Contacts of the helix formed by residues 104 - 118 (chain B) in PDB entry 3L6D
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 ALA 104 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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103B ASN* 1.3 94.9 - - - +
105B GLN* 1.3 59.6 + - - +
106B ASP* 3.4 9.9 - - - +
107B GLU* 2.7 50.2 + - + +
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Residues in contact with GLN 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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200A PHE* 6.2 0.3 - - - -
255A SER* 6.0 2.3 - - - -
103B ASN* 4.2 2.1 + - - +
104B ALA* 1.3 72.2 - - - +
106B ASP* 1.3 66.6 + - - +
108B GLY* 3.7 6.4 + - - -
109B LEU* 4.3 5.9 + - + +
169B TRP* 4.1 19.3 + - - +
170B ASP* 3.7 22.2 + - - +
173B LEU* 3.5 35.2 - - + +
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Residues in contact with ASP 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 ALA* 4.1 7.3 - - - +
105B GLN* 1.3 82.2 + - + +
107B GLU* 1.3 78.4 + - - +
109B LEU* 3.2 20.9 + - - +
110B ALA* 3.5 9.9 + - - +
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Residues in contact with GLU 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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76B ASN* 3.5 39.2 + - - +
80B HIS* 5.1 0.3 + - - -
103B ASN* 3.3 13.1 - - - +
104B ALA* 2.7 49.5 + - + +
106B ASP* 1.3 87.7 - - - +
108B GLY* 1.3 60.7 + - - +
110B ALA* 3.2 10.1 + - - +
111B LEU* 3.0 24.6 + - - +
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Residues in contact with GLY 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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103B ASN* 3.1 23.8 + - - -
104B ALA 3.6 0.6 + - - -
105B GLN 3.7 1.2 + - - -
106B ASP 3.2 0.8 - - - -
107B GLU* 1.3 77.2 - - - +
109B LEU* 1.3 57.6 + - - +
111B LEU* 3.2 7.6 + - - +
112B GLN* 2.9 30.1 + - - +
122B TYR* 4.1 4.8 - - - -
169B TRP* 3.7 25.1 - - - -
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Residues in contact with LEU 109 (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 GLN* 4.9 5.8 - - + +
106B ASP* 3.2 12.4 + - - +
108B GLY* 1.3 75.9 - - - +
110B ALA* 1.3 57.4 + - - +
112B GLN* 3.7 24.8 - - - +
113B GLY* 2.9 25.1 + - - -
169B TRP* 3.8 43.1 - - + +
170B ASP* 5.7 1.8 - - - +
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Residues in contact with ALA 110 (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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80B HIS* 5.1 12.8 - - + +
106B ASP 3.5 7.5 + - - +
107B GLU* 3.2 12.0 + - - +
109B LEU* 1.3 79.7 - - - +
111B LEU* 1.3 57.1 + - - +
113B GLY* 3.3 2.4 + - - +
114B LEU* 2.9 28.2 + - - +
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Residues in contact with LEU 111 (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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76B ASN* 3.4 23.8 - - - +
79B THR* 3.5 28.3 - - + +
80B HIS* 3.7 27.1 - - + +
83B LEU* 4.3 12.3 - - + -
99B ASP* 3.9 18.8 - - - +
103B ASN* 3.8 9.6 - - - +
107B GLU 3.0 18.0 + - - +
108B GLY* 3.6 5.4 - - - +
110B ALA* 1.3 73.7 - - - +
112B GLN* 1.3 66.5 + - - +
114B LEU* 3.5 6.3 - - + +
115B VAL* 2.9 31.7 + - + +
122B TYR* 4.0 16.8 - - + +
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Residues in contact with GLN 112 (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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108B GLY 2.9 16.8 + - - +
109B LEU* 3.7 22.6 - - - +
111B LEU* 1.3 75.5 - - - +
113B GLY* 1.3 56.9 + - - +
115B VAL* 3.2 0.7 + - - +
116B ASN* 2.9 50.0 + - - +
122B TYR* 3.7 27.4 + - + -
145B GLY* 3.1 40.6 + - - -
146B ASP* 4.2 1.9 - - + +
169B TRP* 3.9 13.7 - - + -
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Residues in contact with GLY 113 (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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109B LEU 2.9 16.3 + - - -
110B ALA* 3.6 4.3 - - - -
111B LEU 3.2 0.4 - - - -
112B GLN* 1.3 76.1 - - - +
114B LEU* 1.3 51.1 + - - +
116B ASN* 3.4 6.1 + - - +
117B GLN* 2.8 40.0 + - - +
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Residues in contact with LEU 114 (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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80B HIS* 4.1 28.9 - - + +
83B LEU* 4.1 35.9 - - + +
89B ALA* 6.3 2.0 - - + -
92B LEU* 4.3 12.8 - - + -
110B ALA 2.9 13.1 + - - +
111B LEU* 3.3 11.6 + - + +
113B GLY* 1.3 75.7 - - - +
115B VAL* 1.3 63.9 + - + +
117B GLN* 3.3 12.0 + - - +
118B ALA* 3.2 20.5 + - + +
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Residues in contact with VAL 115 (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 LEU* 4.7 12.6 - - + -
92B LEU* 4.5 19.0 - - + +
97B ILE* 4.1 23.3 - - + -
111B LEU* 2.9 21.9 + - + +
112B GLN 3.9 2.2 - - - +
114B LEU* 1.3 77.1 - - + +
116B ASN* 1.3 61.2 + - - +
118B ALA* 3.2 9.5 + - - +
119B GLY 3.3 0.2 + - - -
120B GLY* 2.9 27.1 + - - -
121B HIS 3.5 40.2 - - - +
122B TYR* 4.0 19.1 - - + +
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Residues in contact with ASN 116 (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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112B GLN* 2.9 36.8 + - - +
113B GLY* 3.7 6.4 + - - +
115B VAL* 1.3 74.1 - - - +
117B GLN* 1.3 57.8 + - - +
119B GLY* 2.8 23.0 + - - -
120B GLY 3.2 18.6 + - - -
121B HIS* 4.1 1.8 + - - +
122B TYR* 4.0 16.6 - - - +
146B ASP* 4.8 7.1 + - - +
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Residues in contact with GLN 117 (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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113B GLY 2.8 22.8 + - - +
114B LEU* 3.5 11.7 - - - +
116B ASN* 1.3 73.4 - - - +
118B ALA* 1.3 59.6 + - - +
119B GLY 3.5 0.5 + - - -
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Residues in contact with ALA 118 (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 ALA* 3.5 29.7 - - + +
92B LEU* 3.8 17.5 - - + -
93B ALA* 3.4 20.8 + - - +
114B LEU* 3.2 10.0 + - + +
115B VAL 3.2 9.1 + - - +
116B ASN 3.1 0.6 - - - -
117B GLN* 1.3 78.8 - - - +
119B GLY* 1.3 60.3 + - - +
120B GLY 3.4 0.2 - - - -
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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