Contacts of the helix formed by residues 91 - 100 (chain B) in PDB entry 1D7K
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 SER 91 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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398A ASN 3.1 21.9 + - - -
399A GLY* 3.7 8.5 - - - -
400A PHE* 3.6 19.3 - - - -
89B CYS 3.7 0.6 - - - -
90B ALA* 1.3 79.9 - - - +
92B LYS* 1.3 60.2 + - - +
93B THR* 3.5 5.0 + - - -
94B GLU* 3.3 14.3 + - - +
95B ILE* 3.0 34.5 + - - +
110B TYR* 3.9 5.1 - - - -
119B GLN* 3.4 13.7 - - - -
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Residues in contact with LYS 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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36A ASP* 4.9 10.3 + - - -
38A ASP* 5.8 2.2 + - - -
91B SER* 1.3 69.8 - - - +
93B THR* 1.3 63.9 + - + +
95B ILE* 3.3 5.5 + - - +
96B GLN* 2.9 60.8 + - - +
110B TYR* 5.0 0.4 + - - -
118B SER 5.7 1.3 - - - +
119B GLN* 3.0 31.0 + - + +
122B TYR* 4.0 41.3 - - + -
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Residues in contact with THR 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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399A GLY* 3.0 36.8 + - - +
401A GLN* 3.2 27.0 + - + +
91B SER* 3.3 2.9 + - - +
92B LYS* 1.3 82.5 - - + +
94B GLU* 1.3 53.7 + - - +
96B GLN* 3.8 18.1 + - - +
97B LEU* 3.0 27.0 + - - +
119B GLN* 6.3 0.9 - - - +
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Residues in contact with GLU 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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398A ASN* 3.3 38.2 + - - +
399A GLY* 4.0 4.2 + - - +
68B VAL* 3.8 27.2 - - + +
69B LLP 3.2 28.0 + - - +
72B ASP* 5.5 3.6 - - + +
88B ASP 4.3 0.7 - - - +
89B CYS* 3.6 16.7 - - + -
90B ALA* 2.8 28.9 + - - +
91B SER* 3.3 10.5 + - - +
93B THR* 1.3 72.1 - - - +
95B ILE* 1.3 68.0 + - - +
97B LEU* 3.2 8.5 + - + +
98B VAL* 3.0 27.7 + - - +
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Residues in contact with ILE 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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89B CYS* 4.0 21.0 - - + -
91B SER 3.0 23.6 + - - +
92B LYS* 3.8 8.1 - - - +
94B GLU* 1.3 76.6 - - - +
96B GLN* 1.3 58.6 + - - +
98B VAL* 3.8 1.2 - - - +
99B GLN* 2.8 50.3 + - - +
108B ILE* 4.2 10.7 - - + +
110B TYR* 4.2 23.8 - - + -
119B GLN 5.8 0.4 - - - +
122B TYR* 3.9 19.7 - - + +
123B ALA* 4.2 26.2 - - + -
128B VAL* 4.1 15.9 - - + -
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Residues in contact with GLN 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 LYS* 2.9 57.3 + - - +
93B THR* 3.8 20.0 - - - +
95B ILE* 1.3 75.4 - - - +
97B LEU* 1.3 64.3 + - - +
99B GLN* 3.7 7.9 - - - +
100B SER* 2.9 24.9 + - - -
122B TYR* 3.0 30.8 - - + +
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Residues in contact with LEU 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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68B VAL* 4.1 17.3 - - + -
72B ASP* 3.7 38.8 - - + +
74B LYS* 4.7 17.9 - - + +
77B VAL* 4.5 7.9 - - + -
93B THR 3.0 19.3 + - - +
94B GLU* 3.5 6.1 - - + +
96B GLN* 1.3 77.6 - - - +
98B VAL* 1.3 66.4 + - + +
100B SER* 2.9 23.9 + - - +
101B LEU* 3.4 31.4 - - + +
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Residues in contact with VAL 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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68B VAL* 4.0 25.8 - - + -
77B VAL* 4.2 14.4 - - + -
87B PHE* 3.7 24.2 - - + -
89B CYS* 4.0 6.1 - - - -
94B GLU 3.0 15.2 + - - +
95B ILE 4.0 1.8 - - - +
97B LEU* 1.3 81.1 - - + +
99B GLN* 1.3 68.6 + - - +
101B LEU* 3.1 16.1 + - - +
102B GLY 3.4 6.8 + - - -
103B VAL* 3.6 35.2 - - + +
108B ILE* 4.2 13.0 - - + -
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Residues in contact with GLN 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 ILE* 2.8 30.8 + - + +
96B GLN* 3.7 9.6 - - - +
98B VAL* 1.3 71.1 - - - +
100B SER* 1.3 56.4 + - - +
102B GLY* 3.0 21.7 + - - -
103B VAL 3.7 17.4 + - - +
105B PRO* 4.4 11.7 - - - +
108B ILE* 3.8 16.6 - - - +
122B TYR* 5.3 4.3 - - - +
126B ASN* 3.2 41.3 + - + +
128B VAL* 4.2 5.7 - - - +
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Residues in contact with SER 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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74B LYS* 5.1 4.0 + - - -
96B GLN 2.9 17.7 + - - -
97B LEU* 2.9 20.8 + - - +
99B GLN* 1.3 70.1 - - - +
101B LEU* 1.3 69.9 + - - +
102B GLY* 3.3 3.3 - - - -
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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