Contacts of the helix formed by residues 108 - 126 (chain A) in PDB entry 1JS3
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 SER 108 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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100A CYS* 3.3 34.0 - - - +
102A GLY* 5.4 0.8 - - - -
104A SER 4.0 2.0 + - - +
105A TRP 2.9 5.3 + - - +
106A ALA 3.0 2.0 - - - -
107A ALA* 1.3 84.1 + - - +
109A PRO* 1.3 74.7 - - - +
110A ALA 3.2 2.0 - - - -
111A CYS* 2.8 22.7 + - - +
112A THR* 3.6 4.5 + - - -
67B GLY 3.9 3.4 - - - -
68B VAL* 3.9 6.2 - - - +
69B THR* 3.0 22.0 + - - -
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Residues in contact with PRO 109 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105A TRP* 2.9 64.5 - - + +
106A ALA* 4.3 1.6 - - - +
108A SER* 1.3 81.3 - - - +
110A ALA* 1.3 58.2 + - - +
112A THR* 3.1 5.5 + - - -
113A GLU* 2.8 31.4 + - - +
31B PRO* 3.8 26.5 - - + -
33B VAL* 4.1 12.1 - - + -
37B TYR* 4.3 4.0 - - + -
67B GLY* 3.0 14.1 - - - +
69B THR* 3.8 2.9 - - - +
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Residues in contact with ALA 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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109A PRO* 1.3 73.7 - - - +
111A CYS* 1.3 63.2 + - - +
113A GLU* 4.2 7.0 - - - +
114A LEU* 2.9 29.1 + - - +
357A PHE* 3.5 16.7 - - + -
37B TYR* 3.5 21.3 - - - +
38B LEU* 4.6 2.0 - - + -
64B ILE* 3.7 22.4 - - + +
67B GLY 2.8 20.9 + - - +
68B VAL* 4.6 1.6 - - + -
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Residues in contact with CYS 111 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
100A CYS* 3.9 11.0 - - - -
102A GLY* 4.0 23.1 - - - -
108A SER* 2.8 26.6 + - - +
110A ALA* 1.3 79.2 - - - +
112A THR* 1.3 61.4 + - - +
115A GLU* 3.8 17.8 - - - +
355A ARG* 4.6 8.1 + - - -
356A ARG 4.0 8.5 - - - -
357A PHE* 3.6 44.7 - - + -
359A SER* 4.0 6.6 + - - -
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Residues in contact with THR 112 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102A GLY 4.4 10.0 + - - -
104A SER 4.3 14.2 + - - -
105A TRP* 4.4 12.3 - - + -
108A SER 3.6 2.9 + - - -
109A PRO 3.1 7.4 + - - -
111A CYS* 1.3 80.0 - - - +
113A GLU* 1.3 65.7 + - - +
115A GLU* 3.3 12.3 + - - +
116A THR* 3.4 13.0 + - - -
343A ILE 3.3 26.2 - - - +
344A THR* 4.2 15.7 + - - +
346A TYR* 3.6 28.5 + - + +
355A ARG* 5.2 2.5 + - - +
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Residues in contact with GLU 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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105A TRP* 2.8 28.7 + - + +
109A PRO 2.8 17.4 + - - +
110A ALA* 4.4 0.2 - - - -
112A THR* 1.3 77.1 - - + +
114A LEU* 1.3 65.0 + - - +
115A GLU 3.3 0.3 + - - -
116A THR* 3.4 7.3 + - - -
117A VAL* 3.4 24.8 + - + +
342A LEU* 4.3 14.2 - - + +
343A ILE 5.5 0.4 - - - -
35B PRO* 3.6 1.7 - - - +
36B GLY* 2.8 29.3 + - - -
37B TYR* 3.2 17.4 + - - -
38B LEU* 3.0 41.9 + - + +
39B ARG 4.4 2.1 + - - +
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Residues in contact with LEU 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 ALA 2.9 18.1 + - - +
113A GLU* 1.3 77.1 - - - +
115A GLU* 1.3 57.3 - - - +
117A VAL* 3.2 2.9 + - - +
118A MET* 2.9 57.9 + - + +
357A PHE* 3.8 5.6 - - + -
359A SER* 3.5 25.4 - - - +
360A LEU* 3.5 29.8 - - + -
363A TRP* 4.0 22.0 - - + -
38B LEU* 3.5 15.5 - - + +
42B ILE* 4.0 17.0 - - + -
64B ILE* 4.5 6.5 - - + -
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Residues in contact with GLU 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 CYS 3.8 8.9 + - - +
112A THR 3.3 10.7 + - - +
113A GLU 3.2 0.2 - - - -
114A LEU* 1.3 80.8 - - - +
116A THR* 1.3 58.2 + - - +
118A MET* 3.3 2.0 + - - +
119A MET* 2.9 36.0 + - + +
143A VAL* 3.6 5.0 - - - +
144A ILE* 2.8 50.0 + - + +
346A TYR* 3.9 11.4 - - + +
355A ARG* 2.7 45.2 + - - -
356A ARG 5.0 4.5 - - - +
357A PHE* 6.1 0.2 - - - -
358A ARG* 5.2 1.6 + - - -
359A SER* 3.4 19.3 + - - -
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Residues in contact with THR 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 THR 3.4 9.9 + - - -
113A GLU* 3.4 8.6 + - - -
114A LEU 3.3 0.6 - - - -
115A GLU* 1.3 77.9 - - - +
117A VAL* 1.3 63.7 + - - +
119A MET* 3.4 5.6 + - - +
120A ASP* 3.1 22.0 + - - +
134A ALA* 3.5 29.8 - - + -
142A GLY 5.2 1.8 - - - +
341A GLY 4.9 0.4 - - - +
342A LEU* 5.7 3.5 - - + +
343A ILE* 3.8 31.5 + - + +
346A TYR* 2.8 22.9 + - - -
39B ARG* 3.6 11.9 - - - +
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Residues in contact with VAL 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 GLU 3.4 15.0 - - - +
114A LEU* 3.2 6.7 + - - +
115A GLU 3.2 0.8 - - - -
116A THR* 1.3 74.3 - - - +
118A MET* 1.3 63.2 + - + +
120A ASP* 3.0 5.4 + - + +
121A TRP* 2.8 47.1 + - + +
38B LEU* 5.1 0.9 - - + -
39B ARG* 4.2 51.8 - - + +
42B ILE* 3.7 32.5 - - + -
43B PRO 4.3 2.7 - - - +
44B ALA* 5.7 1.3 - - - -
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Residues in contact with MET 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 LEU* 2.9 35.6 + - + +
115A GLU* 3.7 6.1 - - - +
117A VAL* 1.3 83.5 - - + +
119A MET* 1.3 59.5 + - - +
121A TRP* 3.3 41.7 + - + +
122A LEU* 2.9 30.3 + - - +
359A SER* 3.8 18.4 - - - +
362A MET* 4.0 22.6 - - + +
363A TRP* 3.6 45.3 - - + +
366A PHE* 4.1 5.1 - - - -
42B ILE* 4.3 1.3 - - + -
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Residues in contact with MET 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 GLU* 2.9 24.9 + - + +
116A THR 3.7 5.2 - - - +
117A VAL 3.1 0.2 - - - -
118A MET* 1.3 78.0 - - - +
120A ASP* 1.3 58.3 + - - +
122A LEU* 4.6 0.9 - - - -
123A GLY 2.9 21.1 + - - -
142A GLY* 3.7 28.0 - - - +
143A VAL* 3.5 12.8 - - - +
144A ILE* 4.4 6.1 - - + -
313A ALA* 3.6 10.3 - - + -
314A MET 3.5 36.8 - - - +
315A TRP* 3.0 45.9 + - + +
362A MET* 3.9 22.2 - - + -
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Residues in contact with ASP 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 THR 3.1 12.9 + - - +
117A VAL* 3.0 8.4 + - + +
119A MET* 1.3 78.2 - - - +
121A TRP* 1.3 68.4 + - + +
123A GLY* 3.1 0.7 + - - +
124A LYS* 2.8 39.6 + - - +
132A PHE 4.9 0.3 - - - +
133A LEU* 3.6 18.3 - - + +
134A ALA* 2.9 25.6 + - - +
135A GLY* 2.8 25.6 + - - -
141A GLY* 5.1 1.4 - - - -
142A GLY 5.2 0.9 + - - -
315A TRP* 5.2 0.9 + - - -
39B ARG* 3.1 25.0 + - - +
44B ALA 5.6 0.7 - - - +
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Residues in contact with TRP 121 (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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117A VAL* 2.8 25.5 + - + +
118A MET* 3.4 36.1 - - + +
120A ASP* 1.3 78.0 - - + +
122A LEU* 1.3 57.1 + - - +
124A LYS* 3.2 6.3 + - - +
125A MET* 3.0 35.0 + - + +
363A TRP* 3.9 26.7 - + - -
366A PHE* 3.9 12.6 - + + -
367A ARG* 4.0 11.7 - - + -
42B ILE* 4.8 2.7 - - + -
43B PRO* 2.8 41.7 + - + -
44B ALA 3.5 19.5 - - - -
45B THR* 3.4 17.5 + - - +
46B ALA* 3.5 29.6 + - + +
47B PRO* 3.9 17.9 - - + -
51B ASP* 5.8 0.2 - - - -
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Residues in contact with LEU 122 (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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118A MET 2.9 16.1 + - - +
121A TRP* 1.3 73.6 - - - +
123A GLY* 1.3 67.0 + - - +
125A MET* 3.3 16.4 + - + +
126A LEU* 3.1 28.2 + - + +
280A ILE* 4.8 2.2 - - + -
299A PHE* 3.8 22.4 - - + -
301A PRO* 4.0 6.1 - - + -
305A LEU* 3.9 18.2 - - + -
313A ALA* 3.9 8.1 - - + -
315A TRP* 3.7 29.4 - - + -
362A MET* 3.5 23.8 - - + -
366A PHE* 3.8 19.5 - - + -
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Residues in contact with GLY 123 (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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119A MET 2.9 17.5 + - - -
120A ASP 3.1 4.0 + - - -
122A LEU* 1.3 75.6 - - - +
124A LYS* 1.3 59.7 + - - +
126A LEU* 3.3 2.4 + - - +
127A GLN 3.1 3.5 + - - -
128A LEU* 3.0 35.4 + - - +
133A LEU* 4.0 18.4 - - - -
315A TRP* 3.7 12.5 - - - -
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Residues in contact with LYS 124 (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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120A ASP* 2.8 26.2 + - - +
121A TRP* 3.6 4.7 - - - +
123A GLY* 1.3 73.4 - - - +
125A MET* 1.3 60.3 + - - +
126A LEU 3.1 1.6 - - - -
127A GLN* 2.9 25.4 + - - +
128A LEU 5.8 0.4 - - - -
133A LEU* 4.1 24.7 - - + -
39B ARG* 6.1 0.8 - - - +
44B ALA* 3.1 40.4 + - - +
45B THR* 4.9 13.7 - - - +
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Residues in contact with MET 125 (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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121A TRP 3.0 20.2 + - - +
122A LEU* 3.3 17.0 + - - +
124A LYS* 1.3 76.4 - - - +
126A LEU* 1.3 59.9 + - - +
127A GLN* 3.2 6.5 + - - +
279A PHE 4.1 0.9 - - - +
280A ILE* 3.4 41.1 - - + +
305A LEU* 5.5 0.4 - - - -
366A PHE* 3.7 38.1 - - + -
371A VAL* 4.1 32.3 - - + -
374A LEU* 4.7 14.8 - - - -
46B ALA* 3.6 25.8 - - + +
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Residues in contact with LEU 126 (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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122A LEU* 3.1 20.8 + - + +
123A GLY 3.7 4.3 - - - +
124A LYS 3.1 0.4 - - - -
125A MET* 1.3 76.2 - - - +
127A GLN* 1.3 64.0 + - - +
128A LEU* 4.0 13.3 - - + -
276A GLY 3.2 27.1 - - - +
279A PHE* 3.5 24.5 - - + -
280A ILE* 3.8 17.3 - - + -
285A ARG* 2.8 27.9 + - - -
288A LEU* 4.3 2.6 - - + +
297A PHE* 3.9 14.4 - - + -
299A PHE* 3.5 28.7 - - + -
315A TRP* 3.7 15.0 - - + -
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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