Contacts of the helix formed by residues 114 - 127 (chain A) in PDB entry 1J7D
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 114 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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14A ARG* 3.9 3.8 - - - -
18A GLU* 3.3 19.3 - - - -
21A GLU* 5.2 3.7 + - - -
73A TYR* 3.3 11.2 - - - -
109A TRP* 4.2 4.9 - - - -
112A SER 4.9 1.5 + - - -
113A TYR* 1.3 78.7 - - - +
115A ILE* 1.3 65.1 + - - +
116A LYS* 3.5 13.9 + - - +
117A VAL* 3.2 25.2 + - - +
118A VAL* 3.0 25.5 + - - +
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Residues in contact with ILE 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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15A LEU* 4.7 0.4 - - + -
18A GLU* 2.9 24.6 + - - +
33A TRP* 3.9 28.5 - - + -
46A TRP* 3.5 51.1 - - + -
48A GLY* 5.7 0.2 - - - -
67A VAL* 4.1 24.0 - - + -
69A CYS* 3.8 17.3 - - - -
73A TYR* 3.3 9.1 + - + +
78A PRO* 5.4 1.6 - - + -
114A SER* 1.3 71.6 - - - +
116A LYS* 1.3 62.7 + - - +
118A VAL* 3.2 8.7 + - + +
119A LEU* 3.0 32.2 + - + +
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Residues in contact with LYS 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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18A GLU* 4.3 0.8 + - - +
21A GLU* 3.3 31.5 + - - +
26A VAL* 3.8 17.6 - - + +
31A VAL* 4.6 0.8 - - + +
33A TRP* 3.6 35.9 - - + -
114A SER* 3.6 14.3 - - - +
115A ILE* 1.3 79.8 - - - +
117A VAL* 1.3 66.5 + - - +
119A LEU* 3.2 4.9 + - - +
120A GLN* 2.9 60.9 + - + +
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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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105A VAL* 3.7 22.7 - - + -
112A SER 5.1 2.2 - - - +
113A TYR* 3.9 23.1 - - + -
114A SER* 3.2 29.2 + - - +
116A LYS* 1.3 89.6 - - - +
118A VAL* 1.3 64.4 + - - +
120A GLN* 3.8 11.7 - - - +
121A GLU* 2.9 23.8 + - + +
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Residues in contact with VAL 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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67A VAL* 5.9 1.6 - - + -
78A PRO* 4.2 9.4 - - + -
80A VAL* 4.0 25.4 - - + -
103A ILE* 6.0 0.2 - - + -
105A VAL* 4.2 14.8 - - + -
106A LEU* 4.0 20.0 - - + -
109A TRP* 3.5 27.6 - - + -
114A SER 3.0 15.8 + - - +
115A ILE* 3.6 8.3 - - + +
117A VAL* 1.3 75.4 - - - +
119A LEU* 1.3 66.1 + - + +
121A GLU* 3.3 3.5 + - - +
122A LEU* 3.0 36.0 + - + +
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Residues in contact with LEU 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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31A VAL* 3.8 15.7 - - + +
32A SER 3.3 30.1 - - - +
33A TRP* 4.0 17.3 - - + -
48A GLY* 3.9 14.4 - - - -
49A MET 4.0 4.9 - - - +
50A ILE* 3.5 29.0 - - + +
65A LEU* 4.2 20.9 - - + -
67A VAL* 4.6 11.4 - - + -
115A ILE* 3.0 24.2 + - + +
116A LYS 3.7 4.0 - - - +
118A VAL* 1.3 79.0 - - + +
120A GLN* 1.3 58.0 + - - +
122A LEU* 3.4 3.7 + - + -
123A ARG* 3.0 26.5 + - - +
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Residues in contact with GLN 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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26A VAL* 4.4 6.1 - - - +
31A VAL* 3.8 26.0 - - + +
116A LYS* 2.9 51.1 + - - +
117A VAL* 3.8 11.8 - - - +
119A LEU* 1.3 75.1 - - - +
121A GLU* 1.3 57.0 + - - +
123A ARG* 3.4 4.0 + - - +
124A ARG* 2.9 28.4 + - - +
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Residues in contact with GLU 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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103A ILE* 4.0 2.5 - - + -
104A PRO* 3.3 20.4 - - - +
105A VAL* 2.9 48.3 + - + +
117A VAL* 2.9 19.0 + - + +
118A VAL 3.5 4.5 - - - +
119A LEU 3.2 0.2 - - - -
120A GLN* 1.3 74.5 - - - +
122A LEU* 1.3 61.9 + - - +
124A ARG* 2.9 37.0 + - - +
125A LEU* 2.8 45.2 + - + +
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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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50A ILE* 3.6 17.7 - - + -
65A LEU* 3.7 29.8 - - + -
80A VAL* 4.2 14.4 - - + -
82A PHE* 4.2 14.8 - - + -
88A MET* 3.3 28.9 - - + +
91A ILE* 4.6 3.4 - - + -
98A VAL* 4.6 5.2 - - + -
103A ILE* 4.1 32.8 - - + -
118A VAL* 3.0 31.2 + - + +
119A LEU* 4.7 1.6 - - + -
121A GLU* 1.3 74.8 - - - +
123A ARG* 1.3 64.5 + - - +
125A LEU* 3.2 1.9 + - + -
126A MET* 3.0 21.0 + - - +
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Residues in contact with ARG 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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28A ASP* 5.2 3.2 + - - -
30A THR* 3.4 49.4 + - - +
31A VAL* 4.1 7.0 - - + -
50A ILE* 3.7 14.9 - - + +
51A ILE* 3.3 22.1 + - - +
52A GLY 5.2 0.4 + - - -
53A PRO* 3.9 10.5 - - + +
54A PRO* 4.0 24.7 - - - +
119A LEU 3.0 17.7 + - - +
120A GLN* 3.7 5.6 - - - +
122A LEU* 1.3 77.7 - - - +
124A ARG* 1.3 62.8 + - - +
126A MET* 3.1 26.6 + - - +
127A MET* 3.3 34.5 + - + +
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Residues in contact with ARG 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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104A PRO* 5.2 4.8 - - - +
120A GLN 2.9 18.2 + - - +
121A GLU* 2.9 40.7 + - - +
123A ARG* 1.3 75.7 - - - +
125A LEU* 1.3 78.1 + - - +
127A MET* 2.9 42.6 + - + +
128A SER* 3.7 5.1 + - - -
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Residues in contact with LEU 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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88A MET* 3.5 15.9 - - + -
102A SER 5.4 0.2 - - - +
103A ILE* 3.8 33.2 - - + -
104A PRO* 4.3 12.3 - - + -
121A GLU* 2.8 41.9 + - + +
122A LEU* 3.2 2.9 + - - -
124A ARG* 1.3 98.3 - - - +
126A MET* 1.3 62.2 + - - +
128A SER* 3.0 25.0 + - - +
130A GLU* 5.9 0.7 - - - +
131A ASN* 2.8 26.1 + - - +
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Residues in contact with MET 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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50A ILE* 3.8 33.0 - - + -
52A GLY* 4.4 2.5 - - - -
53A PRO* 3.6 25.1 - - + -
56A THR* 3.8 1.7 - - - +
58A TYR* 3.2 49.3 - - + -
63A TYR* 4.2 6.1 - - + -
82A PHE* 3.9 22.0 - - + -
86A ILE* 3.7 22.7 - - + -
88A MET* 3.9 12.6 - - - -
122A LEU 3.0 16.0 + - - +
123A ARG* 3.3 11.2 - - - +
124A ARG 3.1 0.6 - - - -
125A LEU* 1.3 76.4 - - - +
127A MET* 1.3 58.9 + - - +
128A SER 3.3 0.2 - - - -
131A ASN* 4.3 2.0 - - - -
132A MET* 3.5 12.8 + - - +
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Residues in contact with MET 127 (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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53A PRO* 3.7 25.1 - - + -
54A PRO 5.5 0.9 - - - +
56A THR* 4.1 11.9 - - + -
123A ARG* 3.3 46.7 - - - +
124A ARG* 2.9 25.6 + - + +
126A MET* 1.3 76.2 - - - +
128A SER* 1.3 66.4 + - - +
129A LYS* 3.6 1.0 + - - +
132A MET* 3.7 14.6 - - - +
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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