Contacts of the helix formed by residues 101 - 122 (chain A) in PDB entry 2JM5
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 PHE 101 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43A PHE* 4.5 0.7 - - + -
47A CYS* 3.4 33.7 - - + -
50A PHE* 3.4 35.9 - + - -
63A ALA* 3.0 39.3 - - + -
66A ILE* 3.6 16.4 - - + -
67A TYR* 3.9 5.4 - - + -
71A ILE* 3.5 38.8 - - + -
89A ILE* 4.2 13.9 - - + -
93A ILE* 4.3 3.1 - - + -
99A HIS* 2.9 2.6 - - - -
100A SER* 1.3 80.5 - - - +
102A ASP* 1.3 52.7 + - - +
103A ALA 3.2 3.1 - - - -
104A ALA* 2.9 15.6 + - + -
105A GLN* 2.7 35.8 + - - +
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Residues in contact with ASP 102 (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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97A THR* 5.1 1.4 + - - -
99A HIS* 2.8 51.6 + - + +
100A SER* 3.2 9.2 - - - +
101A PHE* 1.3 75.9 - - - +
103A ALA* 1.3 73.6 + - - +
105A GLN* 3.3 22.1 - - - +
106A SER* 3.6 9.4 + - - -
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Residues in contact with ALA 103 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85A THR* 3.9 19.1 - - + +
100A SER 4.9 1.5 + - - +
101A PHE 3.2 0.6 - - - -
102A ASP* 1.3 88.6 + - - +
104A ALA* 1.3 62.5 + - - +
106A SER* 3.2 11.4 + - - -
107A ARG* 3.1 29.5 + - - +
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Residues in contact with ALA 104 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43A PHE* 3.8 19.1 - - + -
81A LEU* 3.5 23.3 - - + -
85A THR* 3.6 15.5 - - + +
89A ILE* 3.9 15.5 - - + -
100A SER 5.5 0.2 + - - -
101A PHE* 2.9 9.7 + - - +
103A ALA* 1.3 77.4 - - - +
105A GLN* 1.3 59.4 + - - +
107A ARG* 3.4 0.4 - - - +
108A VAL* 2.9 35.0 + - - +
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Residues in contact with GLN 105 (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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43A PHE* 4.3 1.5 - - + -
44A TRP* 3.2 48.6 - - + +
47A CYS* 5.5 2.0 - - + -
48A GLU* 4.6 22.4 - - + +
99A HIS* 5.8 2.6 - - + +
101A PHE 2.7 11.3 + - - +
102A ASP* 3.3 17.3 - - - +
104A ALA* 1.3 76.4 - - - +
106A SER* 1.3 64.3 + - - +
109A TYR* 3.0 39.2 + - - +
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Residues in contact with SER 106 (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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102A ASP 3.6 10.0 + - - -
103A ALA* 3.2 10.5 + - - -
104A ALA 3.2 0.2 - - - -
105A GLN* 1.3 84.7 + - - +
107A ARG* 1.3 60.8 + - - +
109A TYR* 3.3 12.5 + - - +
110A GLN* 2.9 31.9 + - - +
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Residues in contact with ARG 107 (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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81A LEU* 3.3 28.3 - - + -
82A ASP* 3.7 25.9 + - + +
84A HIS* 5.5 7.1 - - - -
85A THR* 2.7 28.4 + - - +
103A ALA* 3.1 21.6 + - - +
104A ALA* 3.1 2.2 + - - +
106A SER* 1.3 79.4 - - - +
108A VAL* 1.3 57.6 + - - +
110A GLN* 3.1 22.5 + - - +
111A LEU* 2.8 33.0 + - + +
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Residues in contact with VAL 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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40A ASN* 3.3 50.7 - - + +
43A PHE* 3.4 21.5 - - + -
44A TRP* 3.9 8.7 - - + -
79A VAL* 3.7 22.2 - - + -
81A LEU* 4.2 4.0 - - + -
104A ALA 2.9 18.6 + - - +
107A ARG* 1.3 73.6 - - - +
109A TYR* 1.3 61.1 + - - +
111A LEU* 3.3 11.7 - - + +
112A MET* 2.9 33.1 + - + +
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Residues in contact with TYR 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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15A PHE* 3.2 36.0 + + - +
16A ASP* 3.2 43.8 + - + +
19A LEU* 3.4 26.2 - - + -
44A TRP* 3.8 8.4 - - - +
105A GLN* 3.0 31.5 + - - +
106A SER* 3.3 14.4 - - - +
108A VAL* 1.3 76.9 - - - +
110A GLN* 1.3 65.8 + - + +
112A MET* 3.4 4.4 + - - -
113A GLU* 3.0 27.4 + - + +
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Residues in contact with GLN 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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106A SER 2.9 16.6 + - - +
107A ARG* 3.1 34.5 + - - +
109A TYR* 1.3 81.3 - - + +
111A LEU* 1.3 97.0 + - - +
113A GLU* 3.3 10.2 - - + +
114A GLN* 3.0 50.8 + - - +
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Residues in contact with LEU 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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40A ASN* 5.5 7.0 - - - +
79A VAL* 4.3 4.5 - - + -
80A ASN* 3.6 45.8 - - + +
81A LEU* 4.2 3.1 - - - +
82A ASP 5.8 0.9 - - - +
107A ARG* 2.8 21.3 + - + +
108A VAL* 3.3 34.5 - - + +
110A GLN* 1.3 89.9 - - - +
112A MET* 1.3 59.1 + - + +
114A GLN* 3.6 8.0 - - - +
115A ASP* 3.0 35.9 + - + +
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Residues in contact with MET 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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15A PHE* 3.9 8.3 - - + -
28A PHE* 3.6 23.0 - - + -
32A LEU* 3.6 21.3 - - + -
40A ASN* 3.7 18.2 - - + +
41A ILE* 3.4 29.6 - - + -
44A TRP* 3.3 42.6 - - + +
108A VAL* 2.9 22.8 + - + +
109A TYR* 3.9 5.8 - - - +
111A LEU* 1.3 75.2 - - + +
113A GLU* 1.3 53.4 + - - +
115A ASP* 4.8 0.7 - - - -
116A SER* 2.8 14.8 + - - +
117A TYR* 2.7 31.7 + - - +
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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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15A PHE* 3.7 28.7 - - + -
109A TYR* 3.0 19.4 + - + +
110A GLN* 3.3 15.3 - - + +
111A LEU 3.2 0.2 - - - -
112A MET* 1.3 77.3 - - - +
114A GLN* 1.3 79.5 + - - +
117A TYR* 3.0 52.9 + - + +
118A THR* 3.5 11.1 + - - +
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Residues in contact with GLN 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 GLN* 3.1 47.0 + - - +
111A LEU* 3.6 9.2 - - - +
113A GLU* 1.3 91.7 + - - +
115A ASP* 1.3 62.6 + - + +
118A THR* 3.3 20.0 + - - +
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Residues in contact with ASP 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 LEU* 3.0 20.1 + - + +
112A MET* 4.8 0.2 - - - -
114A GLN* 1.3 81.8 - - + +
116A SER* 1.3 70.9 + - - +
118A THR* 3.3 11.8 + - - -
119A ARG* 2.7 50.9 + - - +
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Residues in contact with SER 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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28A PHE* 3.6 18.6 - - - -
31A PHE* 3.4 14.2 - - - -
32A LEU* 3.9 16.3 - - - +
112A MET* 2.8 19.9 + - - +
115A ASP* 1.3 93.8 + - - +
117A TYR* 1.3 52.8 + - - +
118A THR 3.3 2.2 - - - -
119A ARG* 3.3 16.1 + - - +
120A PHE* 2.7 35.2 + - - +
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Residues in contact with TYR 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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11A TRP 2.6 29.3 + - - -
12A GLY 3.3 17.2 + - - -
13A GLU 4.0 1.5 - - - -
14A SER* 3.4 8.2 + - - -
15A PHE* 3.5 40.6 - + + -
18A LEU* 3.6 18.8 - - + -
28A PHE* 3.7 7.6 - - - -
112A MET 2.7 9.0 + - - +
113A GLU* 3.0 45.2 + - - +
116A SER* 1.3 72.2 - - - +
118A THR* 1.3 58.1 + - + +
120A PHE* 3.3 4.0 - + - +
121A LEU* 2.9 61.5 + - + +
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Residues in contact with THR 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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113A GLU* 4.0 12.6 - - - +
114A GLN* 3.3 21.0 + - - +
115A ASP 3.3 17.7 + - - -
117A TYR* 1.3 74.0 - - + +
119A ARG* 1.3 61.1 + - - +
121A LEU* 3.1 31.2 + - + +
122A LYS* 3.3 7.4 + - - +
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Residues in contact with ARG 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 PHE* 3.5 25.9 - - + -
32A LEU* 5.7 0.4 - - - +
35A GLU* 2.6 44.6 + - - -
37A SER* 6.0 0.6 - - - -
115A ASP* 2.7 45.9 + - - +
116A SER* 3.3 22.8 + - - +
118A THR* 1.3 77.3 + - - +
120A PHE* 1.3 52.8 + - - +
122A LYS* 3.1 9.3 + - + +
123A SER* 2.8 33.4 + - - -
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Residues in contact with PHE 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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11A TRP* 5.3 0.2 - - + -
18A LEU* 3.5 39.7 - - + -
27A ALA* 3.5 40.8 - - + -
28A PHE* 3.6 14.6 - + + -
31A PHE* 3.9 22.0 - - + -
116A SER 2.7 22.3 + - - +
117A TYR* 3.3 15.5 - + - +
119A ARG* 1.3 73.5 - - - +
121A LEU* 1.3 65.0 + - + +
123A SER* 2.6 36.1 + - - -
125A ILE* 3.7 11.7 - - + -
126A TYR* 3.1 41.6 - + + +
129A LEU* 4.5 0.2 - - + -
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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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11A TRP 4.6 0.2 - - - +
12A GLY* 3.7 22.9 - - - +
117A TYR* 2.9 58.2 + - + +
118A THR* 3.1 13.0 + - + +
120A PHE* 1.3 82.1 - - + +
122A LYS* 1.3 59.2 + - - +
123A SER 3.8 0.2 + - - -
126A TYR* 3.3 42.8 - - + -
127A LEU* 3.4 13.9 - - - +
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Residues in contact with LYS 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 THR 3.3 8.1 + - - +
119A ARG* 3.1 11.9 + - - +
120A PHE 3.1 0.4 - - - -
121A LEU* 1.3 81.9 - - - +
123A SER* 1.3 62.0 + - - +
124A ASP 3.9 0.5 + - - -
127A LEU* 3.5 26.9 - - + +
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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