Contacts of the helix formed by residues 106 - 120 (chain B) in PDB entry 3D9L
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 ASP 106 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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56B PRO 4.5 3.3 - - - +
57B GLU* 4.7 8.8 - - - +
60B VAL* 3.7 29.0 - - + +
102B CYS* 3.8 10.3 - - + -
103B PRO* 2.7 33.2 + - + +
105B ASP* 1.3 79.0 - - - +
107B LYS* 1.3 64.6 + - - +
108B SER 3.2 2.9 - - - -
109B LYS* 3.1 44.8 + - - +
110B ILE* 3.5 5.9 + - - +
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Residues in contact with LYS 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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100B TYR* 4.0 25.4 - - + -
102B CYS* 3.8 11.6 - - - -
103B PRO 3.6 2.6 + - - +
104B GLY* 3.4 22.9 + - - +
105B ASP 3.3 1.2 - - - -
106B ASP* 1.3 79.7 - - - +
108B SER* 1.3 60.7 + - - +
110B ILE* 3.3 15.3 + - - +
111B VAL* 3.3 15.3 + - + +
135B ALA* 4.0 17.7 - - + +
138B LEU* 3.8 39.0 + - + +
139B GLU* 3.6 31.4 + - - +
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Residues in contact with SER 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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104B GLY 4.8 0.4 + - - -
105B ASP 3.9 12.8 + - - -
107B LYS* 1.3 78.7 - - - +
109B LYS* 1.3 62.0 + - - +
111B VAL* 3.6 7.8 + - - +
112B ARG* 3.1 27.5 + - - +
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Residues in contact with LYS 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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60B VAL* 4.1 30.3 - - + -
63B LEU* 5.2 0.2 - - - -
64B TYR* 4.3 13.9 + - + +
105B ASP* 3.7 13.3 + - - +
106B ASP* 3.1 35.7 + - - +
108B SER* 1.3 80.9 - - - +
110B ILE* 1.3 64.2 + - - +
112B ARG* 3.6 8.8 + - - +
113B VAL* 3.3 26.7 + - - +
3Z PRO* 5.7 0.2 - - - +
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Residues in contact with ILE 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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60B VAL* 4.2 10.8 - - + -
63B LEU* 3.7 18.8 - - + +
96B PHE* 3.5 31.0 - - + -
99B LEU* 3.5 33.9 - - + +
100B TYR* 3.6 35.9 - - + +
102B CYS* 3.7 17.7 - - + -
106B ASP 3.9 7.6 - - - +
107B LYS* 3.3 7.7 + - - +
109B LYS* 1.3 77.0 - - - +
111B VAL* 1.3 62.3 + - - +
113B VAL* 3.1 6.6 + - - +
114B LEU* 3.0 20.9 + - + +
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Residues in contact with VAL 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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100B TYR* 4.4 5.6 - - + +
107B LYS* 3.3 15.7 + - + +
108B SER* 3.9 9.2 - - - +
110B ILE* 1.3 71.6 - - - +
112B ARG* 1.3 67.2 + - - +
114B LEU* 3.2 10.1 + - - +
115B ASN* 2.9 35.1 + - - +
132B LEU* 3.9 19.1 - - + -
135B ALA* 3.7 29.8 - - + -
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Residues in contact with ARG 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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64B TYR* 5.0 3.4 + - - -
108B SER 3.1 19.3 + - - +
109B LYS* 3.7 10.3 - - - +
110B ILE 3.3 0.2 - - - -
111B VAL* 1.3 78.8 - - - +
113B VAL* 1.3 61.4 + - - +
115B ASN* 3.4 7.9 + - + +
116B LEU* 3.0 35.8 + - + +
2Z SEP 2.5 45.0 + - - -
3Z PRO* 3.4 19.0 - - - +
4Z THR* 3.4 19.8 - - - +
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Residues in contact with VAL 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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63B LEU* 3.9 19.7 - - + -
64B TYR* 3.6 29.4 - - + -
67B ASP* 4.2 7.4 - - + +
109B LYS 3.3 14.1 + - - +
110B ILE 3.1 10.3 + - - +
112B ARG* 1.3 78.6 - - + +
114B LEU* 1.3 57.7 + - - +
116B LEU* 3.2 8.8 + - + +
117B TRP* 2.8 65.4 + - + +
3Z PRO* 3.9 15.7 - - + -
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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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96B PHE* 3.6 28.7 - - + -
100B TYR* 3.3 27.4 - - - +
110B ILE* 3.0 18.6 + - + +
111B VAL* 3.2 8.9 + - - +
113B VAL* 1.3 77.2 - - - +
115B ASN* 1.3 56.9 + - - +
117B TRP* 3.4 16.8 + - + +
118B GLN* 3.0 28.8 + - - +
128B ILE* 3.7 14.0 - - + +
131B LEU* 3.6 33.7 - - + -
132B LEU* 3.7 28.0 - - + +
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Residues in contact with ASN 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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111B VAL* 2.9 31.6 + - - +
112B ARG* 3.7 7.6 - - + +
114B LEU* 1.3 73.8 - - - +
116B LEU* 1.3 61.6 + - + +
118B GLN* 3.5 10.5 + - - +
119B LYS* 2.9 30.5 + - - +
132B LEU* 3.7 24.6 - - - +
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Residues in contact with LEU 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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67B ASP* 6.1 0.4 - - - +
112B ARG* 3.0 35.8 + - + +
113B VAL* 3.2 4.9 + - - +
115B ASN* 1.3 74.1 - - + +
117B TRP* 1.3 63.4 + - + +
119B LYS* 3.3 25.3 + - + -
120B ASN* 2.8 46.0 + - - +
122B VAL* 5.2 0.2 - - - -
3Z PRO* 3.7 34.8 - - + +
4Z THR* 3.9 28.3 - - + -
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Residues in contact with TRP 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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63B LEU* 3.5 24.7 - - + -
66B ILE* 3.9 24.9 - - + -
67B ASP* 2.7 36.7 + - - +
70B VAL* 5.7 1.1 - - + +
71B ARG* 5.2 1.5 - - - +
92B ILE* 4.4 6.3 - - + -
96B PHE* 3.7 26.5 - + - -
113B VAL* 2.8 31.2 + - + +
114B LEU* 3.5 22.4 - - + +
115B ASN 3.3 0.2 - - - -
116B LEU* 1.3 80.7 - - + +
118B GLN* 1.3 55.7 + - - +
121B ASN* 3.1 6.4 + - - -
122B VAL* 2.8 57.4 + - + +
123B PHE* 3.5 33.3 + + + -
128B ILE* 3.6 11.2 - - + -
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Residues in contact with GLN 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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114B LEU 3.0 16.4 + - - +
115B ASN* 3.9 10.5 + - - +
117B TRP* 1.3 73.6 - - - +
119B LYS* 1.3 67.9 + - - +
121B ASN* 3.4 17.3 + - - +
123B PHE 4.3 3.5 - - - +
125B SER* 3.6 28.8 - - - +
128B ILE* 3.4 30.0 - - + +
129B GLN* 3.5 22.3 + - - +
132B LEU* 4.4 8.3 - - - +
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Residues in contact with LYS 119 (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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115B ASN 2.9 19.7 + - - +
116B LEU* 3.5 26.2 - - + +
118B GLN* 1.3 79.2 - - - +
120B ASN* 1.3 75.4 + - - +
121B ASN* 3.3 8.5 + - - +
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Residues in contact with ASN 120 (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 ARG* 3.9 10.9 + - - -
79B GLN* 5.3 1.2 + - - -
116B LEU* 2.8 40.1 + - - +
119B LYS* 1.3 92.1 + - - +
121B ASN* 1.3 70.8 + - - +
122B VAL* 3.3 14.5 + - + +
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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