Contacts of the helix formed by residues 126 - 135 (chain A) in PDB entry 4B18
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 GLY 126 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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92A PHE* 3.7 20.8 - - - -
124A THR* 3.0 2.8 + - - +
125A PRO* 1.3 79.3 - - - +
127A VAL* 1.3 57.3 + - - +
128A VAL 3.7 1.3 - - - -
129A ALA* 3.6 13.3 + - - +
130A ARG* 3.1 26.3 + - - +
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Residues in contact with VAL 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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88A ILE* 3.7 30.3 - - + -
91A ILE* 4.3 10.9 - - + +
92A PHE* 4.0 16.8 - - + -
106A PHE* 4.0 9.0 - - + -
121A VAL* 3.8 24.7 - - + +
124A THR* 3.1 21.5 + - + +
125A PRO 3.4 0.8 - - - -
126A GLY* 1.3 72.7 - - - +
128A VAL* 1.3 70.6 + - - +
130A ARG* 3.3 8.7 + - - +
131A PHE* 3.1 43.3 + - + -
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Residues in contact with VAL 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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121A VAL* 4.7 6.1 - - + +
122A ILE* 4.4 20.0 - - + +
124A THR 4.8 0.6 + - - +
125A PRO 5.4 0.2 + - - -
127A VAL* 1.3 74.9 - - - +
129A ALA* 1.3 64.8 + - - +
131A PHE* 2.8 23.2 + - - +
132A VAL* 2.9 12.0 + - + -
151A LEU* 4.1 18.4 - - + -
154A ILE* 4.2 20.6 - - + -
164A ILE* 3.9 35.0 - - + +
165A VAL* 4.5 6.7 - - + -
168A ALA* 4.3 15.0 - - + -
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Residues in contact with ALA 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 PRO 5.6 1.1 - - - +
126A GLY* 3.6 14.2 + - - +
127A VAL 3.5 0.4 - - - -
128A VAL* 1.3 77.9 - - - +
130A ARG* 1.3 57.0 + - - +
132A VAL* 3.2 10.4 + - - +
133A GLU* 2.9 35.4 + - + +
168A ALA* 4.4 12.7 - - + +
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Residues in contact with ARG 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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91A ILE* 2.7 39.3 + - + -
92A PHE* 3.4 33.2 + - + +
93A SER 2.7 29.7 + - - -
99A GLN* 3.0 13.3 - - - +
126A GLY 3.1 14.3 + - - +
127A VAL 3.4 11.2 - - - +
128A VAL 2.9 1.2 + - - -
129A ALA* 1.3 72.7 - - - +
131A PHE* 1.3 66.7 + - - +
133A GLU* 2.9 13.0 + - - +
134A PHE* 2.8 49.5 + - + -
137A ARG* 5.9 0.6 - - - +
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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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91A ILE* 3.4 30.1 - - + -
103A THR* 3.9 26.0 - - + -
106A PHE* 3.5 28.9 - + + -
121A VAL* 4.4 3.8 - - + -
127A VAL* 3.1 36.1 - - + -
128A VAL* 2.8 14.5 + - - +
130A ARG* 1.3 71.6 - - - +
132A VAL* 1.3 58.8 + - - +
134A PHE* 2.8 28.9 + + - +
135A LEU* 3.2 11.8 + - - +
147A SER* 4.1 17.2 - - - +
150A VAL* 3.7 26.0 - - + -
151A LEU* 4.1 21.3 - - + -
154A ILE* 5.0 1.3 - - + -
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Residues in contact with VAL 132 (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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128A VAL* 2.9 13.8 + - + +
129A ALA* 3.6 9.4 - - - +
131A PHE* 1.3 75.7 - - - +
133A GLU* 1.3 72.2 + - - +
135A LEU* 3.2 25.9 + - + +
136A LYS* 4.0 7.1 + - - +
151A LEU* 4.1 13.5 - - + -
165A VAL 4.8 0.7 - - - +
168A ALA* 3.4 36.3 - - + +
169A GLY 4.2 10.1 - - - +
170A ALA* 3.6 29.6 - - + -
173A ILE* 4.5 9.4 - - + +
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Residues in contact with GLU 133 (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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129A ALA* 2.9 19.9 + - + +
130A ARG* 2.9 15.5 + - - +
132A VAL* 1.3 78.8 - - - +
134A PHE* 1.3 71.1 + - + +
135A LEU 3.1 2.2 - - - -
136A LYS* 2.9 61.6 + - - +
137A ARG* 4.1 5.6 - - - +
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Residues in contact with PHE 134 (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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91A ILE* 3.6 26.5 - - + -
99A GLN* 3.7 24.0 - - + -
103A THR* 3.4 23.6 - - - -
130A ARG* 2.8 53.4 + - + -
131A PHE* 2.8 22.0 + + - +
133A GLU* 1.3 74.7 - - + +
135A LEU* 1.3 58.5 + - - -
136A LYS 3.0 0.7 + - - -
137A ARG* 3.3 43.4 + - - +
143A LEU* 3.7 15.4 - - + +
144A GLN* 3.7 12.3 + - - +
147A SER* 3.3 23.1 - - - +
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Residues in contact with LEU 135 (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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131A PHE 3.2 6.7 + - - +
132A VAL* 3.3 20.2 - - + +
133A GLU 3.1 1.4 - - - -
134A PHE* 1.3 76.8 - - - +
136A LYS* 1.3 53.8 + - - +
137A ARG 3.2 0.7 - - - -
144A GLN* 2.6 55.4 + - - +
147A SER* 4.0 5.6 - - - -
148A ALA* 3.8 12.6 - - + +
151A LEU* 3.9 10.8 - - + -
170A ALA 4.6 1.8 - - - +
173A ILE* 3.5 30.2 - - + +
174A PHE* 3.7 44.2 - - + -
177A LEU* 3.9 15.0 - - + +
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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