Contacts of the helix formed by residues 115 - 130 (chain B) in PDB entry 2J0Q
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 THR 115 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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113B ALA 3.9 2.6 - - - +
114B PRO* 1.3 89.9 - - + +
116B ARG* 1.3 63.2 + - - +
117B GLU* 4.0 6.2 + - - +
118B LEU* 3.3 23.0 + - - +
119B ALA 3.1 17.7 + - - -
163B THR* 3.5 11.5 - - - +
336B VAL* 3.6 44.8 + - + +
339B ARG* 5.0 5.7 + - + -
341B LEU* 5.0 1.4 - - - +
3H U 3.7 13.2 - - - +
4H U 3.9 7.6 - - - -
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Residues in contact with ARG 116 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
115B THR* 1.3 72.3 - - - +
117B GLU* 1.3 72.0 + - - +
119B ALA* 3.5 2.4 + - - +
120B VAL* 3.3 28.6 + - - +
141B ILE* 4.1 17.4 - - + +
142B GLY* 3.1 27.4 + - - -
143B GLY* 3.8 4.4 - - - +
163B THR* 3.6 19.7 - - + -
311B MET 5.5 1.4 + - - -
313B GLN* 3.1 42.5 - - - +
316B ARG* 3.3 22.1 - - - +
4H U 3.5 15.6 + - - +
5H U 2.9 26.6 + - - +
6H U 4.3 9.5 + - - -
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Residues in contact with GLU 117 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
115B THR* 3.3 5.4 - - - +
116B ARG* 1.3 82.4 + - - +
118B LEU* 1.3 58.7 + - - +
120B VAL* 3.8 5.9 + - - +
121B GLN* 3.2 25.8 + - - +
307B MET* 5.0 5.8 - - - -
313B GLN* 3.4 14.9 + - - +
316B ARG* 2.8 55.4 + - - +
317B GLU* 4.6 3.5 + - - +
320B MET* 3.9 32.2 - - + +
324B ARG* 4.8 3.5 + - - -
336B VAL* 4.7 2.6 - - + +
337B TRP* 6.0 0.2 - - + -
341B LEU* 3.6 26.1 - - + +
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Residues in contact with LEU 118 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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89B THR* 5.4 3.1 - - + +
113B ALA* 3.8 20.2 - - + -
114B PRO* 4.0 6.7 - - + -
115B THR* 3.3 21.0 + - - +
116B ARG 3.2 0.4 - - - -
117B GLU* 1.3 75.7 - - - +
119B ALA* 1.3 65.7 + - - +
120B VAL 3.2 1.3 - - - -
121B GLN* 4.3 9.0 - - + +
122B ILE* 2.9 32.7 + - + +
187B ASP* 4.2 12.3 - - - +
188B GLU* 3.3 35.0 - - + -
339B ARG* 4.3 6.7 - - + +
340B GLY* 3.7 30.7 - - - +
341B LEU* 3.8 9.4 - - + +
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Residues in contact with ALA 119 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
113B ALA* 4.1 8.2 - - + +
115B THR 3.1 13.2 + - - +
116B ARG 3.5 2.4 + - - +
118B LEU* 1.3 75.9 - - - +
120B VAL* 1.3 57.4 - - - +
122B ILE* 3.4 6.9 - - - +
123B GLN* 3.0 28.4 + - - +
139B ALA* 4.7 2.0 - - + -
141B ILE* 3.4 30.3 - - + -
161B ALA* 3.9 6.8 - - - +
162B GLY* 3.7 28.0 - - - +
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Residues in contact with VAL 120 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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116B ARG 3.3 16.9 + - - +
117B GLU* 4.0 6.1 - - - +
118B LEU 3.2 0.6 - - - -
119B ALA* 1.3 74.3 - - - +
121B GLN* 1.3 60.2 + - - +
123B GLN* 3.3 11.5 + - - +
124B LYS* 2.9 43.8 + - + +
139B ALA* 4.4 11.0 - - + -
141B ILE* 3.6 24.5 - - + -
317B GLU* 6.0 1.6 - - - +
324B ARG* 6.3 0.7 - - - +
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Residues in contact with GLN 121 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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89B THR* 5.8 5.5 - - + +
117B GLU 3.2 15.3 + - - +
118B LEU* 3.3 10.6 + - + +
120B VAL* 1.3 77.6 - - - +
122B ILE* 1.3 64.5 + - - +
124B LYS* 3.1 7.5 + - - +
125B GLY* 2.9 20.8 + - - -
324B ARG* 2.9 36.7 - - - +
340B GLY 3.0 23.3 - - - +
341B LEU* 3.5 16.1 - - - +
342B ASP* 3.0 35.3 + - + +
1413B ANP 4.7 2.9 + - - -
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Residues in contact with ILE 122 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89B THR* 3.8 25.3 - - + +
92B PHE* 3.7 22.9 - - + -
93B SER* 4.6 4.2 + - - +
111B ILE* 3.9 31.9 - - + -
113B ALA* 4.1 16.2 - - + -
118B LEU* 2.9 23.7 + - + +
119B ALA* 3.4 5.4 - - - +
121B GLN* 1.3 75.9 - - - +
123B GLN* 1.3 64.5 + - - +
125B GLY* 3.3 2.8 + - - -
126B LEU* 3.2 24.5 + - + +
161B ALA* 3.8 19.3 - - + -
187B ASP* 4.1 17.5 - - + +
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Residues in contact with GLN 123 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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119B ALA 3.0 15.1 + - - +
120B VAL* 3.4 13.7 + - - +
121B GLN 3.2 0.2 - - - -
122B ILE* 1.3 78.8 - - - +
124B LYS* 1.3 91.2 + - - +
126B LEU* 3.0 22.1 + - - +
127B LEU* 3.1 24.8 + - + +
137B CYS* 3.2 32.9 - - - +
138B HIS* 4.3 2.5 + - - -
139B ALA* 3.2 34.1 + - + +
161B ALA* 4.5 7.2 - - + -
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Residues in contact with LYS 124 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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120B VAL* 2.9 32.7 + - + +
121B GLN* 3.1 6.5 + - - +
123B GLN* 1.3 95.1 - - - +
125B GLY* 1.3 61.2 + - - +
127B LEU* 3.8 12.9 + - + +
128B ALA* 3.2 23.0 + - - +
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Residues in contact with GLY 125 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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56B TYR* 5.1 9.8 - - - -
93B SER* 5.3 3.4 - - - -
121B GLN 2.9 12.5 + - - -
122B ILE 3.3 4.5 + - - -
124B LYS* 1.3 76.9 - - - +
126B LEU* 1.3 59.0 + - - +
128B ALA* 3.5 5.8 - - - +
129B LEU* 3.0 38.4 + - - +
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Residues in contact with LEU 126 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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93B SER* 3.5 32.5 - - - +
96B VAL* 4.6 6.1 - - + -
97B LEU* 3.5 38.8 - - + +
111B ILE* 3.7 28.5 - - + -
122B ILE* 3.2 19.4 + - + +
123B GLN* 3.0 8.3 + - - +
125B GLY* 1.3 74.2 - - - +
127B LEU* 1.3 56.9 + - - +
129B LEU 4.6 0.2 - - - +
130B GLY* 2.7 34.1 + - - -
135B VAL* 4.8 1.6 - - + +
137B CYS* 3.6 28.7 - - - -
159B VAL* 4.0 8.7 - - + -
161B ALA* 5.3 1.1 - - + -
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Residues in contact with LEU 127 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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123B GLN* 3.1 39.4 + - - +
124B LYS* 4.1 13.5 - - + +
126B LEU* 1.3 75.0 - - - +
128B ALA* 1.3 62.8 + - - +
130B GLY 3.3 21.3 - - - +
131B ASP* 3.4 7.6 + - - +
135B VAL* 3.9 14.6 - - - +
136B GLN* 5.3 0.4 - - - -
137B CYS* 3.5 32.1 - - + +
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Residues in contact with ALA 128 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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52B GLY 4.4 4.7 - - - +
56B TYR* 3.7 34.1 - - + +
124B LYS 3.2 19.6 + - - +
125B GLY* 3.5 7.4 - - - +
126B LEU 3.1 0.6 - - - -
127B LEU* 1.3 73.8 - - - +
129B LEU* 1.3 65.3 + - - +
131B ASP* 3.3 22.6 + - - +
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Residues in contact with LEU 129 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48B ASP 4.6 2.1 - - - +
49B LEU* 4.2 12.9 - - + +
52B GLY* 3.7 26.9 - - - +
53B ILE* 4.3 11.0 - - + -
56B TYR* 3.4 40.8 - - + -
58B PHE* 4.3 15.0 - - + -
90B ALA* 4.5 5.8 - - + +
93B SER* 4.1 20.6 - - - -
94B ILE* 3.7 29.2 - - + +
97B LEU* 3.7 14.4 - - + -
125B GLY* 3.0 23.9 + - - +
128B ALA* 1.3 74.2 - - - +
130B GLY* 1.3 57.2 + - - +
131B ASP 3.1 4.7 + - - -
132B TYR 4.6 1.0 + - - -
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Residues in contact with GLY 130 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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97B LEU* 3.5 12.2 - - - +
126B LEU 2.7 19.8 + - - -
127B LEU* 3.3 10.1 - - - +
129B LEU* 1.3 70.7 - - - +
131B ASP* 1.3 60.4 + - - +
132B TYR 3.4 2.0 - - - -
133B MET* 3.7 24.4 + - - -
134B ASN* 4.0 3.5 + - - -
135B VAL* 3.7 18.1 + - - +
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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