Contacts of the helix formed by residues 98 - 105 (chain B) in PDB entry 3DLX
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 98 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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66B LEU* 5.0 1.3 - - - -
69B ILE* 4.0 30.3 - - - -
71B GLU* 6.2 0.4 - - - +
74B ILE* 3.7 15.7 - - - +
93B GLY* 4.7 2.9 - - - -
97B PHE* 1.3 82.5 - - - +
99B LEU* 1.3 59.2 + - - -
101B LEU* 3.0 31.9 + - - +
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Residues in contact with LEU 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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61B VAL* 3.7 33.0 - - + -
69B ILE* 5.4 2.4 - - - +
74B ILE* 4.3 8.2 - - + +
87B ALA* 4.1 6.7 - - + -
89B SER* 2.9 42.8 - - - +
91B ASN 4.6 0.4 - - - +
92B ALA* 4.5 12.8 - - - -
93B GLY* 4.3 4.6 - - - +
97B PHE 3.6 0.6 + - - -
98B GLY* 1.3 67.8 - - - -
100B GLY* 1.3 62.1 + - - +
101B LEU 3.0 6.7 + - - -
102B LEU* 3.1 27.8 + - + +
103B LEU* 3.1 27.3 + - + +
108B ILE* 4.3 12.1 - - + +
111B MET* 3.9 16.2 - - + -
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Residues in contact with GLY 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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92B ALA 3.5 7.7 + - - -
94B VAL 3.2 20.2 - - - -
95B ASP* 3.3 15.4 - - - +
97B PHE 3.5 1.2 + - - -
98B GLY 3.1 1.8 - - - -
99B LEU* 1.3 78.0 - - - +
101B LEU* 1.3 54.9 + - - +
103B LEU* 3.7 6.4 - - - +
104B ARG* 3.1 25.1 + - - +
119B ASN* 3.4 17.8 + - - +
121B GLU* 5.5 1.7 - - - +
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Residues in contact with LEU 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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71B GLU* 5.9 3.8 - - + +
74B ILE* 4.5 10.3 - - + -
75B ASP* 5.4 3.8 - - - +
78B LEU* 3.7 30.6 - - + +
95B ASP 4.2 2.0 - - - +
96B ASN* 3.2 31.2 - - - +
97B PHE* 3.7 19.3 - - + -
98B GLY 3.0 25.8 + - - +
99B LEU 3.0 0.6 - - - -
100B GLY* 1.3 75.8 - - - +
102B LEU* 1.3 64.8 + - - +
103B LEU 3.2 0.2 - - - -
104B ARG* 3.6 4.8 + - + +
105B SER* 3.1 23.9 + - - -
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Residues in contact with LEU 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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61B VAL* 6.0 1.1 - - + -
74B ILE* 4.1 16.8 - - + +
77B LEU* 3.5 37.2 - - + -
78B LEU* 3.4 14.8 - - + +
85B LEU* 4.7 5.2 - - + -
99B LEU* 3.1 26.4 + - + +
101B LEU* 1.3 74.6 - - - +
103B LEU* 1.3 61.7 + - - +
105B SER* 3.3 3.4 + - - -
106B LYS 3.2 2.6 + - - -
107B GLN* 2.8 67.1 + - + +
108B ILE* 3.6 24.0 + - + -
209B LEU* 5.7 0.4 - - + -
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Residues in contact with LEU 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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92B ALA* 4.1 9.2 - - + +
99B LEU 3.1 21.6 + - - +
100B GLY* 3.7 16.6 - - - +
102B LEU* 1.3 75.0 - - - +
104B ARG* 1.3 62.0 + - - +
106B LYS* 2.9 19.3 + - - +
108B ILE* 4.4 13.7 - - + +
111B MET* 4.1 15.7 - - + -
119B ASN* 3.9 13.2 - - - +
121B GLU* 5.1 5.2 - - + -
122B PHE* 4.1 18.4 - - + -
125B GLN* 2.8 29.3 + - - +
131B LEU* 3.6 40.4 - - + -
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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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95B ASP 5.0 4.3 - - - +
100B GLY 3.1 17.2 + - - +
101B LEU* 4.2 4.7 - - + +
103B LEU* 1.3 75.0 - - - +
105B SER* 1.3 56.8 + - - +
106B LYS* 3.4 9.4 + - - +
121B GLU* 4.3 21.5 - - + +
125B GLN* 4.4 1.5 + - - +
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Residues in contact with SER 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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78B LEU* 3.8 6.2 - - - +
101B LEU 3.1 15.8 + - - -
102B LEU* 3.3 9.2 + - - -
103B LEU 3.1 0.8 - - - -
104B ARG* 1.3 74.3 - - - +
106B LYS* 1.3 67.8 + - - +
107B GLN* 2.6 35.2 + - - +
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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