Contacts of the helix formed by residues 109 - 124 (chain A) in PDB entry 2JPO
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 MET 109 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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44A THR 5.3 3.8 - - - +
45A ASP 4.4 5.6 - - - +
46A ARG* 3.2 37.7 - - + -
104A ASN* 3.3 24.2 - - - +
106A ASP* 2.8 22.5 + - - +
108A CYS* 1.3 74.4 - - + +
110A LYS* 1.3 63.9 + - - +
112A ILE* 3.0 32.1 + - + +
113A ASP* 3.0 21.5 + - - +
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Residues in contact with LYS 110 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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98A GLU* 3.1 30.9 + - - +
99A LYS* 6.1 0.4 - - - +
101A ALA* 4.0 12.7 + - + +
102A PRO 4.8 2.9 + - - -
104A ASN* 3.4 27.3 - - - +
105A ASP* 3.6 28.0 - - + -
106A ASP* 3.6 22.2 + - - +
108A CYS 3.5 0.2 - - - -
109A MET* 1.3 76.9 - - - +
111A THR* 1.3 64.2 + - - +
113A ASP* 3.1 9.8 + - - +
114A VAL* 3.0 37.7 + - + +
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Residues in contact with THR 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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49A GLY* 3.7 8.5 - - - +
52A ILE* 3.3 44.9 - - + -
106A ASP 4.9 1.3 + - - -
107A LYS 3.5 14.8 + - - -
108A CYS 3.5 10.0 + - - -
110A LYS* 1.3 77.3 - - - +
112A ILE* 1.3 56.3 + - - +
114A VAL* 3.8 3.6 - - - +
115A ALA* 2.9 32.2 + - - +
138A VAL* 4.7 1.9 - - + +
142A VAL* 3.4 36.0 - - + +
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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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36A PHE* 5.3 0.7 - - - -
43A MET* 3.6 32.5 - - + +
44A THR* 6.2 0.2 - - - -
45A ASP 3.3 25.8 - - - +
46A ARG* 3.6 16.6 - - - -
49A GLY* 3.5 22.7 - - - +
52A ILE* 5.3 0.4 - - + -
108A CYS 3.2 16.7 + - - +
109A MET* 3.0 21.6 + - + +
111A THR* 1.3 73.6 - - - +
113A ASP* 1.3 57.7 + - - +
115A ALA* 3.3 6.0 + - - +
116A MET* 2.8 50.3 + - + +
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Residues in contact with ASP 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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101A ALA* 5.0 1.7 - - + +
102A PRO* 3.7 35.3 - - + +
104A ASN* 4.4 12.3 + - - +
109A MET* 3.0 21.4 + - - +
110A LYS* 3.1 13.0 + - - +
112A ILE* 1.3 77.1 - - - +
114A VAL* 1.3 61.4 + - + +
116A MET* 3.2 17.9 - - - +
117A CYS* 2.9 32.3 + - - +
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Residues in contact with VAL 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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94A ILE* 3.7 26.2 - - + +
97A CYS* 3.7 5.7 - - + +
98A GLU* 3.4 46.4 - - + +
101A ALA* 3.8 19.3 - - + -
110A LYS* 3.0 26.3 + - + +
111A THR* 4.2 4.0 - - - +
113A ASP* 1.3 72.6 - - - +
115A ALA* 1.3 56.4 + - - +
117A CYS* 3.5 6.9 + - - +
118A PHE* 2.9 29.1 + - - +
138A VAL* 5.8 1.1 - - + -
142A VAL* 6.3 2.9 - - + -
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Residues in contact with ALA 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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36A PHE* 4.1 18.4 - - + -
37A TRP* 5.1 5.1 - - + -
43A MET* 5.6 0.2 - - + -
52A ILE* 4.3 16.6 - - + -
111A THR 2.9 20.6 + - - +
112A ILE* 3.6 5.4 - - - +
114A VAL* 1.3 74.0 - - - +
116A MET* 1.3 63.9 + - - +
118A PHE* 3.4 9.0 + - - +
119A LYS* 3.3 19.4 + - - +
138A VAL* 4.1 21.2 - - + +
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Residues in contact with MET 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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36A PHE* 4.2 16.1 - - + -
42A VAL* 3.5 42.0 - - + -
43A MET* 4.2 9.2 - - + +
112A ILE* 2.8 28.5 + - + +
113A ASP* 3.2 26.5 - - - +
115A ALA* 1.3 69.9 - - - +
117A CYS* 1.3 64.6 + - + +
119A LYS* 3.3 12.0 + - - +
120A LYS* 3.1 31.9 + - + +
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Residues in contact with CYS 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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97A CYS* 2.0 52.7 - - + +
100A SER* 5.3 6.1 - - - -
113A ASP 2.9 18.2 + - - +
114A VAL* 3.5 3.8 - - - +
116A MET* 1.3 75.2 - - + +
118A PHE* 1.3 63.1 + - - +
120A LYS* 3.0 12.9 + - - +
121A GLU* 3.0 29.5 + - - +
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Residues in contact with PHE 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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90A LEU* 3.4 43.7 - - + -
93A ILE* 3.4 28.0 - - + +
94A ILE* 3.8 22.9 - - + -
97A CYS* 3.4 2.2 - - - -
114A VAL 2.9 18.4 + - - +
115A ALA* 3.4 11.0 - - - +
116A MET 3.3 0.2 - - - -
117A CYS* 1.3 73.9 - - - +
119A LYS* 1.3 63.9 + - - +
121A GLU* 3.0 6.6 + - - +
122A ILE* 2.9 51.7 + - + +
133A LEU 4.8 2.0 - - - -
134A VAL* 4.3 22.0 - - + -
137A GLU* 3.7 25.4 - - + -
138A VAL* 5.6 3.4 - - + -
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Residues in contact with LYS 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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36A PHE* 3.9 29.9 - - + +
37A TRP* 5.5 4.5 - - - +
39A ASP 4.8 4.0 - - - +
40A ASP* 2.7 41.6 + - + +
41A TYR 2.8 30.0 + - - +
42A VAL* 4.3 8.9 - - - +
115A ALA 3.3 8.0 + - - +
116A MET* 3.3 13.8 + - - +
118A PHE* 1.3 77.6 - - - +
120A LYS* 1.3 69.7 + - + +
122A ILE* 3.2 31.3 + - + +
123A HIS* 3.6 11.7 - - - +
134A VAL* 6.2 2.2 - - + -
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Residues in contact with LYS 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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40A ASP* 4.9 12.9 + - - -
42A VAL* 4.5 19.8 - - - +
116A MET* 3.1 22.0 + - + +
117A CYS* 3.0 13.1 + - - +
119A LYS* 1.3 77.7 - - + +
121A GLU* 1.3 58.9 + - + +
123A HIS* 3.1 41.2 + - + +
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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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93A ILE* 3.4 24.5 - - + +
97A CYS* 3.9 15.9 - - - -
117A CYS* 3.0 19.3 + - - +
118A PHE 3.0 10.2 + - - +
120A LYS* 1.3 71.7 - - + +
122A ILE* 1.3 58.8 + - - +
123A HIS 3.0 2.0 - - - -
124A LYS* 2.8 64.2 + - - +
125A LEU 3.6 1.0 + - - -
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Residues in contact with ILE 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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93A ILE* 4.5 0.2 - - + -
118A PHE* 2.9 49.2 + - + +
119A LYS* 3.2 25.2 + - + +
121A GLU* 1.3 75.6 - - - +
123A HIS* 1.3 63.6 + - + +
125A LEU* 3.3 25.0 + - + +
126A ASN 4.1 0.5 + - - -
127A TRP 4.1 9.6 - - - +
128A VAL* 5.1 4.0 - - + -
129A PRO* 3.7 27.4 - - + -
134A VAL* 3.6 27.4 - - + -
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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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40A ASP* 5.0 11.9 + - - +
119A LYS* 3.6 13.4 + - - +
120A LYS* 3.1 33.6 + - + +
122A ILE* 1.3 77.8 - - + +
124A LYS* 1.3 55.9 + - - +
125A LEU 3.3 0.5 + - - -
126A ASN* 3.0 21.8 + - - -
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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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89A GLN* 4.9 9.3 + - - +
93A ILE* 4.5 13.7 - - + +
121A GLU* 2.8 53.1 + - - +
123A HIS* 1.3 74.1 - - - +
125A LEU* 1.3 76.0 + - + +
126A ASN* 3.1 12.7 + - - +
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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