Contacts of the helix formed by residues 118 - 131 (chain A) in PDB entry 4BPK
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 118 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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113A HIS 4.1 8.5 + - - -
114A ILE* 4.4 0.5 - - - -
115A THR* 2.7 33.4 + - + +
117A GLY* 1.3 81.9 - - - +
119A ALA* 1.3 65.2 + - - +
120A TYR 3.3 2.5 - - - -
121A GLN* 3.4 22.9 + - - +
122A SER* 2.9 30.8 + - - -
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Residues in contact with ALA 119 (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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114A ILE* 3.5 22.2 - - + -
115A THR 2.8 16.6 + - - +
116A PRO 4.1 4.4 + - - +
117A GLY 3.7 0.4 - - - -
118A THR* 1.3 79.2 - - - +
120A TYR* 1.3 63.4 + - - +
122A SER* 3.3 4.9 + - - -
123A PHE* 3.0 22.5 + - - +
150A LEU* 4.7 5.2 - - + +
162A LEU* 3.7 15.5 - - + -
166A ILE* 5.7 1.8 - - + -
169A TRP* 3.6 21.9 - - + -
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Residues in contact with TYR 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 PRO 5.1 1.8 + - - -
117A GLY 5.4 1.2 - - - +
118A THR 3.3 0.2 - - - -
119A ALA* 1.3 78.4 - - - +
121A GLN* 1.3 70.3 + - + +
123A PHE* 3.2 10.3 + + - +
124A GLU* 2.9 55.4 + - + +
169A TRP* 3.3 59.3 - + + -
172A THR* 6.1 0.7 - - - +
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Residues in contact with GLN 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 GLY 3.8 21.1 + - - +
118A THR* 3.6 19.7 - - - +
119A ALA 3.3 0.4 - - - -
120A TYR* 1.3 84.1 - - + +
122A SER* 1.3 61.3 + - - +
124A GLU* 3.5 4.0 + - - -
125A GLN* 3.1 37.3 + - + +
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Residues in contact with SER 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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112A LEU* 5.5 3.1 - - - -
113A HIS 5.1 2.0 + - - -
114A ILE* 5.7 3.6 - - - -
118A THR* 2.9 25.7 + - - -
119A ALA* 3.8 5.4 - - - -
121A GLN* 1.3 75.2 - - - +
123A PHE* 1.3 65.4 + - - +
125A GLN 3.5 0.2 + - - -
126A VAL* 3.2 31.4 + - - +
146A PHE* 4.8 1.3 - - - -
150A LEU* 5.4 10.5 - - - -
1C HT7 4.0 27.1 - - - -
2C ALA* 3.9 11.8 - - - +
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Residues in contact with PHE 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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119A ALA 3.0 13.9 + - - +
120A TYR* 3.2 15.0 + + - +
122A SER* 1.3 77.7 - - - +
124A GLU* 1.3 68.1 + - + +
126A VAL* 3.4 1.2 + - - +
127A VAL* 3.0 57.0 + - + +
143A PHE* 4.0 10.3 - + - -
146A PHE* 3.8 25.4 - + - -
147A GLY* 5.1 2.0 - - - -
150A LEU* 4.1 14.0 - - + +
166A ILE* 4.8 3.6 - - + -
169A TRP* 3.9 41.7 - + + -
170A MET* 3.7 40.2 - - + -
173A TYR* 4.3 8.5 - + + -
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Residues in contact with GLU 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 TYR* 2.9 49.1 + - + +
121A GLN* 4.0 2.4 - - - +
123A PHE* 1.3 79.5 - - + +
125A GLN* 1.3 75.0 + - - +
127A VAL* 3.4 7.6 - - + +
128A ASN* 3.0 58.1 + - - +
173A TYR* 5.8 3.1 - - + -
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Residues in contact with GLN 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 GLN* 3.1 24.0 + - + +
123A PHE 3.3 0.2 - - - -
124A GLU* 1.3 101.0 + - - +
126A VAL* 1.3 65.7 + - - +
128A ASN* 4.5 7.2 + - - +
129A GLU* 3.5 22.5 + - - +
2C ALA* 3.6 22.0 - - + -
3C ARG* 2.7 58.6 + - + +
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Residues in contact with VAL 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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112A LEU* 5.4 2.2 - - + -
122A SER* 3.2 19.7 + - - +
123A PHE 3.8 0.2 - - - +
125A GLN* 1.3 77.8 - - - +
127A VAL* 1.3 59.7 + - - +
129A GLU 3.4 1.4 + - - -
130A LEU* 2.9 29.8 + - + +
146A PHE* 3.6 47.6 - - + -
2C ALA* 3.3 28.9 - - + +
5C ILE* 4.1 13.7 - - + -
6C GLY* 3.5 18.8 - - - +
9C AHP 4.5 6.1 - - + -
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Residues in contact with VAL 127 (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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123A PHE* 3.0 53.2 + - + +
124A GLU* 3.4 13.2 - - - +
126A VAL* 1.3 76.7 - - + +
128A ASN* 1.3 65.3 + - - +
130A LEU* 3.2 8.4 + - + -
131A PHE* 3.1 29.7 + - + -
143A PHE* 3.9 18.8 - - + -
146A PHE* 4.1 13.7 - - + -
173A TYR* 3.7 32.9 + - + -
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Residues in contact with ASN 128 (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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124A GLU* 3.0 47.4 + - - +
125A GLN* 4.5 9.0 + - - +
127A VAL* 1.3 76.9 - - - +
129A GLU* 1.3 59.0 + - - +
131A PHE 3.5 2.6 - - - -
132A ARG* 3.1 44.1 + - - +
173A TYR* 3.2 30.3 + - - -
177A HIS* 4.9 4.0 + - - -
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Residues in contact with GLU 129 (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 GLN 3.5 17.0 + - - +
126A VAL 3.4 3.9 + - - +
127A VAL 3.3 0.4 - - - -
128A ASN* 1.3 75.7 - - - +
130A LEU* 1.3 55.8 + - - +
131A PHE 3.1 0.4 - - - -
132A ARG* 3.3 29.2 + - - +
1196A CD 2.4 26.2 - - - -
3C ARG* 3.4 24.1 - - + +
4C B3E 6.4 0.4 - - - -
6C GLY* 4.1 0.4 - - - -
7C ALA* 3.2 27.4 - - - +
10C ARG* 2.4 64.6 + - - +
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Residues in contact with LEU 130 (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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126A VAL* 2.9 21.7 + - + +
127A VAL* 3.2 9.6 + - + +
129A GLU* 1.3 78.8 - - - +
131A PHE* 1.3 77.3 + - + +
132A ARG 3.4 0.2 - - - -
139A ARG* 3.6 39.9 + - + +
142A ALA* 4.3 4.9 - - + -
143A PHE* 3.7 19.5 - - + +
146A PHE* 5.8 1.8 - - + -
6C GLY* 3.7 10.5 - - - +
9C AHP 4.0 16.4 - - + +
10C ARG* 3.5 44.5 + - - +
13C ALA* 4.2 4.3 - - + -
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Residues in contact with PHE 131 (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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127A VAL* 3.1 25.2 + - + +
128A ASN 3.5 4.3 - - - +
130A LEU* 1.3 90.9 - - + +
132A ARG* 1.3 64.6 + - - +
133A ASP 3.4 2.0 - - - -
134A GLY* 3.3 29.8 + - - +
135A VAL* 3.9 21.5 - - + -
139A ARG* 3.4 47.6 - - + -
140A ILE* 4.0 2.5 - - + -
143A PHE* 3.7 24.5 - + + -
173A TYR* 3.9 20.4 - + - +
178A LEU* 3.7 28.5 - - + -
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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