Contacts of the helix formed by residues 106 - 116 (chain B) in PDB entry 1SAW
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 ARG 106 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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67B ASN* 3.0 25.9 + - - +
69B HIS* 3.1 35.7 + - + +
71B GLU* 3.1 30.9 + - - +
104B THR* 3.0 14.9 + - - +
105B ALA* 1.3 69.6 - - - +
107B ASP* 1.3 66.4 + - - +
109B GLN* 3.0 33.8 + - - +
110B ASP* 3.0 42.9 + - - +
113B LYS* 5.5 1.4 - - - +
123B LYS* 4.5 0.2 - - - +
196B VAL* 3.3 27.5 - - - +
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Residues in contact with ASP 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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64B TYR 4.3 2.9 - - - +
65B THR* 2.5 28.8 + - - -
66B ARG* 2.8 29.0 + - + +
67B ASN* 3.7 20.3 + - + +
105B ALA* 3.7 3.3 - - - +
106B ARG* 1.3 74.8 + - - +
108B VAL* 1.3 69.0 + - - +
110B ASP* 3.7 10.0 + - - +
111B GLU* 3.6 17.7 + - - +
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Residues in contact with VAL 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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64B TYR* 3.5 38.4 - - + +
105B ALA* 3.3 13.9 + - + +
106B ARG 3.3 0.2 - - - -
107B ASP* 1.3 89.1 + - - +
109B GLN* 1.3 64.9 + - - +
111B GLU* 3.4 7.2 + - + +
112B CYS* 3.0 28.2 + - - -
121B LEU* 3.7 29.6 - - + -
122B ALA 3.7 10.8 - - - +
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Residues in contact with GLN 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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104B THR* 4.0 6.4 - - + +
105B ALA 2.9 14.7 + - - +
106B ARG* 3.0 45.0 + - - +
108B VAL* 1.3 74.9 - - - +
110B ASP* 1.3 67.0 - - - +
112B CYS* 3.1 4.1 + - - +
113B LYS* 2.9 51.1 + - + +
119B TRP* 3.7 36.7 - - + -
122B ALA* 3.7 17.7 - - + +
123B LYS* 3.8 13.9 - - - +
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Residues in contact with ASP 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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67B ASN* 5.7 0.3 - - - +
106B ARG* 3.0 37.7 + - - +
107B ASP* 3.9 8.8 - - - +
108B VAL 3.4 0.2 - - - -
109B GLN* 1.3 76.9 - - - +
111B GLU* 1.3 57.3 - - - +
113B LYS* 3.5 15.7 + - - +
114B LYS* 3.0 43.4 + - - +
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Residues in contact with GLU 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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107B ASP 3.6 10.1 + - - +
108B VAL* 3.4 10.9 + - + +
109B GLN 3.2 0.4 - - - -
110B ASP* 1.3 76.2 - - - +
112B CYS* 1.3 65.2 + - - +
114B LYS* 3.2 16.8 + - - +
115B LYS* 3.1 60.5 + - + +
117B LEU* 6.1 0.9 - - + -
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Residues in contact with CYS 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 VAL* 3.0 40.4 + - - -
109B GLN* 3.1 9.4 + - - +
111B GLU* 1.3 72.8 - - - +
113B LYS* 1.3 66.1 + - - +
115B LYS* 3.2 2.1 + - - -
116B GLY 3.0 4.2 + - - -
117B LEU* 3.0 43.2 + - - +
118B PRO 3.4 26.5 - - - +
119B TRP* 4.2 16.8 - - + -
121B LEU* 5.2 3.8 - - - -
122B ALA* 4.6 2.2 - - - -
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Residues in contact with LYS 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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113A LYS 4.8 0.7 - - - +
115A LYS 4.9 0.4 - - - +
116A GLY* 3.3 41.3 + - - +
106B ARG* 5.5 1.4 - - - +
109B GLN* 2.9 43.0 + - + +
110B ASP* 3.6 16.3 + - - +
112B CYS* 1.3 75.6 - - - +
114B LYS* 1.3 63.4 + - + +
116B GLY* 3.2 8.8 + - - -
119B TRP* 3.9 28.1 - - + +
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Residues in contact with LYS 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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113A LYS 5.5 0.7 - - - +
110B ASP* 3.0 29.6 + - - +
111B GLU* 3.5 20.2 - - - +
112B CYS 3.2 0.2 - - - -
113B LYS* 1.3 78.9 - - + +
115B LYS* 1.3 71.5 + - + +
116B GLY 3.3 0.4 + - - -
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Residues in contact with LYS 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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113A LYS* 4.8 2.2 - - - +
111B GLU* 3.1 46.9 + - + +
112B CYS 4.1 0.2 - - - +
114B LYS* 1.3 83.4 - - - +
116B GLY* 1.3 62.1 + - - +
117B LEU* 3.8 31.7 - - + +
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Residues in contact with GLY 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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112A CYS 4.5 4.0 - - - -
113A LYS* 3.3 39.9 + - - +
116A GLY* 4.6 2.7 - - - -
117A LEU 5.5 0.4 - - - -
119A TRP* 3.3 25.9 + - - -
112B CYS 3.0 5.4 + - - -
113B LYS 3.2 9.5 + - - -
114B LYS 3.3 1.2 + - - -
115B LYS* 1.3 78.3 - - - +
117B LEU* 1.3 59.7 + - - +
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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