Contacts of the helix formed by residues 129 - 139 (chain B) in PDB entry 4NAT
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 SER 129 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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102A ARG* 5.7 4.3 - - - -
16B THR* 4.2 5.2 - - - -
92B ARG* 3.5 26.9 - - - +
127B PHE 4.7 1.2 + - - -
128B ILE* 1.3 76.1 - - - +
130B SER* 1.3 66.4 + - - +
131B SER* 3.5 10.5 + - - -
132B ILE* 3.2 25.7 + - - +
133B VAL* 3.1 25.4 + - - +
203B ADP 6.5 0.7 - - - -
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Residues in contact with SER 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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13B ASP* 3.4 29.9 + - - -
14B PRO* 2.7 24.3 + - - +
16B THR* 4.1 10.7 - - - +
19B HIS* 3.3 17.9 + - - -
92B ARG* 4.9 0.4 - - - +
129B SER* 1.3 74.3 - - - +
131B SER* 1.3 63.3 + - - +
133B VAL* 3.4 2.3 + - - +
134B LYS* 3.1 30.6 + - - +
203B ADP 4.2 7.9 + - - -
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Residues in contact with SER 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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129B SER* 3.1 10.6 + - - -
130B SER* 1.3 78.7 - - - +
132B ILE* 1.3 63.3 + - - +
134B LYS* 3.3 14.6 + - - +
135B GLU* 3.1 24.5 + - - +
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Residues in contact with ILE 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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102A ARG* 4.3 10.8 - - + +
103A LEU* 4.0 20.4 - - + -
106A MET* 3.9 40.0 - - + +
201A 2W5 4.0 25.1 - - + -
127B PHE 3.8 13.2 - - - +
128B ILE* 4.3 2.2 - - - -
129B SER* 3.2 29.5 + - - +
131B SER* 1.3 79.7 - - - +
133B VAL* 1.3 65.9 + - + +
135B GLU* 3.3 7.2 + - + +
136B VAL* 3.1 24.3 + - - +
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Residues in contact with VAL 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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106A MET* 5.1 2.0 - - + -
14B PRO* 5.3 2.5 - - + -
16B THR* 3.9 9.6 - - + -
128B ILE* 3.9 22.7 - - + -
129B SER 3.1 18.3 + - - +
130B SER* 3.7 4.9 - - - +
132B ILE* 1.3 81.2 - - + +
134B LYS* 1.3 57.5 + - + +
136B VAL* 3.5 4.5 + - - +
137B ALA* 2.9 27.9 + - - +
143B ILE* 4.4 9.2 - - + +
146B PHE* 4.1 21.1 - - + -
147B VAL* 3.7 15.0 - - + -
155B LEU* 3.7 26.5 - - + -
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Residues in contact with LYS 134 (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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13B ASP* 3.0 45.8 + - - +
14B PRO* 4.3 5.4 - - + -
45B GLY* 5.5 0.2 - - - -
46B THR* 3.1 36.4 - - + +
47B PHE* 4.9 0.2 - - + -
130B SER* 3.1 25.3 + - - +
131B SER* 3.8 9.3 - - - +
133B VAL* 1.3 73.5 - - - +
135B GLU* 1.3 66.2 + - - +
137B ALA* 3.8 6.3 - - - +
138B ALA* 3.0 24.9 + - - +
155B LEU* 3.9 21.5 - - + -
159B PHE* 4.0 13.9 - - + -
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Residues in contact with GLU 135 (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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201A 2W5 3.6 41.6 + - + +
131B SER* 3.1 15.9 + - - +
132B ILE* 3.4 18.6 - - + +
133B VAL 3.3 0.2 - - - -
134B LYS* 1.3 78.9 - - - +
136B VAL* 1.3 64.0 + - - +
138B ALA* 3.2 11.4 + - - +
139B TYR* 3.1 50.6 + - - -
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Residues in contact with VAL 136 (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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74A LEU* 4.7 2.0 - - + -
106A MET* 4.1 11.2 - - + -
110A LEU* 4.0 23.3 - - + -
201A 2W5 3.8 26.7 - - + -
132B ILE 3.1 16.0 + - - +
133B VAL* 3.9 3.4 - - - +
135B GLU* 1.3 78.4 - - - +
137B ALA* 1.3 62.9 + - - +
139B TYR* 3.3 8.0 + - - +
140B ARG 3.2 3.8 + - - -
141B ALA* 3.1 45.5 + - + +
143B ILE* 3.5 20.0 - - + -
146B PHE* 4.1 10.5 - - + -
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Residues in contact with ALA 137 (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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133B VAL 2.9 22.5 + - - +
134B LYS* 3.8 2.5 - - - +
135B GLU 3.3 0.2 - - - -
136B VAL* 1.3 73.9 - - - +
138B ALA* 1.3 55.5 + - - +
140B ARG* 2.8 27.6 + - - +
141B ALA 4.9 0.4 - - - -
143B ILE* 4.0 28.3 - - + -
155B LEU* 4.2 8.7 - - + +
156B LYS* 5.9 1.8 - - + -
159B PHE* 3.7 31.9 - - + +
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Residues in contact with ALA 138 (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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134B LYS 3.0 13.9 + - - +
135B GLU* 3.4 13.9 - - - +
137B ALA* 1.3 75.7 - - - +
139B TYR* 1.3 62.7 + - + +
140B ARG* 3.0 22.4 + - - -
159B PHE* 3.7 28.8 - - + -
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Residues in contact with TYR 139 (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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73A GLY* 3.5 42.2 + - - -
74A LEU* 3.6 30.1 - - + -
201A 2W5 3.6 24.0 - - - -
202A EPE 3.3 20.8 - - - +
135B GLU* 3.1 48.8 + - - -
136B VAL 3.3 7.4 + - - +
137B ALA 3.2 0.8 - - - -
138B ALA* 1.3 78.3 - - + +
140B ARG* 1.3 72.9 + - - +
141B ALA 3.2 0.7 + - - -
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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