Contacts of the helix formed by residues 108 - 129 (chain D) 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 D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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103D TRP* 3.6 22.0 - + - -
104D ALA* 2.9 20.8 + - + +
106D GLY 3.5 1.8 - - - -
107D HIS* 1.3 102.1 - + + +
109D THR* 1.3 66.1 + - + +
112D ALA* 2.9 32.3 + - - +
411D GLU 5.0 8.5 - - - +
412D GLY 6.0 0.4 - - - -
413D MET* 3.6 25.1 - - + -
417D GLU* 2.6 30.0 + - - -
129E HIS* 3.9 9.5 + + - -
130E ALA* 3.5 42.6 - - + -
133E VAL* 4.9 10.5 - - + +
134E ARG* 3.3 19.6 + - + +
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Residues in contact with THR 109 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105D LYS* 3.5 9.8 + - - -
108D TYR* 1.3 79.4 - - + +
110D GLU* 1.3 72.0 + - - +
111D GLY 3.1 1.1 + - - -
112D ALA* 4.2 0.5 - - - +
113D GLU* 3.5 15.6 + - - +
411D GLU* 3.0 46.8 + - - +
134E ARG* 4.9 17.6 - - + +
137E LYS* 5.1 8.7 - - + -
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Residues in contact with GLU 110 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70D LEU* 3.2 25.5 - - + +
97D SER* 3.9 22.1 + - - +
98D GLY* 4.2 20.2 + - - +
99D ALA 4.9 0.9 - - - +
105D LYS* 2.9 50.5 + - + +
109D THR* 1.3 74.7 - - - +
111D GLY* 1.3 63.4 + - - +
113D GLU* 3.4 18.4 - - - +
114D LEU* 4.0 1.7 + - - +
411D GLU* 4.9 0.9 - - - +
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Residues in contact with GLY 111 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70D LEU* 4.2 0.7 - - - -
105D LYS 2.7 15.1 + - - -
106D GLY* 3.1 27.6 - - - -
108D TYR 4.5 0.2 - - - -
109D THR 3.1 1.2 - - - -
110D GLU* 1.3 69.3 - - - +
112D ALA* 1.3 65.8 + - - -
113D GLU 3.0 1.6 - - - -
114D LEU 2.7 17.5 + - - -
115D VAL* 3.4 4.5 - - - +
149D MET* 3.2 23.2 - - - +
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Residues in contact with ALA 112 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
108D TYR* 2.9 25.4 + - - +
109D THR 4.2 0.7 - - - +
111D GLY* 1.3 70.1 - - - +
113D GLU* 1.3 64.4 + - - +
114D LEU 3.1 1.9 + - - -
115D VAL* 3.3 26.9 + - - +
116D ASP* 4.3 7.4 - - - +
152D LEU* 4.0 9.7 - - + +
134E ARG* 3.3 26.5 - - - +
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Residues in contact with GLU 113 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97D SER* 5.5 6.5 - - - +
109D THR 3.5 10.4 + - - +
110D GLU* 3.4 20.2 - - - +
111D GLY 2.7 3.8 + - - -
112D ALA* 1.3 74.5 - - - +
114D LEU* 1.3 62.4 + - + +
116D ASP* 5.1 2.6 + - - +
117D SER* 5.3 2.3 + - - -
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Residues in contact with LEU 114 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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68D VAL* 4.4 8.7 - - + -
69D ASP 3.6 19.1 - - - +
70D LEU* 4.7 4.0 - - + -
93D VAL* 3.5 27.8 - - + +
94D PHE 3.3 24.5 - - - +
95D GLY* 4.1 5.6 - - - -
110D GLU 4.7 3.6 - - - +
111D GLY 2.7 14.1 + - - +
113D GLU* 1.3 78.3 - - + +
115D VAL* 1.3 67.0 + - - +
116D ASP 2.7 2.6 + - - -
117D SER* 2.7 35.5 + - - +
118D VAL* 3.6 11.7 + - + -
149D MET* 3.9 11.4 - - + -
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Residues in contact with VAL 115 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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111D GLY 3.4 4.5 - - - +
112D ALA* 3.3 33.0 - - - +
114D LEU* 1.3 71.1 - - - +
116D ASP* 1.3 60.4 + - - +
118D VAL* 3.0 9.7 + - - +
119D LEU* 2.7 44.3 + - + +
149D MET* 4.3 9.9 - - + +
152D LEU* 3.3 28.3 - - + -
153D LEU* 4.7 10.9 - - + +
156D LYS* 3.8 30.5 - - + -
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Residues in contact with ASP 116 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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112D ALA 4.3 6.2 - - - +
113D GLU 5.6 2.0 - - - +
114D LEU 2.7 5.4 + - - +
115D VAL* 1.3 83.6 - - - +
117D SER* 1.3 56.4 + - - +
119D LEU* 3.6 11.3 - - - +
120D ASP* 2.8 44.4 + - - +
156D LYS* 5.0 9.6 + - - -
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Residues in contact with SER 117 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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93D VAL* 4.3 10.9 - - - +
113D GLU 5.3 2.4 + - - -
114D LEU* 2.7 32.0 + - - +
116D ASP* 1.3 73.6 - - - +
118D VAL* 1.3 58.7 + - - -
120D ASP* 4.1 7.9 - - - +
121D VAL* 3.6 20.6 - - - +
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Residues in contact with VAL 118 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7D ILE* 5.5 0.4 - - + -
66D ILE* 4.0 8.1 - - + -
68D VAL* 3.5 45.1 - - + -
93D VAL* 3.7 25.4 - - + -
114D LEU* 3.8 13.9 - - + -
115D VAL* 3.0 9.5 + - - +
117D SER* 1.3 73.7 - - - +
119D LEU* 1.3 59.3 + - - +
120D ASP 3.0 1.6 - - - -
121D VAL* 2.6 25.5 + - - +
122D VAL* 2.9 22.4 + - + +
149D MET* 5.1 2.0 - - - -
153D LEU* 3.7 22.4 - - + -
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Residues in contact with LEU 119 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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115D VAL* 2.7 21.8 + - + +
116D ASP* 3.6 10.3 - - - +
118D VAL* 1.3 74.1 - - - +
120D ASP* 1.3 54.5 + - - +
122D VAL* 3.4 12.7 - - + +
123D ARG* 2.9 51.9 + - - +
153D LEU* 4.3 11.9 - - + +
156D LYS* 3.7 60.6 - - + +
157D ILE* 4.2 16.2 - - + -
160D GLU* 3.6 12.7 - - - +
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Residues in contact with ASP 120 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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116D ASP* 2.8 28.3 + - - +
117D SER* 4.1 10.7 - - - +
118D VAL 3.0 0.2 + - - -
119D LEU* 1.3 74.6 - - - +
121D VAL* 1.3 62.3 + - + +
123D ARG* 3.5 30.2 + - - +
124D LYS* 4.0 14.2 + - - +
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Residues in contact with VAL 121 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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66D ILE* 3.9 11.2 - - + -
90D ASP 4.3 16.4 - - - +
91D ASN* 3.4 34.8 - - - +
93D VAL* 4.9 5.8 - - + -
117D SER 3.6 16.2 - - - +
118D VAL* 2.6 13.4 + - - +
120D ASP* 1.3 77.3 - - + +
122D VAL* 1.3 65.6 + - - +
123D ARG 3.1 1.1 - - - -
124D LYS* 3.4 19.1 + - + +
125D GLU* 3.3 22.4 + - + +
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Residues in contact with VAL 122 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5D VAL* 5.4 1.4 - - + +
7D ILE* 3.9 28.5 - - + -
66D ILE* 4.1 17.3 - - + -
118D VAL* 3.0 30.7 - - + +
119D LEU* 3.4 12.6 - - + +
121D VAL* 1.3 75.7 - - - +
123D ARG* 1.3 62.9 - - - +
125D GLU* 3.2 2.8 + - - +
126D SER* 2.8 32.7 + - - -
135D PHE* 4.4 13.3 - - + -
153D LEU* 5.0 0.9 - - + -
157D ILE* 3.7 25.6 - - + -
160D GLU* 5.5 0.4 - - - +
161D TYR* 4.5 8.1 - - + -
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Residues in contact with ARG 123 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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119D LEU* 2.9 39.5 + - - +
120D ASP* 3.5 42.0 + - - +
121D VAL 3.1 0.4 - - - -
122D VAL* 1.3 80.1 - - + +
124D LYS* 1.3 59.4 + - - +
126D SER* 4.1 0.3 - - - -
127D GLU* 3.2 44.9 + - - +
160D GLU* 2.5 44.9 + - - +
161D TYR* 3.8 12.8 - - - +
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Residues in contact with LYS 124 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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88D ARG* 5.1 17.7 - - - +
90D ASP* 6.0 3.1 - - - -
120D ASP 4.0 12.8 + - - +
121D VAL* 3.4 20.4 + - + +
122D VAL 3.2 0.6 - - - -
123D ARG* 1.3 78.0 - - - +
125D GLU* 1.3 65.8 + - + +
127D GLU* 3.7 3.0 + - - +
128D SER* 3.1 24.3 + - - -
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Residues in contact with GLU 125 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5D VAL* 4.6 6.5 - - + -
54D ASN* 3.2 28.3 + - - +
62D VAL* 5.6 0.9 - - - +
63D PRO 4.8 2.3 - - - +
64D ARG* 3.4 27.3 - - + +
65D ALA 4.8 1.0 + - - -
66D ILE* 3.9 23.3 - - + -
88D ARG* 3.0 30.8 + - - +
91D ASN* 3.3 17.2 - - - +
121D VAL 3.3 11.6 + - - +
122D VAL 3.2 7.3 + - - +
124D LYS* 1.3 78.6 - - + +
126D SER* 1.3 63.9 + - - +
128D SER* 3.3 6.6 + - - -
129D CYS* 3.2 23.0 + - - -
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Residues in contact with SER 126 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5D VAL* 4.3 9.8 - - - +
122D VAL 2.8 18.0 + - - -
123D ARG 4.1 0.4 - - - -
125D GLU* 1.3 73.0 - - - +
127D GLU* 1.3 59.1 + - - +
128D SER 3.0 4.3 - - - -
129D CYS* 2.9 31.6 + - - +
132D LEU* 3.9 26.5 - - - +
135D PHE* 4.5 7.6 - - - -
161D TYR* 3.4 24.9 - - - -
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Residues in contact with GLU 127 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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123D ARG* 3.2 41.6 + - + +
124D LYS* 3.9 3.8 - - - +
126D SER* 1.3 78.9 - - - +
128D SER* 1.3 60.4 + - - +
129D CYS 3.4 5.2 - - - +
161D TYR* 5.0 5.2 - - + +
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Residues in contact with SER 128 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54D ASN* 4.1 18.8 + - - +
124D LYS* 3.1 19.0 + - - -
125D GLU* 3.5 8.3 - - - -
126D SER 3.0 0.8 - - - -
127D GLU* 1.3 78.9 - - - +
129D CYS* 1.3 65.6 + - - +
130D ASP* 3.5 2.8 + - - +
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Residues in contact with CYS 129 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3D GLU* 3.1 28.3 - - - +
5D VAL* 4.3 3.8 - - - -
54D ASN* 4.5 2.4 - - - +
64D ARG* 3.7 27.1 - - - -
125D GLU 3.2 15.8 + - - -
126D SER 2.9 18.5 + - - +
127D GLU* 4.0 4.7 - - - +
128D SER* 1.3 78.6 - - - +
130D ASP* 1.3 65.3 + - - +
131D CYS* 4.5 0.3 - - - -
132D LEU* 4.1 30.5 + - + +
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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