO* 3.1 15.8 + - + +
93B ILE* 3.8 12.8 - - + +
95B LYS* 1.3 76.5 - - + +
97B ILE* 1.3 62.9 + - - +
99B GLU* 3.4 20.5 + - - +
100B LYS* 3.2 24.4 + - - +
128B LEU* 4.3 14.7 - - + +
132B GLY* 2.8 29.7 + - - +
133B THR* 5.1 0.7 - - - -
134B ALA* 4.1 21.9 + - + +
192B LEU* 4.4 23.1 - - + -
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Residues in contact with ILE 97 (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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89B PRO* 4.1 11.2 - - + -
93B ILE* 3.0 33.4 + - + +
94B ARG* 3.7 4.7 - - - +
96B LYS* 1.3 77.3 - - + +
98B GLU* 1.3 58.1 + - + +
100B LYS 3.4 0.5 + - - -
101B PHE* 2.8 38.3 + - + +
103B SER 4.0 9.9 - - - +
104B PHE* 4.1 12.1 - - + +
107B PHE* 3.6 47.8 - - + -
126B LEU* 4.6 7.9 - - + -
134B ALA* 5.2 1.3 - - + -
185B TRP* 3.7 31.9 - - + -
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Residues in contact with GLU 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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94B ARG* 2.9 58.5 + - + +
95B LYS* 3.8 6.9 - - - +
97B ILE* 1.3 78.5 - - + +
99B GLU* 1.3 61.6 + - + +
102B GLY* 2.8 40.1 + - - +
103B SER* 4.2 17.6 - - - +
104B PHE* 4.8 4.4 + - + +
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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
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95B LYS* 2.9 29.5 + - - +
96B LYS* 3.7 28.5 + - - +
97B ILE 3.3 0.2 - - - -
98B GLU* 1.3 76.8 - - + +
100B LYS* 1.3 59.2 + - + +
133B THR* 6.5 1.6 - - + -
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Residues in contact with LYS 100 (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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96B LYS 3.2 15.5 + - - +
99B GLU* 1.3 78.6 - - - +
101B PHE* 1.3 92.3 + - + +
102B GLY 3.6 0.4 - - - -
129B LYS* 5.3 4.0 - - - +
133B THR* 5.4 7.6 - - - +
134B ALA* 3.3 28.5 - - + +
135B ASP* 3.6 28.1 + - - -
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Residues in contact with PHE 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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97B ILE* 2.8 26.6 + - - +
100B LYS* 1.3 104.1 - - + +
102B GLY* 1.3 57.9 + - - +
103B SER 3.2 15.5 - - - +
106B ALA* 3.2 21.0 - - + +
107B PHE* 3.5 49.6 - + + +
110B ASP* 3.5 32.3 - - + -
126B LEU* 4.7 8.7 - - + -
134B ALA* 4.9 3.6 - - + -
135B ASP* 4.6 0.9 - - - -
136B ILE* 3.9 29.2 - - + -
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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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98B GLU* 2.8 30.4 + - - +
100B LYS 3.6 1.0 - - - -
101B PHE* 1.3 75.8 - - - +
103B SER* 1.3 62.0 + - - +
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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