Contacts of the helix formed by residues 118 - 130 (chain B) in PDB entry 3SI5
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 118 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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75B LEU* 3.6 18.6 - - + +
114B ARG 5.1 1.8 + - - +
115B TYR* 2.8 27.5 + - + +
116B TYR 3.5 0.7 - - - +
117B SER* 1.3 76.3 - - - +
119B PRO* 1.4 65.7 - - - +
120B ARG* 2.8 60.8 + - - +
121B PHE* 2.8 19.8 + - - +
122B LEU* 3.1 12.3 + - - +
151B LEU* 4.2 1.5 - - - +
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Residues in contact with PRO 119 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117B SER 3.4 9.4 - - - +
118B ASP* 1.4 90.8 - - - +
120B ARG* 1.3 56.9 + - + +
122B LEU* 3.6 3.8 + - + +
123B ASN* 2.9 27.2 + - - +
151B LEU* 4.0 22.9 - - + -
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Residues in contact with ARG 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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73B ASP* 3.0 38.4 + - - -
75B LEU* 3.7 20.6 - - + +
76B ASP* 3.5 26.1 + - - +
79B ASP* 3.5 35.8 - - - +
115B TYR* 4.3 2.0 - - - -
118B ASP* 2.8 33.9 + - - +
119B PRO* 1.3 78.6 - - + +
121B PHE* 1.3 60.1 + - - +
123B ASN* 3.4 10.0 + - - +
124B LEU* 3.4 25.8 + - - +
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Residues in contact with PHE 121 (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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75B LEU* 3.8 15.3 - - + +
106B VAL* 5.8 2.5 - - + -
109B LEU* 3.7 44.2 - - + -
110B GLN* 5.7 0.2 - - - -
111B GLY 5.4 1.6 - - - -
112B GLU 4.8 0.2 - - - -
115B TYR* 3.3 43.5 - + + +
116B TYR* 3.7 29.4 - + - -
118B ASP 2.8 5.7 + - - +
120B ARG* 1.3 76.0 - - - +
122B LEU* 1.3 64.4 + - - +
124B LEU* 3.1 25.7 + - + +
125B TRP* 3.1 49.2 - + - -
147B ILE* 3.8 18.2 - - + -
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Residues in contact with LEU 122 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118B ASP 3.1 5.4 + - - +
119B PRO* 3.8 7.6 - - + +
121B PHE* 1.3 76.1 - - - +
123B ASN* 1.3 63.3 + - - +
125B TRP* 3.1 7.9 + - - +
126B LEU* 2.9 49.1 + - + +
142B LEU* 3.8 26.5 - - + -
147B ILE* 5.2 2.4 - - + +
148B GLY* 4.7 9.9 - - - -
151B LEU* 3.7 35.9 - - + -
153B GLN* 4.1 12.3 - - + -
154B PHE* 3.7 34.8 - - + +
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Residues in contact with ASN 123 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79B ASP* 4.5 13.3 + - - -
82B ILE* 5.1 6.9 - - - +
86B GLU* 5.2 2.4 + - - -
119B PRO 2.9 20.0 + - - +
120B ARG* 3.4 10.9 + - - +
121B PHE 3.2 0.2 - - - -
122B LEU* 1.3 75.8 - - - +
124B LEU* 1.3 61.1 + - - +
126B LEU* 3.4 9.3 + - - +
127B LYS* 2.9 56.8 + - - +
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Residues in contact with LEU 124 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75B LEU* 3.8 24.2 - - + -
78B TRP* 5.1 5.6 - - + +
79B ASP* 5.3 3.8 - - - +
82B ILE* 4.0 29.6 - - + -
102B LEU* 4.1 14.0 - - + +
105B ALA* 4.0 22.9 - - + -
106B VAL* 4.4 15.0 - - + -
109B LEU* 3.9 16.8 - - + -
120B ARG 3.5 12.8 - - - +
121B PHE* 3.1 16.3 + - + +
123B ASN* 1.3 79.9 - - - +
125B TRP* 1.3 53.3 + - + +
127B LYS* 3.3 3.3 + - - +
128B LEU* 2.8 35.4 + - - +
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Residues in contact with TRP 125 (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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106B VAL* 3.6 40.1 - - + +
110B GLN* 6.2 2.7 - - - -
121B PHE* 3.1 59.8 + + - -
122B LEU* 3.1 5.7 + - - +
124B LEU* 1.3 78.4 - - + +
126B LEU* 1.3 55.7 + - - +
128B LEU* 3.1 16.2 + - + +
129B GLY* 2.7 33.8 + - - -
138B MET* 3.9 12.4 - - + +
141B TYR* 3.8 20.0 - + - -
142B LEU* 3.5 39.0 - - + -
147B ILE* 4.1 18.7 - - + +
215Y PHE* 3.7 31.9 - + - -
219Y ILE* 4.3 5.4 - - + -
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Residues in contact with LEU 126 (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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122B LEU* 2.9 53.3 + - + +
123B ASN* 3.8 9.4 - - - +
125B TRP* 1.3 73.3 - - - +
127B LYS* 1.3 62.1 + - + +
129B GLY* 3.4 1.7 + - - -
130B ARG* 3.3 34.6 + - - +
138B MET* 4.3 8.0 - - + +
139B TYR* 3.8 33.1 + - + +
153B GLN* 3.9 26.2 - - + +
154B PHE* 5.1 2.5 - - + -
157B SER* 4.2 14.4 - - - +
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Residues in contact with LYS 127 (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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82B ILE* 3.8 14.9 - - + +
86B GLU* 2.7 44.6 + - - +
98B MET* 3.5 15.2 - - - +
102B LEU* 3.7 22.6 - - + +
123B ASN* 2.9 42.5 + - - +
124B LEU* 3.7 4.0 - - - +
126B LEU* 1.3 73.4 - - + +
128B LEU* 1.3 64.7 + - - +
130B ARG* 3.2 36.0 + - - +
131B LEU* 3.8 10.0 + - - +
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Residues in contact with LEU 128 (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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102B LEU* 3.8 25.2 - - + +
103B GLU* 3.8 28.0 - - + +
106B VAL* 4.3 9.6 - - + -
124B LEU 2.8 21.2 + - - +
125B TRP* 3.5 27.6 - - + +
127B LYS* 1.3 71.0 - - - +
129B GLY* 1.3 62.1 + - - +
131B LEU* 3.0 16.4 + - - +
132B CYS* 3.4 19.9 + - - -
138B MET* 5.6 0.4 - - + -
213Y ILE* 4.0 18.8 - - + +
215Y PHE* 4.2 9.0 - - + -
218Y PHE* 3.8 27.6 - - + -
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Residues in contact with GLY 129 (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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125B TRP 2.7 18.8 + - - -
126B LEU 3.7 3.8 - - - -
127B LYS 3.2 0.4 - - - -
128B LEU* 1.3 68.0 - - - +
130B ARG* 1.3 56.2 + - - +
131B LEU 3.0 10.1 + - - -
132B CYS* 3.1 19.7 + - - +
135B PRO* 3.5 25.5 - - - +
138B MET* 3.9 24.2 - - - +
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Residues in contact with ARG 130 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
126B LEU* 3.3 26.6 + - - +
127B LYS* 3.2 24.5 + - - +
129B GLY* 1.3 73.5 - - - +
131B LEU* 1.3 67.1 + - + +
132B CYS 3.5 3.5 - - - +
135B PRO* 5.4 2.9 - - - -
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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