Contacts of the helix formed by residues 110 - 127 (chain B) in PDB entry 2P2Q
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 TYR 110 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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81B CYS 3.2 26.5 - - - -
82B LEU* 4.4 11.9 - - + +
85B HIS* 3.7 20.6 - + + -
86B LEU* 3.8 12.7 - - + +
89B ASN* 3.7 16.8 - - + +
90B GLY 3.2 7.1 + - - +
92B ARG* 2.8 35.6 + - + -
94B ALA* 3.6 24.0 - - + -
109B SER* 1.3 72.4 - - - +
111B ARG* 1.3 57.3 + - - +
113B LEU* 3.3 1.8 + - - +
114B HIS* 2.9 30.8 + - - +
321B LEU* 3.3 16.6 + - + +
324B GLY* 3.1 30.2 - - - -
325B ALA 2.9 28.7 + - - -
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Residues in contact with ARG 111 (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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86B LEU* 3.3 46.7 + - + +
87B GLN* 5.3 0.8 + - - +
90B GLY* 2.8 41.0 + - - +
91B ASP* 3.6 21.1 + - - +
109B SER* 3.3 4.2 - - - +
110B TYR* 1.3 73.8 - - - +
112B GLU* 1.3 58.0 + - + +
114B HIS* 3.6 4.3 + - - +
115B ARG* 3.1 27.2 + - + +
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Residues in contact with GLU 112 (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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107B HIS 3.7 7.1 - - - +
108B ILE* 3.6 16.0 - - + +
109B SER* 2.9 37.0 + - - +
111B ARG* 1.3 75.4 - - + +
113B LEU* 1.3 60.1 + - - +
115B ARG* 3.6 9.0 + - - +
116B ASP* 3.1 35.5 + - - +
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Residues in contact with LEU 113 (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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82B LEU* 3.5 23.6 - - + -
94B ALA* 3.9 21.1 - - + -
95B ILE* 4.1 21.5 - - + -
108B ILE* 3.8 16.7 - - + +
109B SER 3.1 16.2 + - - +
110B TYR 3.7 2.9 - - - +
112B GLU* 1.3 71.9 - - - +
114B HIS* 1.3 61.3 + - - +
116B ASP* 3.4 4.1 + - - +
117B VAL* 3.0 35.3 + - + +
143B PRO* 5.2 2.5 - - + +
147B VAL* 4.0 25.4 - - + +
150B LEU* 4.0 19.7 - - + -
321B LEU* 4.1 12.6 - - + -
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Residues in contact with HIS 114 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82B LEU* 4.2 17.3 - - + +
83B ASP* 3.3 42.6 + - - -
86B LEU* 3.5 35.0 - - + +
110B TYR 2.9 16.0 + - - +
111B ARG* 3.7 6.2 + - - +
113B LEU* 1.3 76.1 - - - +
115B ARG* 1.3 67.0 + - - +
117B VAL* 3.3 2.1 + - - +
118B CYS* 2.9 52.3 + - - -
154B ARG* 4.0 3.7 + - - -
246B PRO 5.3 2.7 - - - -
247B GLU* 6.0 1.6 - - - -
248B HIS 5.2 0.4 + - - -
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Residues in contact with ARG 115 (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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111B ARG* 3.1 16.4 + - + +
112B GLU* 3.6 9.6 - - - +
113B LEU 3.3 0.2 - - - -
114B HIS* 1.3 85.4 + - - +
116B ASP* 1.3 71.4 + - - +
118B CYS* 3.3 6.3 + - - +
119B ARG* 3.1 42.1 + - - +
246B PRO* 3.6 38.5 - - + +
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Residues in contact with ASP 116 (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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108B ILE* 5.7 2.4 - - - +
112B GLU* 3.1 23.4 + - - +
113B LEU* 3.9 5.0 - - - +
114B HIS 3.3 0.2 - - - -
115B ARG* 1.3 79.8 - - - +
117B VAL* 1.3 56.6 + - - +
119B ARG* 2.8 34.3 + - - -
120B PHE* 2.9 29.8 + - - +
147B VAL* 4.0 22.0 - - + +
241B ILE* 3.5 13.9 - - + +
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Residues in contact with VAL 117 (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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78B ALA* 4.9 0.2 - - + -
82B LEU* 3.8 22.9 - - + -
113B LEU* 3.0 21.5 + - + +
114B HIS 3.8 3.4 - - - +
116B ASP* 1.3 73.2 - - - +
118B CYS* 1.3 61.1 + - - +
120B PHE* 4.4 0.7 - - - +
121B ALA* 2.7 30.1 + - - +
147B VAL* 4.0 25.4 - - + +
150B LEU* 3.5 30.3 - - + +
151B ALA* 3.9 17.7 - - - +
154B ARG* 3.9 21.3 - - + +
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Residues in contact with CYS 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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114B HIS* 2.9 49.2 + - - -
115B ARG* 3.3 5.8 + - - +
117B VAL* 1.3 76.9 - - - +
119B ARG* 1.3 54.8 + - - +
121B ALA* 3.4 4.2 + - - +
122B ASN* 3.0 33.1 + - - -
154B ARG* 3.8 21.1 - - - +
245B SER 4.1 2.7 - - - -
246B PRO 3.0 26.2 - - - +
248B HIS* 3.8 19.3 - - + +
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Residues in contact with ARG 119 (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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115B ARG* 3.1 29.6 + - - +
116B ASP* 2.8 32.6 + - - +
118B CYS* 1.3 75.0 - - - +
120B PHE* 1.3 52.3 + - - +
122B ASN 3.6 0.2 + - - -
123B THR* 2.7 34.8 + - - -
241B ILE* 3.4 47.4 + - + +
242B GLU* 4.0 20.8 + - - +
244B ALA* 3.4 16.1 - - - +
245B SER 3.5 10.5 - - - +
246B PRO* 3.5 28.9 - - + -
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Residues in contact with PHE 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 ASP 2.9 17.6 + - - +
117B VAL 4.0 0.2 - - - +
119B ARG* 1.3 73.7 - - - +
121B ALA* 1.3 60.5 + - - +
122B ASN 3.3 0.2 - - - -
123B THR* 3.3 21.4 - - + -
124B LEU* 3.0 62.6 + - + +
147B VAL* 3.8 10.8 - - + -
148B ALA* 3.8 26.9 - - + -
151B ALA* 3.5 19.5 - - + -
184B ILE* 4.0 12.3 - - + -
218B ILE* 4.0 15.3 - - + -
237B TRP* 3.5 45.3 - + - -
240B LEU* 5.8 0.7 - - + -
241B ILE* 4.0 11.4 - - + +
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Residues in contact with ALA 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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117B VAL 2.7 21.9 + - - +
118B CYS 3.5 5.2 - - - +
120B PHE* 1.3 72.3 - - - +
122B ASN* 1.3 61.8 + - - +
124B LEU* 3.5 4.6 + - - +
125B LEU* 3.1 30.4 + - - +
151B ALA* 3.6 12.9 - - + +
154B ARG* 4.0 18.8 - - - -
155B ILE* 3.8 22.3 - - + +
248B HIS* 4.1 7.6 - - + -
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Residues in contact with ASN 122 (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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118B CYS 3.0 16.5 + - - +
119B ARG 3.8 3.4 - - - +
120B PHE 3.3 0.4 - - - -
121B ALA* 1.3 73.2 - - - +
123B THR* 1.3 56.0 + - - +
125B LEU* 3.3 8.4 + - - +
126B ASP* 2.7 49.6 + - - +
244B ALA* 4.2 7.4 - - + -
245B SER* 2.7 37.6 + - - +
247B GLU 2.9 25.0 + - - +
248B HIS* 3.4 17.8 - - - +
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Residues in contact with THR 123 (chain B).
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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119B ARG 2.7 20.5 + - - -
120B PHE* 3.3 29.4 - - + -
122B ASN* 1.3 75.6 - - - +
124B LEU* 1.3 61.9 + - - +
126B ASP* 3.4 7.3 + - - +
127B LEU* 3.1 24.1 + - + +
218B ILE* 4.6 5.6 - - + -
240B LEU* 3.5 48.4 + - + +
241B ILE* 3.9 2.8 - - - -
244B ALA* 3.5 14.3 - - - +
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Residues in contact with LEU 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 PHE* 3.0 44.3 + - + +
121B ALA* 3.8 4.5 - - - +
122B ASN 3.3 0.2 - - - -
123B THR* 1.3 76.2 - - - +
125B LEU* 1.3 56.6 + - - +
127B LEU* 2.9 23.6 + - - +
129B ILE* 3.1 26.6 + - + +
135B VAL* 5.0 3.6 - - + -
151B ALA* 3.7 26.0 - - + -
152B CYS* 3.9 22.4 - - - +
155B ILE* 3.9 19.5 - - + -
182B LEU* 3.5 32.3 - - + -
184B ILE* 4.4 3.1 - - + -
218B ILE* 4.5 3.4 - - + -
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Residues in contact with LEU 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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121B ALA 3.1 22.6 + - - +
122B ASN* 3.6 10.8 - - - +
124B LEU* 1.3 75.7 - - - +
126B ASP* 1.3 59.8 + - - +
128B GLY* 3.1 17.5 + - - -
129B ILE 3.7 19.4 - - - +
130B LYS* 5.2 4.9 - - + +
131B LYS 6.0 0.2 - - - +
155B ILE* 3.9 21.1 - - + -
248B HIS* 3.5 31.0 - - + +
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Residues in contact with ASP 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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122B ASN* 2.7 35.4 + - - +
123B THR* 3.7 7.5 + - - +
124B LEU 3.3 0.2 - - - -
125B LEU* 1.3 75.2 - - - +
127B LEU* 1.3 62.1 + - + +
128B GLY* 3.2 1.6 + - - -
244B ALA* 4.6 13.0 - - - +
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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 THR 3.1 13.2 + - - +
124B LEU* 2.9 13.1 + - - +
126B ASP* 1.3 80.6 - - + +
128B GLY* 1.3 59.7 + - - +
129B ILE* 3.4 8.2 + - + +
181B ARG* 4.0 8.8 + - - -
182B LEU* 4.4 14.8 - - + -
215B GLU* 5.1 1.2 - - - +
216B HIS* 4.2 26.0 + - + +
218B ILE* 3.7 31.4 - - + -
235B LEU* 3.8 30.5 - - + -
240B LEU* 4.5 8.5 - - + -
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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