Contacts of the helix formed by residues 119 - 129 (chain A) in PDB entry 4N1T
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 ASP 119 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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72A PHE* 3.3 13.4 - - + -
117A TRP* 3.3 6.4 - - - +
118A PRO* 1.3 78.6 - - - +
120A ASP* 1.3 66.6 + - - +
122A TYR* 3.0 16.5 + - - +
123A TRP* 2.9 35.1 + - - +
137A PHE* 3.7 35.7 - - + -
139A PHE* 3.3 6.7 - - + -
145A ILE* 3.7 11.4 - - + +
201A 2GD 2.9 43.7 + - - -
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Residues in contact with ASP 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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32A TRP 4.5 1.0 - - - +
33A ASN* 3.8 9.0 - - - +
113A PHE* 4.0 4.5 - - + -
116A MET* 3.3 39.4 - - + +
117A TRP* 3.1 20.0 + - - +
119A ASP* 1.3 82.1 - - - +
121A SER* 1.3 58.2 + - - +
123A TRP* 3.5 18.3 - - - +
124A PHE* 2.9 40.3 + - + +
201A 2GD 2.7 31.6 + - - -
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Residues in contact with SER 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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113A PHE* 3.6 36.8 + - - +
117A TRP 4.4 0.4 + - - -
118A PRO* 3.3 15.5 + - - +
119A ASP 3.1 0.6 - - - -
120A ASP* 1.3 80.2 - - - +
122A TYR* 1.3 65.5 + - - +
125A PRO* 3.4 17.0 - - - +
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Residues in contact with TYR 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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118A PRO* 3.8 11.2 - - + -
119A ASP* 3.0 13.0 + - - +
121A SER* 1.3 84.1 - - - +
123A TRP* 1.3 62.0 + - - +
124A PHE 3.7 0.2 - - - -
125A PRO* 3.7 8.7 - - - +
126A LEU* 4.1 9.0 - - - +
137A PHE* 3.9 19.3 - + + -
145A ILE* 4.1 19.6 - - + +
148A TYR* 3.3 43.6 - + + -
150A LEU* 3.7 22.3 - - + +
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Residues in contact with TRP 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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9A LEU* 3.9 22.2 - - + -
11A LEU* 4.2 7.6 - - + -
33A ASN* 5.2 1.1 - - - -
70A ILE* 3.4 25.7 - - + +
85A VAL* 4.4 3.6 - - + -
119A ASP* 2.9 49.2 + - + -
120A ASP* 3.5 22.1 - - - +
122A TYR* 1.3 76.0 - - - +
124A PHE* 1.3 89.5 + + - +
125A PRO 3.3 2.7 - - - -
126A LEU* 3.0 16.2 + - - +
127A LEU* 3.1 34.2 + - + -
133A PHE* 3.5 33.6 - + + -
137A PHE* 4.2 6.7 - + - -
150A LEU* 4.0 17.5 - - + -
201A 2GD 3.8 11.9 - - - -
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Residues in contact with PHE 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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11A LEU* 3.7 26.9 - - + -
18A VAL* 4.0 24.9 - - + -
20A LEU* 4.2 8.1 - - + -
34A GLY 5.9 0.2 - - - -
111A ILE* 3.6 33.7 - - + -
113A PHE* 3.7 14.1 - + + -
116A MET* 4.1 21.8 - - + -
120A ASP* 2.9 24.0 + - + +
123A TRP* 1.3 102.3 - + - +
125A PRO* 1.4 64.3 - - + +
127A LEU* 3.0 11.4 + - + +
128A LEU* 2.9 41.7 + - + +
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Residues in contact with PRO 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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113A PHE* 4.5 13.5 - - + -
120A ASP 3.6 0.9 - - - +
121A SER 3.4 26.2 - - - +
122A TYR 3.7 6.1 - - - +
123A TRP 3.5 3.4 - - - -
124A PHE* 1.4 94.8 - - + +
126A LEU* 1.3 63.4 + - + +
128A LEU* 3.4 14.9 + - + +
129A GLN* 3.2 25.9 + - - +
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Residues in contact with LEU 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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122A TYR 4.1 8.1 - - - +
123A TRP* 3.0 11.0 + - - +
125A PRO* 1.3 76.6 - - + +
127A LEU* 1.3 63.7 + - - +
129A GLN* 3.2 7.7 + - - +
130A LYS 3.2 4.2 + - - -
131A LYS* 2.8 43.0 + - + +
133A PHE* 4.1 24.2 - - + -
150A LEU* 3.7 34.3 - - + -
151A ARG* 6.1 0.2 - - - -
152A GLU* 3.3 34.3 - - + +
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Residues in contact with LEU 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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11A LEU* 3.8 30.1 - - + -
13A LEU* 3.7 28.3 - - + +
18A VAL* 5.9 0.2 - - + -
67A VAL* 3.7 29.8 - - + -
85A VAL* 4.1 1.3 - - + -
87A CYS* 4.2 12.3 - - + -
123A TRP* 3.1 33.9 + - + +
124A PHE* 3.0 18.1 + - + +
126A LEU* 1.3 74.4 - - - +
128A LEU* 1.3 71.8 + - + +
130A LYS* 3.1 15.9 + - - +
131A LYS 4.2 8.2 + - - -
133A PHE* 4.5 4.8 - - + -
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Residues in contact with LEU 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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13A LEU* 3.8 32.4 - - + +
108A LEU* 4.2 27.7 - - + +
111A ILE* 3.7 22.4 - - + -
113A PHE* 5.5 3.4 - - + -
124A PHE* 2.9 39.8 + - + +
125A PRO* 3.6 16.2 - - + +
126A LEU 3.2 0.2 - - - -
127A LEU* 1.3 78.2 - - + +
129A GLN* 1.3 56.7 + - - +
130A LYS* 3.2 13.2 + - - +
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Residues in contact with GLN 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* 3.2 14.9 + - - +
126A LEU* 3.2 10.5 + - - +
128A LEU* 1.3 76.5 - - + +
130A LYS* 1.3 71.6 + - - +
131A LYS* 3.2 40.6 + - + +
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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