Contacts of the helix formed by residues 61 - 71 (chain B) in PDB entry 4ICX
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 61 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7B GLN* 3.4 27.2 + - - +
60B ILE* 1.3 79.9 - - - +
62B ARG* 1.3 68.3 + - - +
63B LYS* 3.3 33.6 + - - +
64B ALA* 3.1 14.2 + - + +
65B LEU* 3.0 24.4 + - - +
27C MSE 5.6 0.3 - - - +
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Residues in contact with ARG 62 (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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7B GLN* 4.2 4.7 + - - +
8B LEU* 4.0 23.3 - - + +
60B ILE 3.9 1.2 + - - -
61B ASP* 1.3 76.5 + - - +
63B LYS* 1.3 68.3 + - - +
65B LEU* 3.5 12.3 + - + +
66B HIS 3.6 6.8 + - - -
23C ARG 5.1 0.4 + - - -
24C PRO* 3.2 26.9 + - - +
25C LYS* 3.7 6.3 - - - +
26C HIS* 3.3 32.8 + - - +
27C MSE 3.5 20.8 - - + +
45C ASP* 2.7 31.9 + - - +
46C HIS 4.7 0.4 - - - +
84C PRO* 3.7 34.3 - - + +
85C VAL* 5.8 1.3 - - + -
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Residues in contact with LYS 63 (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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61B ASP* 3.3 17.8 + - - +
62B ARG* 1.3 80.2 - - - +
64B ALA* 1.3 70.2 + - + +
66B HIS* 3.0 18.3 + - - +
67B GLN* 3.1 30.0 + - - +
27C MSE 3.5 29.8 - - + -
42C ASP* 3.8 17.6 + - - +
43C PRO* 4.3 23.4 + - + +
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Residues in contact with ALA 64 (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 LYS* 6.4 0.2 - - - +
60B ILE* 4.1 16.4 - - + -
61B ASP* 3.1 23.1 + - + +
63B LYS* 1.3 83.7 - - + +
65B LEU* 1.3 56.1 - - - +
67B GLN* 3.4 15.2 + - - +
68B HIS* 3.0 42.1 + - + +
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Residues in contact with LEU 65 (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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8B LEU* 3.8 27.1 - - + -
10B ILE* 4.9 0.4 - - + -
60B ILE* 4.1 16.3 - - + +
61B ASP 3.0 11.6 + - - +
62B ARG* 3.7 8.3 - - - +
63B LYS 3.2 0.4 - - - -
64B ALA* 1.3 75.1 - - - +
66B HIS* 1.3 62.5 + - - +
68B HIS* 4.1 4.0 - - - +
69B ARG* 3.2 39.5 + - - +
99B LEU* 4.3 22.2 - - + +
132B LEU* 3.9 34.5 - - + -
84C PRO 3.4 22.4 - - - +
85C VAL* 4.3 4.7 - - - -
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Residues in contact with HIS 66 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62B ARG 3.6 7.2 + - - +
63B LYS* 3.0 12.6 + - - +
65B LEU* 1.3 78.9 - - - +
67B GLN* 1.3 58.2 + - - +
69B ARG* 3.4 10.9 + - + +
70B LEU* 3.1 48.7 + - + +
27C MSE 6.1 0.2 - - - -
29C VAL* 4.9 5.3 - - - +
43C PRO* 3.4 30.0 - - + +
82C LEU* 3.6 41.5 - - + +
84C PRO* 5.0 9.5 + - + +
87C SER* 4.1 19.2 + - - -
89C LYS* 5.9 3.3 - - + +
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Residues in contact with GLN 67 (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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105A THR* 5.0 0.2 - - - +
106A LYS* 3.6 49.5 + - + +
63B LYS* 3.1 27.1 + - - +
64B ALA* 3.8 19.6 - - - +
66B HIS* 1.3 76.8 - - - +
68B HIS* 1.3 59.3 + - + +
70B LEU* 3.3 15.8 + - + +
71B GLN* 3.1 35.1 + - - +
42C ASP* 2.8 40.0 + - - +
43C PRO* 5.0 7.4 - - + -
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Residues in contact with HIS 68 (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 LYS* 5.2 9.8 + - - -
34B PHE* 3.6 10.2 - + - -
35B ASP* 3.3 41.5 + - + -
60B ILE* 3.5 28.8 - - + +
64B ALA* 3.0 29.2 + - - +
65B LEU* 4.1 2.2 - - - +
66B HIS 3.4 0.2 - - - -
67B GLN* 1.3 74.3 - - + +
69B ARG* 1.3 63.9 + - - +
70B LEU 3.2 0.4 - - - -
71B GLN* 3.9 9.9 + - - -
72B ARG* 3.3 2.1 + - - -
73B THR* 2.9 52.1 + - + +
99B LEU* 3.6 21.7 - - + +
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Residues in contact with ARG 69 (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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65B LEU* 3.2 37.2 + - + +
66B HIS* 3.6 11.1 + - - +
67B GLN 3.3 0.2 - - - -
68B HIS* 1.3 78.8 - - - +
70B LEU* 1.3 61.3 + - - +
72B ARG* 3.6 23.4 + - - +
99B LEU* 3.8 18.5 + - + +
100B ARG* 4.1 37.9 + - + +
102B ALA 3.5 20.8 + - - -
132B LEU* 4.3 2.4 - - - +
84C PRO 3.6 15.2 + - - -
85C VAL 3.2 25.7 + - - -
86C THR 5.1 2.2 + - - -
87C SER* 3.8 29.2 + - - -
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Residues in contact with LEU 70 (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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105A THR* 5.2 11.4 - - + -
106A LYS 4.0 21.8 - - - +
108A ALA* 3.9 18.8 + - - +
66B HIS* 3.1 42.1 + - + +
67B GLN* 3.4 22.2 - - + +
68B HIS 3.2 0.2 - - - -
69B ARG* 1.3 75.0 - - - +
71B GLN* 1.3 56.1 + - - +
72B ARG* 3.1 12.4 + - - +
43C PRO* 5.7 2.7 - - + -
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Residues in contact with GLN 71 (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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13A SER* 5.1 7.1 + - - -
15A LEU* 6.3 1.2 - - - +
55A GLU* 5.6 1.6 + - - -
106A LYS* 3.4 41.5 + - + +
107A GLN 3.5 17.6 + - - +
108A ALA* 4.0 8.3 - - - +
109A PRO* 3.4 22.8 - - + +
129A SER* 4.2 18.4 + - - -
67B GLN 3.1 20.0 + - - +
68B HIS* 3.6 11.1 + - - -
70B LEU* 1.3 73.5 - - - +
72B ARG* 1.3 69.9 + - - +
73B THR* 3.1 21.2 + - - +
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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