Contacts of the helix formed by residues 107 - 123 (chain A) in PDB entry 1J7I
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 107 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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101A GLU* 4.1 18.1 + - - -
102A TYR* 4.3 9.7 - - - -
104A ASP* 4.8 9.6 + - - +
105A GLU 4.2 4.5 + - - -
106A GLN* 1.3 75.8 - - - +
108A PRO* 1.4 77.1 - - - +
109A GLU* 3.1 4.6 + - - -
110A LYS* 3.4 18.0 + - - +
111A ILE* 4.0 7.3 + - - +
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Residues in contact with PRO 108 (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 GLU 3.2 16.4 - - - +
106A GLN* 4.4 0.7 - - - -
107A SER* 1.4 92.2 - - - +
109A GLU* 1.3 67.1 + - + +
111A ILE* 3.0 26.0 + - + +
112A ILE* 3.4 10.9 + - - +
232A ILE* 3.8 32.7 - - + +
237A TYR* 3.2 39.3 - - + +
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Residues in contact with GLU 109 (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 SER 3.1 2.3 + - - +
108A PRO* 1.3 82.2 - - + +
110A LYS* 1.3 64.2 + - - +
112A ILE* 3.1 18.8 + - - +
113A GLU* 3.4 15.5 + - - +
237A TYR* 4.6 8.9 - - + -
240A LEU* 4.6 19.9 - - + +
244A LEU* 5.8 0.2 - - - +
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Residues in contact with LYS 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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101A GLU* 4.8 14.9 + - - +
107A SER* 3.4 10.1 + - - +
108A PRO 3.3 0.8 - - - -
109A GLU* 1.3 79.6 - - - +
111A ILE* 1.3 64.6 + - + +
113A GLU* 3.4 16.4 + - + +
114A LEU* 3.3 28.7 + - + +
198A VAL* 5.3 2.1 - - - +
201A GLY* 3.5 37.0 - - - +
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Residues in contact with ILE 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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98A CYS* 5.3 9.9 - - - +
101A GLU* 3.5 29.6 - - + +
102A TYR* 3.7 24.5 - - + -
107A SER 4.1 8.3 - - - +
108A PRO* 3.0 18.8 + - + +
110A LYS* 1.3 74.1 - - + +
112A ILE* 1.3 71.2 + - + +
114A LEU* 2.8 25.9 + - + +
115A TYR* 3.0 43.6 + - + +
231A ASP* 5.7 2.5 - - + -
232A ILE* 5.2 11.0 - - + -
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Residues in contact with ILE 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 PRO 3.5 13.7 - - - +
109A GLU* 3.1 7.8 + - - +
111A ILE* 1.3 76.0 - - + +
113A GLU* 1.3 51.4 + - - +
115A TYR* 3.0 11.3 + - + +
116A ALA* 2.8 31.9 + - - +
228A ILE* 3.7 33.0 - - + -
232A ILE* 4.0 11.9 - - + -
237A TYR* 4.0 29.2 - - + +
240A LEU* 4.2 6.7 - - + -
241A PHE* 3.4 41.4 - - + +
244A LEU* 4.1 11.2 - - + -
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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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109A GLU* 3.4 13.3 + - + +
110A LYS* 3.4 18.6 + - - +
112A ILE* 1.3 79.8 - - - +
114A LEU* 1.3 51.9 + - - +
116A ALA* 3.3 9.1 - - + +
117A GLU* 2.8 32.5 + - + +
120A ARG* 4.9 5.0 + - - +
201A GLY 5.5 2.8 - - - +
202A LYS* 4.6 13.2 + - - -
244A LEU* 4.2 15.1 - - + +
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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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98A CYS* 3.9 26.9 - - - -
101A GLU* 5.2 5.6 - - - +
110A LYS* 3.3 22.9 + - + +
111A ILE* 2.8 15.7 + - + +
113A GLU* 1.3 75.8 - - - +
115A TYR* 1.3 65.7 + - + +
116A ALA 3.1 0.2 - - - -
117A GLU* 3.3 17.3 + - - +
118A CYS* 2.8 39.0 + - - -
196A ILE* 5.7 3.4 - - + -
198A VAL* 3.9 26.2 - - + -
201A GLY 3.6 23.3 - - - +
203A VAL* 4.0 11.9 - - + +
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Residues in contact with TYR 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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98A CYS* 5.0 6.5 - - - -
111A ILE* 3.0 35.2 + - + +
112A ILE* 3.0 10.7 + - - +
114A LEU* 1.3 80.8 - - + +
116A ALA* 1.3 57.0 - - - +
118A CYS* 3.6 5.6 - - - +
119A ILE* 3.0 34.1 + - - +
191A LEU* 6.1 0.2 - - + -
193A ASP* 3.3 21.5 - - + +
196A ILE* 3.9 26.9 - - + -
224A CYS* 3.8 28.2 - - + -
227A SER* 3.2 24.1 - - - -
228A ILE* 3.8 36.6 - - + -
231A ASP* 4.4 2.8 + - - +
241A PHE* 4.0 14.4 - - + -
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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 ILE 2.8 12.9 + - - +
113A GLU* 3.3 15.5 - - + +
115A TYR* 1.3 74.0 - - - +
117A GLU* 1.3 64.3 + - - +
119A ILE* 3.3 4.0 + - - +
120A ARG* 3.1 40.3 + - - +
241A PHE* 4.1 1.5 - - + -
244A LEU* 4.3 17.0 - - + -
245A LEU* 3.5 27.3 - - + +
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Residues in contact with GLU 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* 2.8 19.1 + - + +
114A LEU* 3.6 12.6 - - - +
116A ALA* 1.3 74.8 - - - +
118A CYS* 1.3 65.1 - - - +
120A ARG* 3.5 20.9 + - + +
121A LEU* 3.0 29.3 + - + +
201A GLY 4.5 0.7 - - - +
202A LYS* 3.5 29.0 + - - +
203A VAL* 3.0 45.0 + - + +
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Residues in contact with CYS 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* 2.8 32.6 + - - +
115A TYR* 3.6 7.9 - - - +
117A GLU* 1.3 73.1 - - - +
119A ILE* 1.3 64.2 + - - +
121A LEU* 3.2 20.3 + - - +
122A PHE* 3.4 24.9 + - + -
191A LEU* 4.9 8.5 - - + -
196A ILE* 3.8 38.1 - - - -
203A VAL* 4.0 9.2 - - - -
206A PHE* 3.9 21.3 - - + -
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Residues in contact with ILE 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 TYR 3.0 21.6 + - - +
116A ALA 3.7 4.0 - - - +
117A GLU 3.3 0.2 - - - -
118A CYS* 1.3 75.9 - - - +
120A ARG* 1.3 64.6 + - - +
122A PHE* 3.1 19.3 + - + +
123A HIS* 3.0 45.3 - - + +
191A LEU* 4.7 0.7 - - + -
217A LYS 5.7 0.2 - - - +
220A ASP* 3.6 39.0 - - + -
221A ILE* 4.3 9.4 - - + +
224A CYS* 4.2 15.5 - - - -
241A PHE* 4.3 11.9 - - + -
245A LEU* 3.8 24.5 - - + -
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Residues in contact with ARG 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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113A GLU* 4.9 5.7 + - - +
116A ALA* 3.1 31.6 + - - +
117A GLU* 3.6 29.0 - - + +
119A ILE* 1.3 81.7 - - + +
121A LEU* 1.3 65.0 + - + +
123A HIS* 3.4 10.8 + - + +
124A SER* 3.3 23.0 + - - -
244A LEU* 4.9 9.9 + - - +
245A LEU* 4.8 8.4 - - + +
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Residues in contact with LEU 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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70A LYS 5.6 4.5 - - - +
71A LEU* 3.5 28.3 - - + -
72A PRO* 4.9 5.8 - - + -
117A GLU* 3.0 20.5 + - + +
118A CYS* 3.2 8.3 - - - +
119A ILE 3.0 0.2 - - - -
120A ARG* 1.3 80.8 - - + +
122A PHE* 1.3 59.0 + - + +
124A SER* 2.6 25.6 + - - +
125A ILE* 3.5 12.0 - - - +
203A VAL* 3.8 28.7 - - + -
206A PHE* 4.4 8.1 - - + -
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Residues in contact with PHE 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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71A LEU* 3.9 23.8 - - + -
118A CYS* 3.4 25.1 - - + -
119A ILE* 3.1 14.7 + - + +
121A LEU* 1.3 77.4 - - - +
123A HIS* 1.3 61.2 + + + +
124A SER 2.9 5.6 - - - -
125A ILE* 2.9 27.5 + - - +
185A VAL* 4.0 2.0 - - - +
186A PHE* 3.1 49.4 - + + +
188A HIS* 4.1 20.0 - + + -
191A LEU* 4.2 15.9 - - + -
206A PHE* 4.1 27.8 - + - -
220A ASP* 3.3 26.5 - - - -
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Residues in contact with HIS 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 ILE* 3.0 46.2 + - + +
120A ARG* 3.4 12.1 + - + +
122A PHE* 1.3 81.0 - + + +
124A SER* 1.3 57.0 + - - +
125A ILE 3.5 2.4 - - - +
183A GLU* 6.0 0.2 + - - -
185A VAL* 3.5 28.8 - - + +
186A PHE 5.1 1.1 - - - -
217A LYS* 4.0 38.9 + - + +
220A ASP* 6.2 0.2 - - - +
221A ILE* 5.0 6.9 - - + +
247A ILE* 6.1 1.8 - - + -
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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