Contacts of the helix formed by residues 119 - 134 (chain B) in PDB entry 1SA4
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 PRO 119 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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117B PRO* 3.4 11.0 - - + +
118B ILE* 1.3 88.4 - - + +
120B GLN* 1.3 66.1 + - - +
121B ILE* 3.2 4.7 - - + +
122B VAL* 3.0 28.3 + - + +
123B ALA* 3.0 19.6 + - - +
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Residues in contact with GLN 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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118B ILE 3.3 3.1 + - - -
119B PRO* 1.3 71.3 - - - +
121B ILE* 1.3 68.0 + - + +
123B ALA* 3.3 8.1 + - + +
124B THR* 2.8 32.8 + - - -
167B GLU* 4.9 1.7 - - - +
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Residues in contact with ILE 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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85A ASN* 6.3 0.7 - - - -
87B ARG* 5.0 4.3 - - - +
119B PRO* 3.2 4.1 - - + +
120B GLN* 1.3 80.3 - - + +
122B VAL* 1.3 69.5 + - + +
124B THR* 3.4 6.4 + - - +
125B ASP* 3.0 40.1 + - - +
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Residues in contact with VAL 122 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87A VAL* 5.6 1.3 - - + -
86B LEU* 3.3 35.4 - - + -
87B ARG* 3.9 26.2 - - - +
118B ILE* 4.0 13.2 - - + -
119B PRO* 3.0 29.9 + - + +
121B ILE* 1.3 74.7 - - + +
123B ALA* 1.3 67.7 + - - +
125B ASP* 3.2 2.6 + - - +
126B VAL* 2.9 28.4 + - + +
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Residues in contact with ALA 123 (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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118B ILE* 4.0 16.5 - - + +
119B PRO 3.0 12.1 + - - +
120B GLN* 3.5 15.0 - - - +
122B VAL* 1.3 78.2 - - - +
124B THR* 1.3 61.4 + - - +
126B VAL* 3.4 1.2 + - - -
127B CYS* 3.1 29.1 + - - -
163B ILE* 3.6 30.5 - - + +
165B THR* 5.7 3.4 - - + -
167B GLU* 5.0 0.9 - - - +
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Residues in contact with THR 124 (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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120B GLN* 2.8 34.8 + - - -
121B ILE* 3.7 9.3 - - - +
122B VAL 3.2 0.2 - - - -
123B ALA* 1.3 73.9 - - - +
125B ASP* 1.3 65.7 + - - +
127B CYS* 3.3 3.9 + - - +
128B GLN* 3.0 46.8 + - + +
167B GLU* 3.4 32.5 + - - +
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Residues in contact with ASP 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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85A ASN* 3.4 38.5 - - - +
87A VAL* 3.7 7.8 - - + +
87B ARG* 2.6 35.3 + - - +
121B ILE* 3.0 30.2 + - - +
122B VAL 3.2 4.9 + - - +
124B THR* 1.3 75.9 - - - +
126B VAL* 1.3 65.9 + - - +
128B GLN* 3.3 16.9 + - - +
129B PHE* 2.9 24.3 + - - +
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Residues in contact with VAL 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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87A VAL* 4.2 21.5 - - + -
86B LEU* 4.4 15.9 - - + -
104B CYS* 4.3 12.8 - - + -
108B LEU* 4.1 18.8 - - + -
122B VAL* 2.9 32.2 + - + +
123B ALA* 3.7 5.8 - - - +
125B ASP* 1.3 75.7 - - - +
127B CYS* 1.3 63.9 + - - +
129B PHE* 3.1 2.6 + - - +
130B LEU* 2.9 44.2 + - + +
163B ILE* 3.9 16.2 - - + -
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Residues in contact with CYS 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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123B ALA 3.1 22.6 + - - -
124B THR* 3.3 9.2 + - - +
126B VAL* 1.3 78.4 - - - +
128B GLN* 1.3 57.2 + - + +
130B LEU* 3.2 2.3 + - - +
131B GLU* 2.9 29.5 + - - +
160B LEU* 4.2 10.5 - - - -
163B ILE* 3.8 12.6 - - - -
167B GLU* 4.1 18.4 - - + +
168B ALA* 3.6 39.5 - - - -
171B ILE* 4.2 16.1 - - + +
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Residues in contact with GLN 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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84A PRO* 4.5 16.2 - - + +
85A ASN* 4.3 11.4 + - - +
124B THR* 3.0 34.8 + - + +
125B ASP* 3.6 21.6 - - - +
126B VAL 3.3 0.2 - - - -
127B CYS* 1.3 75.1 - - + +
129B PHE* 1.3 61.2 + - - +
131B GLU* 3.3 16.4 + - - +
132B LEU* 3.2 28.8 + - + +
167B GLU* 5.5 1.8 - - - +
171B ILE* 5.6 0.7 - - - -
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Residues in contact with PHE 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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82A ASP* 3.8 22.2 - - - +
86A PRO* 5.8 0.4 - - + -
87A VAL* 3.4 35.0 - - + +
88A VAL* 3.8 14.1 - - + -
100B ARG* 3.3 59.2 - - + -
104B CYS* 3.9 14.4 - - - -
125B ASP 2.9 11.5 + - - +
126B VAL 3.6 2.2 - - - +
128B GLN* 1.3 78.5 - - - +
130B LEU* 1.3 69.7 + - + +
132B LEU* 3.1 18.4 + - + +
133B CYS* 3.2 37.5 + - - -
144B PRO* 3.9 8.3 - - + -
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Residues in contact with LEU 130 (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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101B PRO* 4.1 32.8 - - + -
104B CYS* 4.2 6.1 - - + -
126B VAL* 2.9 35.8 + - + +
127B CYS 3.8 3.8 - - - +
129B PHE* 1.3 85.2 - - + +
131B GLU* 1.3 64.9 + - - +
133B CYS* 3.0 12.3 + - + +
134B GLN 3.1 9.4 + - - -
140B PHE* 3.3 21.8 - - + -
156B ALA* 3.9 18.4 - - + +
159B ALA* 4.0 11.0 - - + -
160B LEU* 3.7 34.3 - - + +
171B ILE* 4.7 0.4 - - + -
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Residues in contact with GLU 131 (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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127B CYS 2.9 12.7 + - - +
128B GLN* 3.4 18.0 - - - +
130B LEU* 1.3 77.8 - - - +
132B LEU* 1.3 64.8 + - + +
134B GLN* 3.2 24.5 + - - +
171B ILE* 3.7 40.0 - - + +
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Residues in contact with LEU 132 (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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81A ASN* 3.5 28.0 - - - +
82A ASP* 3.6 8.7 - - - +
83A GLY* 3.5 34.1 - - - +
128B GLN* 3.4 16.6 - - + +
129B PHE* 3.1 12.7 + - + +
131B GLU* 1.3 80.7 - - + +
133B CYS* 1.3 60.3 + - - +
134B GLN 3.3 4.8 + - - +
144B PRO* 3.5 28.5 - - + +
145B GLY 4.1 4.2 + - - -
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Residues in contact with CYS 133 (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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101B PRO* 4.1 13.5 - - + -
129B PHE* 3.2 50.7 + - - -
130B LEU* 3.0 13.0 + - - +
132B LEU* 1.3 76.2 - - - +
134B GLN* 1.3 63.7 + - - +
135B SER* 3.5 1.0 + - - -
140B PHE* 4.1 5.6 - - + -
141B GLY* 2.9 38.5 + - - +
143B GLY* 3.9 29.3 - - - +
144B PRO* 4.0 0.7 - - - -
145B GLY 5.6 0.8 + - - -
146B GLN 4.8 2.8 - - - +
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Residues in contact with GLN 134 (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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130B LEU 3.1 4.6 + - - +
131B GLU* 3.2 20.2 + - - +
132B LEU 4.1 4.0 - - - +
133B CYS* 1.3 78.1 - - - +
135B SER* 1.3 72.2 + - - +
136B PRO* 4.0 2.8 - - - +
139B GLY 3.5 19.1 + - - +
140B PHE* 3.5 37.6 - - + -
171B ILE* 2.9 25.0 - - - +
172B ILE* 3.7 2.2 - - - +
173B ASN* 2.9 42.1 + - + +
177B LEU* 5.9 0.4 - - - +
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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