Contacts of the helix formed by residues 123 - 134 (chain B) in PDB entry 1NDD
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 VAL 123 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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121B ASP 3.9 0.6 + - - -
122B LYS* 1.3 72.5 - - - +
124B GLU* 1.3 63.2 + - - +
126B ILE* 3.0 21.7 + - + +
127B LYS* 3.0 14.3 + - - +
143B LEU* 4.3 10.1 - - + -
150B MET* 3.6 42.8 - - + +
151B ASN 3.2 28.3 - - - +
152B ASP* 3.6 15.5 + - - +
154B LYS 2.8 15.7 + - - +
155B THR 4.5 4.9 - - - -
159B TYR* 3.8 17.9 - - + -
161B ILE* 5.4 0.2 - - + -
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Residues in contact with GLU 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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122B LYS* 3.1 6.0 - - + -
123B VAL* 1.3 76.4 - - - +
125B ARG* 1.3 56.4 + - - +
127B LYS* 3.3 7.3 + - - +
128B GLU* 2.9 44.3 + - + +
138B PRO* 3.6 27.0 - - - +
139B GLN* 5.9 1.0 - - - +
152B ASP* 3.2 46.4 + - + +
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Residues in contact with ARG 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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117B ILE* 5.6 0.4 - - + -
121B ASP* 3.5 35.6 + - + +
122B LYS* 2.8 25.7 + - + +
124B GLU* 1.3 76.3 - - - +
126B ILE* 1.3 63.2 + - - +
128B GLU* 3.1 11.3 + - - +
129B ARG* 2.8 66.3 + - + +
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Residues in contact with ILE 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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103B ILE* 4.2 11.2 - - + -
105B VAL* 5.1 1.8 - - + -
115B ILE* 4.9 3.1 - - + +
117B ILE* 3.8 38.4 - - + -
121B ASP* 5.1 2.7 - - + -
122B LYS 3.8 8.5 - - - +
123B VAL* 3.0 14.5 + - + +
125B ARG* 1.3 75.7 - - - +
127B LYS* 1.3 62.6 + - - +
129B ARG* 3.1 9.0 + - - +
130B VAL* 3.0 28.0 + - + +
143B LEU* 3.8 17.9 - - + -
150B MET* 4.0 23.6 - - + -
156B ALA* 4.4 7.4 - - + -
161B ILE* 4.4 7.4 - - + -
167B LEU* 4.0 16.6 - - + -
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Residues in contact with LYS 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 VAL* 3.0 15.2 + - - +
124B GLU* 3.5 14.6 - - - +
125B ARG 3.2 0.2 - - - -
126B ILE* 1.3 77.0 - - - +
128B GLU* 1.3 56.7 + - - +
130B VAL* 3.2 1.3 + - - -
131B GLU* 2.9 24.9 + - - +
138B PRO* 3.8 30.3 + - + +
141B GLN* 2.9 58.2 + - + +
142B ARG* 4.4 3.2 - - - +
143B LEU* 3.6 33.1 - - + +
150B MET 4.5 6.6 + - - -
152B ASP* 2.7 34.2 + - - +
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Residues in contact with GLU 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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124B GLU* 2.9 33.6 + - + +
125B ARG* 3.1 15.2 + - - +
127B LYS* 1.3 75.9 - - - +
129B ARG* 1.3 66.8 + - - +
131B GLU* 3.0 28.3 + - - +
132B GLU* 3.0 37.9 + - - +
138B PRO* 3.6 14.5 - - + +
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Residues in contact with ARG 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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115B ILE* 3.6 32.5 - - + +
116B ASP 4.4 11.0 + - - +
117B ILE* 4.4 8.5 - - + -
121B ASP* 5.7 1.4 + - - -
125B ARG* 2.8 66.7 + - + +
126B ILE 3.1 8.0 + - - +
128B GLU* 1.3 80.4 - - - +
130B VAL* 1.3 61.5 + - - +
132B GLU* 3.3 39.7 + - - +
133B LYS* 3.2 22.5 + - - +
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Residues in contact with VAL 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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105B VAL* 4.4 27.8 - - + -
113B ILE* 4.7 11.0 - - + -
115B ILE* 4.5 11.2 - - + -
126B ILE* 3.0 23.2 + - + +
127B LYS* 3.4 2.2 - - - +
129B ARG* 1.3 77.2 - - - +
131B GLU* 1.3 52.3 + - - +
133B LYS 3.2 1.6 + - - -
134B GLU* 2.8 42.0 + - + +
136B ILE* 4.9 4.3 - - + -
141B GLN* 3.4 32.1 - - - +
143B LEU* 5.1 3.8 - - + -
169B LEU* 4.0 19.7 - - + -
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Residues in contact with GLU 131 (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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127B LYS 2.9 12.6 + - - +
128B GLU* 3.0 30.7 + - - +
130B VAL* 1.3 77.2 - - - +
132B GLU* 1.3 60.8 + - + +
135B GLY* 2.7 34.5 + - - +
136B ILE 3.2 29.4 - - - +
137B PRO* 4.2 6.7 - - - +
138B PRO* 3.2 20.2 - - + +
141B GLN* 3.9 0.4 - - - +
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Residues in contact with GLU 132 (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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128B GLU* 3.0 21.8 + - - +
129B ARG* 3.4 44.9 + - - +
130B VAL 3.3 0.2 - - - -
131B GLU* 1.3 77.1 - - + +
133B LYS* 1.3 63.1 + - + +
135B GLY 5.0 0.2 + - - -
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Residues in contact with LYS 133 (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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113B ILE* 4.5 13.2 - - + +
114B GLU* 3.3 24.6 + - - +
115B ILE* 3.6 23.1 - - + +
129B ARG 3.2 10.4 + - - +
130B VAL 3.2 4.5 + - - +
132B GLU* 1.3 82.8 - - + +
134B GLU* 1.3 77.2 + - + +
135B GLY 3.9 0.2 - - - -
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Residues in contact with GLU 134 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
113B ILE* 3.3 34.6 - - + +
130B VAL* 2.8 23.0 + - + +
133B LYS* 1.3 89.9 - - - +
135B GLY* 1.3 60.8 + - - +
136B ILE* 3.4 11.3 + - + +
237C PRO* 4.4 0.7 - - - +
240C GLN* 2.9 50.4 + - - +
273C LEU* 3.5 42.6 - - + +
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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