Contacts of the helix formed by residues 94 - 105 (chain B) in PDB entry 1D8L
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 94 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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33B THR* 5.2 9.9 - - - +
89B ILE 4.4 0.5 - - - +
90B LEU* 4.8 4.7 - - - +
93B MET* 1.3 82.6 - - - +
95B ALA* 1.3 66.2 + - - +
96B GLN* 2.9 19.1 + - - +
97B GLN* 3.0 30.8 + - - +
98B PHE* 3.7 15.4 + - - +
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Residues in contact with ALA 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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67B GLN* 6.0 0.4 - - + -
68B GLU* 4.5 23.1 - - + +
71B LEU* 4.3 14.7 - - + +
90B LEU* 4.5 9.2 - - + +
94B SER* 1.3 75.2 + - - +
96B GLN* 1.3 68.3 + - - +
97B GLN 3.4 0.7 + - - -
98B PHE* 3.5 4.5 + - - +
99B VAL* 3.4 22.2 + - - +
139B LEU* 3.7 26.0 - - + +
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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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94B SER* 2.9 8.2 + - - +
95B ALA* 1.3 81.1 - - - +
97B GLN* 1.3 66.6 + - + +
99B VAL* 3.4 11.3 + - - +
100B ASN* 3.5 25.6 + - - +
138B ASP 5.2 0.3 - - - +
139B LEU* 3.2 41.6 + - + +
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Residues in contact with GLN 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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93B MET* 3.7 23.9 - - + +
94B SER* 3.0 41.8 + - - +
95B ALA 3.4 0.2 - - - -
96B GLN* 1.3 75.1 - - + +
98B PHE* 1.3 64.8 + - - +
100B ASN* 3.0 23.5 + - - +
101B ALA* 3.3 10.5 + - - +
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Residues in contact with PHE 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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71B LEU* 3.5 30.3 - - + -
75B LEU* 3.9 8.5 - - + -
89B ILE* 3.4 36.8 - - + +
90B LEU* 5.9 0.2 - - + -
93B MET* 4.3 10.6 - - - -
94B SER 3.7 8.8 + - - +
95B ALA* 3.5 9.6 + - - +
97B GLN* 1.3 77.7 - - - +
99B VAL* 1.3 63.3 + - - +
101B ALA* 3.3 10.3 + - - +
102B VAL* 3.2 31.5 + - + +
110B LEU* 4.2 23.6 - - + -
124B LEU* 4.8 6.3 - - + -
128B MET* 3.5 29.2 - - + -
132B PHE* 3.5 25.8 - + - -
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Residues in contact with VAL 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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71B LEU* 4.4 3.8 - - + -
95B ALA 3.4 13.4 + - - +
96B GLN* 3.4 9.6 + - - +
97B GLN 3.2 1.2 + - - -
98B PHE* 1.3 80.0 - - + +
100B ASN* 1.3 64.2 + - - +
102B VAL* 3.5 2.1 + - - +
103B GLU* 3.3 26.0 + - + +
132B PHE* 3.5 39.9 - - + -
139B LEU* 4.1 24.0 - - + -
140B PHE 3.9 23.6 - - - +
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Residues in contact with ASN 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 GLN* 3.5 30.1 + - - +
97B GLN* 3.0 10.3 + - - +
99B VAL* 1.3 77.7 - - - +
101B ALA* 1.3 54.7 + - - +
103B GLU* 3.0 7.7 + - - +
104B ARG* 2.8 49.2 + - + +
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Residues in contact with ALA 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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93B MET* 5.9 0.4 - - - -
97B GLN 3.3 7.2 + - - +
98B PHE* 3.3 15.2 + - - +
100B ASN* 1.3 79.8 - - - +
102B VAL* 1.3 52.8 + - - +
104B ARG* 3.9 15.4 - - - +
105B GLU* 2.7 29.8 + - - -
106B GLU 3.1 21.9 + - - +
109B ALA* 4.9 8.3 - - + -
110B LEU* 4.4 20.0 - - + -
125B ILE* 4.0 3.4 - - - +
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Residues in contact with VAL 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 PHE* 3.2 36.2 + - + +
100B ASN 3.2 0.4 - - - -
101B ALA* 1.3 76.9 - - + +
103B GLU* 1.3 56.5 + - - +
104B ARG 3.6 0.2 + - - -
105B GLU 3.6 1.4 + - - -
110B LEU* 5.4 1.8 - - + -
124B LEU 5.3 0.2 - - - -
125B ILE* 3.2 41.7 - - + +
128B MET* 3.5 19.1 - - + -
129B LYS* 2.6 58.2 + - + +
132B PHE* 4.0 14.8 - - + -
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Residues in contact with GLU 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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99B VAL* 3.3 20.5 + - + +
100B ASN* 3.0 9.8 + - - +
102B VAL* 1.3 78.0 - - - +
104B ARG* 1.3 59.1 + - - +
105B GLU* 4.8 4.7 - - - +
129B LYS* 4.6 14.4 + - - +
132B PHE* 4.2 23.1 - - + +
133B LYS* 6.1 0.9 - - - +
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Residues in contact with ARG 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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100B ASN* 2.8 29.2 + - + +
101B ALA* 3.7 11.3 - - - +
103B GLU* 1.3 72.6 - - - +
105B GLU* 1.3 73.3 + - - +
106B GLU* 3.1 49.6 + - + +
109B ALA* 4.6 12.1 - - - +
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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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101B ALA 2.7 18.0 + - - -
103B GLU 3.5 3.4 - - - +
104B ARG* 1.3 79.5 - - - +
106B GLU* 1.3 57.8 + - - +
107B VAL* 3.1 10.1 + - - +
125B ILE* 3.7 19.8 - - + +
126B VAL* 6.0 1.6 - - - +
129B LYS* 3.3 36.4 + - - +
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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