Contacts of the helix formed by residues 109 - 120 (chain A) in PDB entry 3SWL
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 109 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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105A THR 4.8 0.2 + - - -
107A GLY* 4.3 7.8 + - - -
108A LEU* 1.3 78.8 + - - +
110A ILE* 1.3 64.9 + - - +
111A PHE 3.4 1.1 + - - -
112A ALA* 3.6 9.2 + - + +
113A LYS* 2.7 52.5 + - - +
136A ALA* 3.7 17.6 - - - +
139A VAL* 5.4 5.7 - - - +
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Residues in contact with ILE 110 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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107A GLY* 3.1 18.1 + - - +
108A LEU 3.4 0.2 - - - -
109A ASP* 1.3 77.4 - - - +
111A PHE* 1.3 57.9 - - - +
113A LYS* 3.2 5.0 + - - +
114A PHE* 2.9 26.3 + - - +
133A LEU* 4.2 13.3 - - + +
136A ALA* 3.4 44.4 - - + +
137A LEU* 3.8 13.0 - - + +
140A LEU* 3.7 31.4 - - + -
180A LEU* 5.1 2.2 - - + -
183A LYS* 6.2 0.4 - - + -
184A LEU* 4.1 23.3 - - + -
187A VAL* 4.2 16.6 - - + -
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Residues in contact with PHE 111 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25A PRO* 4.5 10.8 - - + -
26A PHE* 5.3 6.5 - + - -
107A GLY 4.7 0.6 + - - -
108A LEU 4.6 5.3 + - - +
109A ASP 3.4 0.8 - - - -
110A ILE* 1.3 80.9 - - - +
112A ALA* 1.3 56.8 + - - +
114A PHE* 3.2 34.9 + + - +
115A SER* 2.8 40.7 + - - -
183A LYS* 3.7 56.1 - - + +
186A ILE* 3.8 26.5 - - + -
187A VAL* 4.0 0.7 - - + -
233A TYR* 3.6 20.9 - - - -
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Residues in contact with ALA 112 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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108A LEU 5.4 0.4 + - - -
109A ASP* 3.6 10.5 + - + +
110A ILE 3.4 0.4 - - - -
111A PHE* 1.3 76.2 - - - +
113A LYS* 1.3 55.2 + - + +
115A SER* 3.2 7.8 + - - -
116A ALA* 2.8 36.1 + - - +
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Residues in contact with LYS 113 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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109A ASP* 2.7 49.4 + - - +
110A ILE* 3.2 7.6 + - - +
112A ALA* 1.3 74.6 - - + +
114A PHE* 1.3 63.2 + - - +
116A ALA* 3.6 6.7 + - - +
117A TYR* 3.2 22.5 + - - +
129A LEU* 4.6 4.1 - - - +
132A GLY* 3.9 25.1 - - - +
133A LEU* 4.1 22.5 - - - +
135A LYS* 6.2 0.9 - - - -
136A ALA* 4.3 7.6 - - + -
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Residues in contact with PHE 114 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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110A ILE 2.9 13.4 + - - +
111A PHE* 3.4 40.4 - + - +
113A LYS* 1.3 77.4 - - - +
115A SER* 1.3 68.2 + - - +
117A TYR* 3.2 3.7 + + - +
118A ILE* 3.0 53.0 + - + +
133A LEU* 4.2 17.9 - - + +
186A ILE* 3.8 8.7 - - + -
187A VAL* 3.6 22.2 - - + -
190A VAL* 3.7 25.4 - - + -
191A CYS* 3.7 24.9 - - - -
233A TYR* 3.7 25.8 - + - -
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Residues in contact with SER 115 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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111A PHE* 2.8 27.3 + - - -
112A ALA* 3.3 12.3 - - - -
114A PHE* 1.3 84.0 - - - +
116A ALA* 1.3 59.1 + - - +
117A TYR 3.0 2.2 + - - -
118A ILE* 4.3 3.4 - - - -
119A LYS* 2.2 54.1 + - - +
233A TYR* 5.2 4.3 + - - -
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Residues in contact with ALA 116 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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112A ALA 2.8 20.2 + - - +
113A LYS* 4.0 7.4 - - - +
114A PHE 3.4 0.4 - - - -
115A SER* 1.3 72.5 - - - +
117A TYR* 1.3 56.2 + - - +
119A LYS* 4.1 5.9 - - - +
120A ASN* 3.3 27.2 + - - +
129A LEU* 3.9 20.6 - - + +
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Residues in contact with TYR 117 (chain A).
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 3.2 14.9 + - - +
114A PHE* 3.2 12.1 + - - +
115A SER 3.0 0.4 - - - -
116A ALA* 1.3 76.1 - - - +
118A ILE* 1.3 73.5 + - + +
119A LYS 3.5 0.2 + - - -
120A ASN* 3.6 14.2 + - - +
126A ASN* 4.1 12.7 + - - +
129A LEU* 4.0 18.4 - - + +
130A GLU* 3.6 48.0 + - + +
133A LEU* 3.9 17.0 - - + -
191A CYS* 3.8 22.9 - - - -
195A ARG* 3.3 59.2 + - + +
197A PHE* 3.8 12.1 - - + +
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Residues in contact with ILE 118 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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114A PHE* 3.0 48.4 + - + +
115A SER* 4.1 6.7 - - - +
117A TYR* 1.3 84.2 - - + +
119A LYS* 1.3 65.6 + - + +
120A ASN 3.8 0.2 - - - +
190A VAL* 3.7 21.1 - - + +
191A CYS* 5.7 0.7 - - - -
194A TYR* 4.1 6.7 - - + -
195A ARG* 3.3 46.3 + - + +
233A TYR* 4.4 10.8 - - + -
236A VAL* 3.4 19.1 - - + +
237A ALA* 3.8 22.4 - - + +
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Residues in contact with LYS 119 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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115A SER* 2.2 46.7 + - - +
116A ALA* 4.1 4.7 - - - +
118A ILE* 1.3 78.8 - - + +
120A ASN* 1.3 68.2 + - - +
121A SER* 3.3 5.4 + - - -
233A TYR* 5.4 6.5 - - - -
236A VAL* 3.9 45.6 - - + +
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Residues in contact with ASN 120 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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116A ALA 3.3 9.1 + - - +
117A TYR 3.7 7.6 + - - +
118A ILE 3.5 8.0 - - - +
119A LYS* 1.3 80.5 - - - +
121A SER* 1.3 59.3 + - - +
122A ASN* 3.3 29.3 + - - +
125A LEU* 3.0 41.0 + - - +
126A ASN* 4.2 12.3 + - - +
129A LEU* 3.4 26.3 - - + +
195A ARG* 3.8 13.7 + - - -
236A VAL 5.2 1.0 - - - +
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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