Contacts of the helix formed by residues 131 - 141 (chain A) in PDB entry 2NDG
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 131 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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96A GLU* 3.4 44.3 - - + +
129A ASN 4.1 0.8 + - - -
130A PRO* 1.3 72.9 - - - +
132A GLU* 1.3 75.7 + - - +
133A ASP* 4.0 14.0 + - + +
134A PHE* 2.9 9.4 + - + +
135A ARG* 2.9 19.4 + - - +
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Residues in contact with GLU 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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1A GLY* 3.3 34.8 + - - +
130A PRO 3.8 0.6 + - - -
131A THR* 1.3 76.6 + - - +
133A ASP* 1.3 55.9 + - - +
135A ARG* 3.5 23.6 + - - +
136A ARG* 2.6 48.7 + - + +
139A LEU* 5.5 0.3 - - - +
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Residues in contact with ASP 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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96A GLU* 5.2 3.4 - - - +
131A THR* 3.2 14.0 + - + +
132A GLU* 1.3 79.2 - - - +
134A PHE* 1.3 60.1 + - - +
136A ARG* 2.7 35.3 + - - +
137A LYS* 2.9 36.8 + - - +
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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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50A PHE* 4.7 11.0 - + + -
92A PHE* 5.0 5.6 - + + -
93A LYS 3.7 13.0 - - - -
94A ASN* 3.8 20.9 - - - -
96A GLU* 3.1 28.7 + - + +
97A GLU* 6.0 1.3 - - + -
127A PHE* 3.5 43.3 - + + -
130A PRO* 3.7 17.3 - - + -
131A THR* 2.9 12.9 + - + +
133A ASP* 1.3 77.9 - - - +
135A ARG* 1.3 66.8 + - - +
137A LYS* 3.0 17.7 + - - +
138A LEU* 2.9 56.8 + - + +
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Residues in contact with ARG 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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8A CYS* 3.5 36.5 - - - +
9A ALA 5.7 0.2 - - - -
10A VAL* 3.6 22.8 - - - +
130A PRO* 4.2 19.5 - - + +
131A THR 2.9 15.4 + - - +
132A GLU* 3.5 21.5 + - - +
134A PHE* 1.3 73.8 - - - +
136A ARG* 1.3 55.5 + - - +
138A LEU* 3.2 8.5 + - - +
139A LEU* 2.8 71.7 + - + +
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Residues in contact with ARG 136 (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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132A GLU* 2.6 30.7 + - + +
133A ASP* 2.7 45.6 + - - +
135A ARG* 1.3 74.0 - - - +
137A LYS* 1.3 92.8 + - - +
139A LEU* 3.5 12.4 + - - +
140A LYS* 3.2 46.5 + - - +
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Residues in contact with LYS 137 (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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49A HIS* 3.1 35.0 - - + +
50A PHE* 4.1 7.6 - - + -
93A LYS* 2.9 45.4 + - + -
94A ASN* 5.1 0.2 - - - +
96A GLU* 4.9 1.0 + - - -
133A ASP* 2.9 30.6 + - - +
134A PHE* 3.0 17.2 + - - +
136A ARG* 1.3 98.6 - - - +
138A LEU* 1.3 65.9 + - - +
139A LEU 3.1 1.8 - - - -
140A LYS* 3.0 20.8 + - - +
141A ALA* 3.1 10.6 + - - +
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Residues in contact with LEU 138 (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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10A VAL* 3.2 43.8 - - + +
11A GLN 5.5 1.4 - - - +
12A VAL* 3.4 23.8 - - + +
50A PHE* 3.4 26.4 - - + -
127A PHE* 3.9 14.1 - - + -
130A PRO* 4.6 0.9 - - + -
134A PHE* 2.9 66.0 + - + +
135A ARG* 3.5 3.8 - - - +
137A LYS* 1.3 76.4 - - - +
139A LEU* 1.3 60.6 + - - +
141A ALA* 3.3 16.8 - - - +
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Residues in contact with LEU 139 (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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10A VAL* 4.5 11.9 - - + -
132A GLU* 5.5 0.9 - - - +
135A ARG* 2.8 78.1 + - + +
136A ARG* 3.6 9.6 - - - +
137A LYS 3.1 0.2 - - - -
138A LEU* 1.3 74.4 - - - +
140A LYS* 1.3 64.5 + - - +
141A ALA 3.1 7.7 + - - +
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Residues in contact with LYS 140 (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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49A HIS* 3.2 38.4 + - + +
136A ARG* 3.2 41.1 + - - +
137A LYS* 3.0 13.1 + - - +
139A LEU* 1.3 77.3 - - - +
141A ALA* 1.3 66.8 + - - +
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Residues in contact with ALA 141 (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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12A VAL* 5.5 0.2 - - + -
44A HIS 3.7 6.7 - - - +
45A SER* 3.4 17.9 - - - -
46A ASN* 2.7 42.6 + - - +
49A HIS* 3.9 4.0 - - - -
50A PHE* 3.2 40.2 - - + -
137A LYS 3.1 6.0 + - - +
138A LEU 3.3 16.2 - - - +
139A LEU 3.1 5.8 - - - +
140A LYS* 1.3 83.0 - - - +
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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