Contacts of the helix formed by residues 108 - 127 (chain B) in PDB entry 1SA0
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 TYR 108 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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103B TRP* 3.7 17.5 - + - -
104B ALA* 2.9 21.2 + - + +
106B GLY 3.5 1.8 - - - -
107B HIS* 1.3 99.3 - + - +
109B THR* 1.3 66.4 + - - +
112B ALA* 2.9 35.3 + - - +
411B GLU 4.9 6.7 - - - +
413B MET* 3.6 29.4 - - + -
417B GLU* 2.7 29.6 + - - -
78E HIS* 3.8 11.4 + + - -
79E GLU* 3.7 32.3 - - + -
82E VAL* 3.5 32.8 - - + -
83E ILE* 4.9 11.3 - - - +
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Residues in contact with THR 109 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105B LYS* 3.6 8.8 + - - -
108B TYR* 1.3 78.1 - - + +
110B GLU* 1.3 71.7 + - - +
111B GLY 3.0 1.3 + - - -
112B ALA* 4.3 0.7 - - - +
113B GLU* 3.6 14.9 + - - +
411B GLU* 3.1 46.5 + - - +
83E ILE* 4.7 13.0 - - + +
86E ALA* 4.5 15.0 - - + -
87E ILE* 5.7 6.7 - - + -
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Residues in contact with GLU 110 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70B LEU* 3.2 25.8 - - + +
97B SER* 4.0 24.8 + - - +
98B GLY* 4.2 15.1 + - - +
99B ALA 5.0 0.7 - - - +
105B LYS* 2.9 49.5 + - + +
109B THR* 1.3 76.0 - - - +
111B GLY* 1.3 63.5 + - - +
113B GLU* 3.3 19.2 - - - +
114B LEU* 4.1 1.7 + - - +
411B GLU* 5.0 1.4 - - - +
163C LYS* 6.1 1.0 - - - +
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Residues in contact with GLY 111 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70B LEU* 4.2 0.4 - - - -
105B LYS 2.7 11.4 + - - -
106B GLY* 3.1 27.6 - - - -
108B TYR 4.3 0.2 - - - -
109B THR 3.0 1.8 - - - -
110B GLU* 1.3 73.4 - - - +
112B ALA* 1.3 53.2 + - - -
113B GLU 2.9 1.6 - - - -
114B LEU 2.7 29.5 + - - -
115B VAL* 3.4 5.0 + - - -
149B MET* 3.3 23.5 - - - +
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Residues in contact with ALA 112 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
108B TYR* 2.9 27.7 + - - +
109B THR 4.3 0.7 - - - +
111B GLY* 1.3 68.1 - - - -
113B GLU* 1.3 62.9 + - - +
114B LEU 3.1 1.2 + - - -
115B VAL* 3.3 27.6 + - + +
116B ASP* 4.5 6.8 + - - +
152B LEU* 4.0 8.0 - - + +
79E GLU* 6.4 2.0 - - + -
83E ILE* 5.8 4.9 - - + -
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Residues in contact with GLU 113 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97B SER* 5.5 6.5 - - - +
109B THR 3.6 10.4 + - - +
110B GLU* 3.3 21.6 - - - +
111B GLY 2.7 3.0 + - - -
112B ALA* 1.3 75.5 - - - +
114B LEU* 1.3 63.1 + - + +
116B ASP* 5.1 2.6 + - - +
117B SER* 5.4 1.9 + - - -
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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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68B VAL* 4.5 8.5 - - + -
69B ASP 3.6 17.7 - - - +
70B LEU* 4.7 2.9 - - + -
93B VAL* 3.5 27.4 - - + +
94B PHE 3.3 25.1 - - - +
95B GLY* 4.1 5.6 - - - -
110B GLU 4.7 3.1 - - - +
111B GLY 2.7 14.5 + - - +
113B GLU* 1.3 76.6 - - + +
115B VAL* 1.3 67.4 + - - +
116B ASP 3.2 2.2 - - - -
117B SER* 2.7 30.5 + - - +
118B VAL* 3.6 12.0 + - + -
149B MET* 3.9 13.0 - - + -
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Residues in contact with VAL 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 GLY 3.4 4.0 - - - +
112B ALA* 3.3 33.7 - - - +
114B LEU* 1.3 72.1 - - - +
116B ASP* 1.3 60.1 + - - +
118B VAL* 3.0 9.6 + - - +
119B LEU* 2.7 43.2 + - + +
149B MET* 4.4 9.5 - - + +
152B LEU* 3.4 27.1 - - + -
153B LEU* 4.7 10.7 - - + +
156B LYS* 3.7 32.5 - - + -
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Residues in contact with ASP 116 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
112B ALA 4.5 5.7 + - - +
113B GLU 5.7 2.0 - - - +
114B LEU 2.8 4.6 + - - -
115B VAL* 1.3 83.1 - - - +
117B SER* 1.3 51.1 + - - +
119B LEU* 3.6 11.1 - - - +
120B ASP* 2.7 49.3 + - - +
156B LYS* 4.8 11.6 + - - -
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Residues in contact with SER 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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93B VAL* 4.3 10.0 - - - +
113B GLU 5.4 2.1 + - - -
114B LEU* 2.7 32.8 + - - +
116B ASP* 1.3 74.1 - - - +
118B VAL* 1.3 58.5 + - - -
120B ASP* 4.1 7.4 - - - -
121B VAL* 3.5 22.3 + - - +
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Residues in contact with VAL 118 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7B ILE* 5.5 0.4 - - + -
66B ILE* 4.1 13.9 - - + -
68B VAL* 3.5 44.6 - - + -
93B VAL* 3.6 25.1 - - + -
114B LEU* 3.8 14.1 - - + +
115B VAL* 3.0 8.6 + - - +
117B SER* 1.3 76.0 - - - +
119B LEU* 1.3 58.9 + - - +
120B ASP 2.9 1.6 - - - -
121B VAL* 2.6 27.8 + - - +
122B VAL* 2.9 15.7 + - + +
149B MET* 5.1 2.0 - - - -
153B LEU* 3.7 23.3 - - + -
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Residues in contact with LEU 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 VAL* 2.7 20.3 + - + +
116B ASP* 3.6 12.1 - - - +
118B VAL* 1.3 73.2 - - - +
120B ASP* 1.3 58.1 + - - +
122B VAL* 3.3 12.4 - - - +
123B ARG* 2.9 49.5 + - - +
153B LEU* 4.4 12.5 - - + +
156B LYS* 3.7 60.6 - - + +
157B ILE* 4.3 15.9 - - + -
160B GLU* 3.7 12.7 - - - +
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Residues in contact with ASP 120 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116B ASP* 2.7 37.9 + - - +
117B SER* 4.1 5.9 + - - -
118B VAL 2.9 0.4 + - - -
119B LEU* 1.3 72.2 - - - +
121B VAL* 1.3 63.3 + - - +
123B ARG* 2.7 37.0 - - + +
124B LYS* 4.2 10.7 + - - +
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Residues in contact with VAL 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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66B ILE* 3.9 11.0 - - + -
90B ASP 4.3 17.3 - - - +
91B ASN* 3.3 34.8 - - - +
93B VAL* 4.9 6.5 - - + -
117B SER 3.5 16.8 - - - +
118B VAL* 2.6 17.5 + - - +
120B ASP* 1.3 75.6 - - - +
122B VAL* 1.3 63.6 + - - +
123B ARG 3.1 0.9 - - - -
124B LYS* 3.4 7.8 + - + +
125B GLU* 3.3 22.3 + - - +
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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
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5B VAL* 5.4 1.4 - - + +
7B ILE* 3.9 28.5 - - + -
66B ILE* 4.0 17.5 - - + -
118B VAL* 3.1 29.8 - - + +
119B LEU* 3.3 13.0 - - + +
121B VAL* 1.3 76.5 - - - +
123B ARG* 1.3 64.0 + - + +
125B GLU* 3.2 1.4 + - - +
126B SER* 2.9 32.9 + - - -
135B PHE* 4.4 13.3 - - + -
153B LEU* 5.0 0.7 - - + -
157B ILE* 3.8 24.0 - - + -
160B GLU* 5.5 0.4 - - - +
161B TYR* 4.6 8.5 - - + -
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Residues in contact with ARG 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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119B LEU* 2.9 37.6 + - - +
120B ASP* 2.7 41.6 - - + +
121B VAL 3.1 0.2 - - - -
122B VAL* 1.3 79.8 - - + +
124B LYS* 1.3 55.9 + - - +
126B SER* 4.0 0.2 - - - -
127B GLU* 3.2 47.9 + - - +
160B GLU* 2.6 42.8 + - - +
161B TYR* 3.8 11.4 - - - +
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Residues in contact with LYS 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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88B ARG* 6.1 1.8 - - - +
120B ASP 4.2 10.0 + - - +
121B VAL* 3.4 10.9 + - + +
122B VAL 3.2 0.6 - - - -
123B ARG* 1.3 77.2 - - - +
125B GLU* 1.3 65.8 + - + +
127B GLU* 4.6 2.1 - - - +
128B SER* 3.2 22.7 + - - -
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Residues in contact with GLU 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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5B VAL* 4.6 6.7 - - + -
54B ASN* 3.2 27.3 + - - +
62B VAL* 5.6 1.0 - - - +
63B PRO 4.9 1.7 - - - +
64B ARG* 3.3 28.5 - - + +
65B ALA 4.9 0.9 + - - -
66B ILE* 3.9 22.4 - - + -
88B ARG* 2.8 31.6 + - - +
91B ASN* 3.4 16.4 - - - +
121B VAL* 3.3 13.0 + - + +
122B VAL 3.2 7.5 + - - +
124B LYS* 1.3 76.0 - - + +
126B SER* 1.3 64.0 + - - +
128B SER* 3.3 5.9 + - - -
129B CYS* 3.2 23.9 + - - -
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Residues in contact with SER 126 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5B VAL* 4.3 10.0 - - - +
122B VAL 2.9 18.3 + - - -
123B ARG 4.0 0.2 - - - -
125B GLU* 1.3 73.2 - - - +
127B GLU* 1.3 58.5 + - - +
128B SER 2.9 4.0 - - - -
129B CYS* 2.9 30.9 + - - +
132B LEU* 4.1 21.7 - - - +
135B PHE* 4.5 8.1 - - - -
161B TYR* 3.3 29.2 - - - -
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Residues in contact with GLU 127 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
123B ARG* 3.2 41.9 + - + +
124B LYS* 4.6 3.1 - - - +
126B SER* 1.3 78.9 - - - +
128B SER* 1.3 60.1 + - - +
129B CYS 4.0 4.5 - - - +
161B TYR* 5.1 5.2 - - + +
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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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
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