Contacts of the helix formed by residues 136 - 149 (chain G) in PDB entry 2J28
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 ASP 136 (chain G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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32G LEU* 3.6 36.6 - - + +
33G THR 5.3 3.8 - - - +
34G ARG* 5.4 4.5 + - - -
119G GLY* 5.0 1.0 + - - -
120G ILE* 3.8 5.4 - - + +
135G ALA* 1.3 77.0 - - - +
137G LYS* 1.3 61.9 + - - +
138G GLN* 2.9 34.8 + - - +
139G VAL* 4.6 14.7 - - + +
140G ILE* 3.1 23.6 + - - +
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Residues in contact with LYS 137 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2746B U 3.6 27.0 - - - +
2747B G 3.0 29.0 + - - -
73G SER* 4.1 22.8 + - - +
82G PHE* 3.5 44.0 - - + -
135G ALA 3.0 5.1 + - - -
136G ASP* 1.3 71.8 + - - +
138G GLN* 1.3 67.7 + - - +
140G ILE* 3.1 15.3 - - + +
141G GLY* 3.0 16.6 + - - -
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Residues in contact with GLN 138 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2744B G 5.5 0.4 - - - +
2745B C 3.6 13.9 + - - +
2746B U 3.8 14.3 - - - +
2759B G 3.3 23.0 + - - -
2760B C 3.6 21.7 + - - +
2761B A 5.6 0.2 + - - -
34G ARG* 5.2 14.7 + - - +
136G ASP* 2.9 19.3 + - - +
137G LYS* 1.3 72.9 - - - +
139G VAL* 1.3 72.2 + - + +
140G ILE 2.8 4.3 + - - -
141G GLY* 2.8 13.9 + - - -
142G GLN* 3.3 27.0 + - - +
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Residues in contact with VAL 139 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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117G PRO* 3.5 44.2 - - + -
118G ALA 4.9 8.3 - - - +
120G ILE* 3.4 20.0 - - + -
136G ASP* 3.8 15.5 + - + +
138G GLN* 1.3 81.8 - - + +
140G ILE* 1.3 60.8 + - - +
142G GLN* 3.3 15.2 - - - +
143G VAL* 3.0 27.1 + - + +
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Residues in contact with ILE 140 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2746B U 5.8 1.1 - - - +
82G PHE* 4.3 17.5 - - + +
83G THR* 5.5 1.8 - - - +
84G LYS* 4.5 17.0 - - + -
120G ILE* 3.3 23.6 - - + +
132G LEU* 3.7 15.7 - - + +
133G LYS* 4.1 3.1 - - - -
134G GLY 3.4 29.4 - - - +
136G ASP 3.1 22.0 + - - +
137G LYS* 3.1 22.2 - - + +
138G GLN 2.8 1.0 + - - -
139G VAL* 1.3 76.9 - - - +
141G GLY* 1.3 66.3 + - - +
143G VAL* 3.1 6.8 - - - +
144G ALA* 2.9 22.2 + - + +
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Residues in contact with GLY 141 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2745B C 2.9 36.9 - - - +
2746B U 4.3 4.5 - - - -
137G LYS 3.0 6.3 + - - -
138G GLN 2.8 10.3 + - - -
140G ILE* 1.3 77.9 - - - +
142G GLN* 1.3 61.7 + - - -
144G ALA* 2.8 24.7 + - - +
145G ALA* 3.2 5.0 + - - +
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Residues in contact with GLN 142 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2744B G 5.5 1.8 - - - +
2745B C 2.6 19.0 + - - +
2760B C 4.3 1.0 + - - -
2761B A 3.8 37.9 - - - +
114G HIS* 6.2 0.2 + - - -
117G PRO* 4.0 26.1 - - - +
138G GLN* 3.3 19.4 + - - +
139G VAL* 3.3 26.8 - - - +
141G GLY* 1.3 72.7 - - - +
143G VAL* 1.3 62.4 + - - +
145G ALA* 3.2 4.8 + - - +
146G ASP* 2.6 46.6 + - + +
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Residues in contact with VAL 143 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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114G HIS* 3.7 29.6 - - + +
116G LEU* 4.6 16.6 - - + -
117G PRO* 4.6 9.4 - - + -
120G ILE* 4.8 8.3 - - + -
132G LEU* 3.5 20.6 - - + -
139G VAL* 3.0 22.9 - - + +
140G ILE* 3.1 11.9 - - - +
142G GLN* 1.3 82.6 - - + +
144G ALA* 1.3 65.2 + - - +
146G ASP* 3.7 7.4 - - - -
147G LEU* 3.2 31.7 + - + +
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Residues in contact with ALA 144 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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84G LYS* 4.4 20.9 - - + +
86G LEU* 3.0 26.8 - - - +
132G LEU* 4.3 15.5 - - + -
140G ILE* 2.9 14.5 + - + +
141G GLY* 2.8 17.8 + - - +
143G VAL* 1.3 79.8 - - - +
145G ALA* 1.3 56.2 + - - +
148G ARG 3.6 3.8 + - - -
163G TYR* 3.1 20.7 - - + +
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Residues in contact with ALA 145 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2744B G 3.8 23.8 - - - +
2745B C 4.4 6.1 - - - +
141G GLY 3.2 4.7 + - - +
142G GLN* 3.2 5.9 + - - +
144G ALA* 1.3 77.0 - - - +
146G ASP* 1.3 55.6 + - - +
147G LEU 2.8 5.3 + - - -
148G ARG* 3.2 9.4 + - + +
149G ALA* 2.6 39.4 + - + +
163G TYR* 2.9 20.2 + - - +
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Residues in contact with ASP 146 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2761B A 4.6 11.4 + - - -
114G HIS* 3.5 28.7 - - - +
142G GLN* 2.6 32.0 + - - +
143G VAL* 3.7 11.2 - - - -
145G ALA* 1.3 71.9 - - - +
147G LEU* 1.3 57.8 + - - +
149G ALA* 3.7 10.4 - - - +
150G TYR* 2.9 26.8 + - - -
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Residues in contact with LEU 147 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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86G LEU* 4.3 22.7 - - + -
102G ILE* 4.1 24.9 - - + -
104G LEU* 4.4 16.9 - - + +
114G HIS* 4.1 27.4 - - + -
130G ILE* 4.9 8.5 - - + -
132G LEU* 4.8 12.3 - - + -
143G VAL* 3.2 32.3 + - + +
144G ALA 4.0 3.4 - - - +
145G ALA 2.8 1.6 + - - -
146G ASP* 1.3 74.7 - - - +
148G ARG* 1.3 56.5 + - - +
149G ALA 2.9 0.9 - - - -
150G TYR* 2.7 39.5 + - + +
161G VAL* 3.9 6.6 - - + +
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Residues in contact with ARG 148 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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86G LEU* 4.1 4.9 - - + +
144G ALA 3.6 5.6 + - - +
145G ALA* 3.4 18.6 + - - +
147G LEU* 1.3 78.9 - - - +
149G ALA* 1.3 71.3 + - - +
151G ARG 2.9 27.0 + - - +
152G ARG* 3.3 42.4 + - - +
153G PRO* 3.0 30.0 - - - +
161G VAL* 3.2 36.1 + - + +
162G ARG* 4.7 0.7 - - - +
163G TYR* 3.4 34.1 - - - -
166G GLU* 3.3 21.1 + - - -
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Residues in contact with ALA 149 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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145G ALA* 2.6 26.2 + - + +
146G ASP* 3.7 11.2 - - - +
147G LEU 2.9 0.2 + - - -
148G ARG* 1.3 81.3 - - - +
150G TYR* 1.3 60.6 + - - +
151G ARG* 2.9 8.3 + - - -
152G ARG* 4.2 16.9 + - + +
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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
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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