Contacts of the helix formed by residues 110 - 128 (chain A) in PDB entry 2P2B
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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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81A CYS 3.2 27.1 - - - -
82A LEU* 4.3 12.5 - - + +
85A HIS* 3.8 24.0 - + + +
86A LEU* 3.7 8.5 - - + +
89A ASN* 3.6 22.2 - - + +
90A GLY* 3.5 5.1 + - - +
92A ARG* 2.9 24.4 + - + -
93A THR 3.9 4.0 - - - -
94A ALA* 3.5 29.2 - - + -
109A SER* 1.3 71.0 - - - +
111A ARG* 1.3 57.2 + - - +
113A LEU* 3.5 1.9 + - - +
114A HIS* 2.9 32.1 + - - +
321A LEU* 3.4 15.1 - - + +
324A GLY* 3.1 28.7 - - - -
325A ALA 2.6 26.2 + - - -
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Residues in contact with ARG 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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86A LEU* 3.2 48.0 + - + +
87A GLN* 5.1 2.6 + - - +
90A GLY* 2.9 29.6 + - - +
91A ASP* 3.0 28.3 + - - +
109A SER* 3.7 3.8 - - - +
110A TYR* 1.3 77.1 - - - +
112A GLU* 1.3 57.8 + - + +
114A HIS* 3.7 4.0 + - - +
115A ARG* 3.1 32.1 + - + +
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Residues in contact with GLU 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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107A HIS 3.4 15.9 - - - +
108A ILE* 3.5 10.5 - - + +
109A SER* 2.9 40.4 + - - +
111A ARG* 1.3 75.0 - - + +
113A LEU* 1.3 66.3 + - - +
115A ARG* 3.3 9.2 + - - +
116A ASP* 3.1 27.8 + - - +
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Residues in contact with LEU 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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82A LEU* 3.5 24.9 - - + -
94A ALA* 3.9 17.0 - - + -
95A ILE* 3.9 32.1 - - + -
108A ILE* 3.8 16.8 - - + +
109A SER 2.9 16.1 + - - +
110A TYR 3.9 3.1 - - - +
112A GLU* 1.3 73.4 - - - +
114A HIS* 1.3 60.6 + - - +
116A ASP* 3.3 4.3 + - + +
117A VAL* 2.9 42.5 + - + +
143A PRO* 5.0 0.7 - - + +
147A VAL* 3.7 30.1 - - + +
150A LEU* 4.2 12.6 - - + -
321A LEU* 4.2 6.1 - - + -
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Residues in contact with HIS 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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82A LEU* 4.2 17.4 - - + +
83A ASP* 3.3 43.8 + - - -
86A LEU* 3.7 33.5 - - + +
110A TYR 2.9 19.5 + - - +
111A ARG* 3.7 5.5 + - - +
113A LEU* 1.3 75.5 - - - +
115A ARG* 1.3 62.5 + - - +
117A VAL* 3.2 2.9 + - - +
118A CYS* 2.9 57.4 + - - -
154A ARG* 3.8 3.1 + - - -
246A PRO 5.3 2.9 - - - -
247A GLU* 6.0 2.0 - - - -
248A HIS 5.3 0.4 + - - -
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Residues in contact with ARG 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 ARG* 3.1 19.3 + - + +
112A GLU* 3.7 8.1 - - - +
113A LEU 3.2 0.2 - - - -
114A HIS* 1.3 85.5 - - - +
116A ASP* 1.3 61.2 + - - +
118A CYS* 3.4 6.5 + - - +
119A ARG* 2.9 40.5 + - - +
246A PRO* 3.5 38.6 + - + +
247A GLU* 4.7 7.5 + - - -
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Residues in contact with ASP 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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108A ILE* 5.9 1.9 - - - +
112A GLU* 3.1 19.4 + - - +
113A LEU* 3.8 4.3 - - - +
115A ARG* 1.3 77.8 - - - +
117A VAL* 1.3 58.6 - - - +
119A ARG* 2.5 38.3 + - - -
120A PHE* 2.8 31.2 + - - +
147A VAL* 3.6 23.5 - - + +
241A ILE* 3.7 10.4 - - + +
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Residues in contact with VAL 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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82A LEU* 3.8 23.8 - - + -
113A LEU* 2.9 25.2 + - + +
114A HIS 3.7 4.5 - - - +
116A ASP* 1.3 75.9 - - - +
118A CYS* 1.3 54.7 + - - +
120A PHE* 3.3 1.3 + - - -
121A ALA* 2.7 33.4 + - - +
147A VAL* 4.1 19.3 - - - -
150A LEU* 3.7 32.1 - - + +
151A ALA* 3.7 24.0 - - - +
154A ARG* 3.9 17.5 - - + +
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Residues in contact with CYS 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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114A HIS* 2.9 47.9 + - - +
115A ARG 3.5 5.2 - - - +
117A VAL* 1.3 72.9 - - - +
119A ARG* 1.3 64.7 + - - +
121A ALA* 3.5 4.2 + - - +
122A ASN* 3.2 26.9 + - - -
154A ARG* 3.7 22.9 - - - +
245A SER 4.1 2.0 - - - -
246A PRO 3.2 24.7 - - - +
248A HIS* 3.8 18.6 - - + +
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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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115A ARG* 2.9 27.9 + - - +
116A ASP* 2.5 31.9 + - - +
118A CYS* 1.3 76.0 - - - +
120A PHE* 1.3 58.7 + - - +
122A ASN* 3.3 0.7 + - - +
123A THR* 2.9 23.2 + - - -
241A ILE* 3.4 46.9 + - + +
242A GLU* 4.0 20.0 + - - +
244A ALA* 3.2 23.7 - - + +
245A SER 3.5 7.6 + - - -
246A PRO* 3.5 24.9 - - + -
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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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116A ASP 2.8 21.4 + - - +
117A VAL 4.0 1.8 - - - +
119A ARG* 1.3 70.2 - - - +
121A ALA* 1.3 60.1 + - - +
123A THR* 3.3 21.9 - - + -
124A LEU* 2.9 42.5 + - + +
147A VAL* 3.8 9.9 - - + -
148A ALA* 3.8 18.6 - - + -
151A ALA* 3.5 18.2 - - + -
184A ILE* 3.7 31.2 - - + -
218A ILE* 4.0 18.8 - - + -
237A TRP* 3.5 44.0 - + - -
240A LEU* 5.5 0.9 - - + -
241A ILE* 4.0 11.4 - - + +
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Residues in contact with ALA 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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117A VAL 2.7 21.8 + - - +
118A CYS 3.7 5.4 - - - +
120A PHE* 1.3 72.6 - - - +
122A ASN* 1.3 56.5 + - - +
124A LEU* 3.3 6.2 + - - +
125A LEU* 2.9 34.2 + - - +
151A ALA* 3.7 12.7 - - + +
154A ARG* 4.1 18.8 - - - -
155A ILE* 3.8 22.2 - - + +
248A HIS* 4.1 9.4 - - + -
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Residues in contact with ASN 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 CYS 3.2 11.0 + - - -
119A ARG 3.6 6.5 - - - +
121A ALA* 1.3 74.2 - - - +
123A THR* 1.3 57.2 + - - +
125A LEU* 3.1 8.6 + - - +
126A ASP* 2.8 48.5 + - - +
244A ALA* 4.2 7.2 - - + -
245A SER* 2.7 36.1 + - - +
247A GLU 2.9 23.8 + - - +
248A HIS* 3.5 19.0 - - - +
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Residues in contact with THR 123 (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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119A ARG 2.9 17.8 + - - -
120A PHE* 3.3 28.3 - - + -
122A ASN* 1.3 75.8 - - - +
124A LEU* 1.3 62.5 + - - +
126A ASP* 3.5 5.7 + - - +
127A LEU* 3.0 23.8 + - + +
218A ILE* 4.4 6.1 - - + -
240A LEU* 3.5 55.1 + - + +
241A ILE* 3.8 8.3 - - - -
244A ALA* 3.5 6.9 - - - +
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Residues in contact with LEU 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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120A PHE* 2.9 36.8 + - + +
121A ALA* 3.5 7.9 - - - +
123A THR* 1.3 75.7 - - - +
125A LEU* 1.3 63.7 + - - +
127A LEU* 3.1 13.6 + - + +
128A GLY 3.3 0.3 + - - -
129A ILE* 3.1 31.3 + - + +
135A VAL* 5.1 1.3 - - + -
151A ALA* 3.9 13.2 - - + -
152A CYS* 3.8 39.3 - - - +
155A ILE* 3.8 20.4 - - + -
182A LEU* 3.6 31.2 - - + -
184A ILE* 4.3 2.5 - - + -
218A ILE* 4.7 4.0 - - + -
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Residues in contact with LEU 125 (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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121A ALA 2.9 22.2 + - - +
122A ASN* 3.1 10.5 + - - +
124A LEU* 1.3 74.3 - - - +
126A ASP* 1.3 61.1 - - - +
128A GLY* 3.0 20.6 + - - -
129A ILE 3.5 18.2 + - - +
130A LYS* 5.0 6.7 - - + -
131A LYS 5.8 0.4 - - - +
155A ILE* 3.9 22.0 - - + +
248A HIS* 3.5 33.2 - - + +
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Residues in contact with ASP 126 (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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122A ASN* 2.8 34.0 + - - +
123A THR* 3.8 6.6 + - - +
125A LEU* 1.3 76.4 - - - +
127A LEU* 1.3 60.6 + - - +
128A GLY* 3.4 1.0 + - - -
244A ALA* 5.3 6.8 - - - +
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Residues in contact with LEU 127 (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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123A THR* 3.0 16.6 + - + +
124A LEU* 3.1 9.3 + - - +
126A ASP* 1.3 78.3 - - - +
128A GLY* 1.3 57.6 + - - +
129A ILE* 3.5 8.4 - - + +
181A ARG* 5.2 3.8 + - - -
182A LEU* 4.0 20.6 - - + -
215A GLU* 5.6 0.9 - - - +
216A HIS* 4.1 27.0 + - + +
218A ILE* 3.9 28.5 - - + -
235A LEU* 3.7 28.0 - - + -
240A LEU* 4.7 11.0 - - + -
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Residues in contact with GLY 128 (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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125A LEU 3.0 12.1 + - - -
126A ASP 3.2 1.7 - - - -
127A LEU* 1.3 79.1 - - - +
129A ILE* 1.3 65.1 + - - +
130A LYS* 3.5 12.0 + - - +
133A ASP* 3.8 0.2 - - - +
181A ARG* 2.8 25.9 + - - -
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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