Contacts of the helix formed by residues 120 - 129 (chain A) in PDB entry 4U7D
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 120 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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118A GLY* 3.3 1.7 - - - -
119A LYS* 1.3 80.5 + - - +
121A LEU* 1.3 64.4 + - - +
122A CYS 3.0 1.0 + - - -
123A TYR* 3.2 21.8 + - - -
124A GLN* 3.2 31.7 + - - +
147A GLN* 2.9 36.1 + - - -
219A ASP* 5.2 2.6 + - - -
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Residues in contact with LEU 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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83A LEU* 4.0 14.4 - - + -
87A PHE* 3.7 42.0 - - + -
89A LEU* 3.8 25.4 - - + -
92A PHE* 4.3 6.3 - - + -
96A GLN* 3.4 40.8 - - + +
100A ILE* 4.3 3.7 - - + +
118A GLY* 3.9 4.1 + - - +
120A SER* 1.3 78.7 - - - +
122A CYS* 1.3 58.6 + - - +
123A TYR 3.1 5.6 + - - -
124A GLN* 3.7 7.3 + - - +
125A LEU* 3.1 39.6 + - + +
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Residues in contact with CYS 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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96A GLN* 3.9 34.3 - - - -
99A THR* 4.0 20.0 - - + -
100A ILE* 3.8 14.7 - - + +
103A THR* 4.3 5.4 + - - -
111A LEU* 3.8 21.8 - - + -
118A GLY 3.9 11.9 - - - -
119A LYS 3.1 14.5 + - - +
120A SER 3.0 1.0 + - - -
121A LEU* 1.3 78.3 - - - +
123A TYR* 1.3 57.1 + - - +
126A PRO* 3.5 16.9 - - - +
251A ILE* 3.7 15.4 - - + +
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Residues in contact with TYR 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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103A THR* 5.8 0.4 - - - -
119A LYS 4.2 1.8 - - - -
120A SER* 3.5 21.0 - - - -
122A CYS* 1.3 77.7 - - - +
124A GLN* 1.3 84.1 + - + +
125A LEU 3.3 1.6 - - - -
126A PRO* 3.6 7.3 - - - +
127A ALA* 3.3 21.0 + - - +
134A THR* 4.0 9.5 - - + +
136A VAL* 3.8 20.2 - - + +
147A GLN* 2.9 24.7 + - - -
186A LEU* 4.0 8.1 - - + -
188A TYR* 3.5 19.0 + - - -
215A ARG* 5.0 2.2 - - - +
217A ALA* 3.7 15.5 - - + -
219A ASP* 4.0 14.1 + - - -
251A ILE* 3.8 22.2 - - + -
253A LEU* 3.6 34.3 - - + -
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Residues in contact with GLN 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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87A PHE* 4.2 21.0 - - + -
120A SER* 3.2 28.5 + - - +
121A LEU* 3.7 7.6 + - - +
123A TYR* 1.3 91.7 - - + +
125A LEU* 1.3 62.7 + - - +
127A ALA* 3.3 16.5 - - - +
128A LEU* 3.3 15.2 - - - +
147A GLN* 3.3 28.1 + - - +
150A VAL* 6.1 1.9 - - - +
151A LEU* 4.1 17.2 - - + +
186A LEU* 4.0 18.1 - - + +
188A TYR* 3.2 21.1 + - - +
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Residues in contact with LEU 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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79A VAL* 3.9 27.8 - - + +
82A ILE* 4.0 22.7 - - + -
83A LEU* 4.1 26.9 - - + +
87A PHE* 4.0 22.0 - - + -
92A PHE* 4.6 9.9 - - + -
100A ILE* 4.2 12.8 - - + -
121A LEU* 3.1 18.4 + - + +
124A GLN* 1.3 75.5 - - - +
126A PRO* 1.3 75.8 - - + +
128A LEU* 2.9 16.5 + - - +
129A CYS* 3.2 29.8 + - - -
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Residues in contact with PRO 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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100A ILE* 4.0 17.9 - - + -
103A THR* 4.6 6.1 - - + -
104A MET* 3.7 24.1 - - + +
122A CYS 3.5 21.3 - - - +
123A TYR* 3.6 12.1 - - - +
125A LEU* 1.3 98.0 - - + +
127A ALA* 1.3 62.9 + - - +
129A CYS* 2.8 15.1 + - + +
130A SER* 3.1 15.6 + - - -
215A ARG* 3.5 27.3 + - - +
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Residues in contact with ALA 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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123A TYR 3.3 7.8 + - - +
124A GLN 3.3 13.2 - - - +
125A LEU 3.3 0.4 - - - -
126A PRO* 1.3 78.6 - - - +
128A LEU* 1.3 60.7 + - + +
130A SER* 3.4 12.5 + - - +
132A GLY 4.0 3.5 - - - +
133A PHE* 5.2 0.6 - - - -
134A THR* 3.2 30.0 + - - +
185A LYS* 2.9 41.0 - - - +
186A LEU* 3.8 10.3 - - + -
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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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78A LYS* 5.2 2.1 + - - +
82A ILE* 4.2 18.3 - - + +
86A VAL* 4.0 21.3 - - + -
87A PHE* 4.0 26.5 - - + -
124A GLN 3.3 15.3 - - - +
125A LEU 2.9 10.3 + - - +
127A ALA* 1.3 76.3 - - + +
129A CYS* 1.3 58.5 + - - +
130A SER 3.2 10.1 + - - +
156A ILE* 4.2 24.2 - - + -
185A LYS* 3.9 31.0 + - + +
186A LEU* 4.6 2.9 - - + -
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Residues in contact with CYS 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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78A LYS* 3.8 31.9 + - + +
79A VAL* 4.1 13.0 - - - -
82A ILE* 3.2 28.3 - - - -
104A MET* 3.1 32.0 - - + +
125A LEU* 3.3 31.9 - - - +
126A PRO 2.8 5.6 + - - +
128A LEU* 1.3 76.1 - - - +
130A SER* 1.3 58.1 + - - +
215A ARG* 4.9 0.2 + - - -
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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