Contacts of the helix formed by residues 63 - 73 (chain A) in PDB entry 3IKH
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 63 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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61A GLY 3.3 0.9 - - - +
62A ASN* 1.3 76.3 - - - +
64A SER* 1.3 65.8 + - - +
65A ASN* 4.1 4.9 - - - -
66A GLY 2.9 14.4 + - - -
67A ALA* 3.2 12.5 + - - +
70A ARG* 4.8 0.9 + - - -
88A GLN* 2.7 11.7 - - - +
89A HIS* 2.5 57.4 - - - +
31C LYS* 4.5 9.9 + - - +
34C GLN* 4.5 23.9 + - - +
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Residues in contact with SER 64 (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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63A ASP* 1.3 74.6 - - - +
65A ASN* 1.3 69.8 + - - +
67A ALA* 3.4 7.2 + - - +
68A TRP* 3.1 23.5 + - - +
13C GLU* 5.0 2.6 + - - -
34C GLN* 4.8 11.6 + - - -
64C SER* 4.4 17.9 - - - -
65C ASN* 4.9 16.6 + - - -
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Residues in contact with ASN 65 (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 VAL* 3.5 23.4 - - + +
13A GLU* 3.2 19.9 + - - +
31A LYS* 5.1 1.2 + - - -
34A GLN* 3.7 20.1 + - - +
63A ASP* 3.3 6.2 + - - +
64A SER* 1.3 89.3 + - - +
66A GLY* 1.3 58.0 + - - +
68A TRP* 3.6 6.0 - - - +
69A ILE* 2.9 34.0 + - - +
89A HIS* 3.5 14.6 - - + +
91A ASP* 3.0 27.1 + - - +
13C GLU* 5.9 0.4 - - - -
31C LYS* 3.6 10.6 - - - +
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Residues in contact with GLY 66 (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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60A THR* 4.6 0.2 - - - -
61A GLY 3.7 6.3 - - - -
63A ASP* 2.9 14.6 + - - -
65A ASN* 1.3 74.5 - - - +
67A ALA* 1.3 65.8 + - - +
69A ILE* 3.2 3.0 + - - +
70A ARG* 3.0 35.9 + - - +
89A HIS* 2.5 29.6 + - - -
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Residues in contact with ALA 67 (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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63A ASP 3.2 10.9 + - - +
64A SER* 3.4 9.2 + - - +
66A GLY* 1.3 74.6 - - - +
68A TRP* 1.3 57.5 + - - +
70A ARG* 3.4 21.1 + - - +
71A GLN* 2.9 30.6 + - - +
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Residues in contact with TRP 68 (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 VAL* 3.9 21.1 - - + -
34A GLN* 3.5 49.7 + - + +
35A ASP* 3.8 10.8 - - - -
36A ILE* 3.7 31.6 - - + -
64A SER 3.1 17.1 + - - +
65A ASN* 3.6 7.9 - - - +
67A ALA* 1.3 74.4 - - - +
69A ILE* 1.3 60.1 + - - +
71A GLN* 3.2 14.2 + - - +
72A GLN* 2.8 72.8 + - + +
118B ASP* 4.5 21.4 + - + +
119B GLU* 6.3 0.4 - - - +
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Residues in contact with ILE 69 (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 ILE* 3.4 40.6 - - + +
10A THR* 3.9 24.0 - - - +
11A VAL* 3.5 20.2 - - + -
36A ILE* 3.8 11.2 - - + +
60A THR* 4.0 14.4 - - + -
65A ASN 2.9 19.1 + - - +
66A GLY 3.2 6.5 + - - +
68A TRP* 1.3 78.4 - - + +
70A ARG* 1.3 59.1 + - - +
71A GLN 3.1 0.2 + - - -
72A GLN 3.8 0.2 - - - -
73A ILE* 2.9 30.8 + - - +
80A LEU* 4.7 3.8 - - + -
89A HIS* 3.1 31.2 - - + +
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Residues in contact with ARG 70 (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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60A THR* 2.7 41.9 + - + +
61A GLY 3.0 23.4 + - - -
62A ASN* 4.8 1.6 - - - +
63A ASP 4.8 1.8 + - - -
66A GLY 3.0 17.0 + - - +
67A ALA* 3.5 26.6 - - - +
69A ILE* 1.3 79.2 - - - +
71A GLN* 1.3 61.0 + - - +
73A ILE* 3.3 19.5 - - - +
74A LYS* 3.4 14.4 - - - +
80A LEU* 4.7 8.1 - - + -
82A PRO 6.0 0.2 - - - -
83A ASP* 5.6 0.7 - - - +
84A GLY* 3.2 23.8 + - - +
85A HIS* 3.2 28.3 + - - +
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Residues in contact with GLN 71 (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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67A ALA 2.9 17.3 + - - +
68A TRP* 3.6 16.6 - - - +
70A ARG* 1.3 76.3 - - - +
72A GLN* 1.3 107.0 + - - +
74A LYS* 3.2 27.5 + - + +
75A ASN* 4.3 6.9 + - - -
119B GLU* 4.4 19.1 + - - +
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Residues in contact with GLN 72 (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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36A ILE* 3.4 19.6 - - + +
68A TRP* 2.8 63.0 + - + +
71A GLN* 1.3 98.1 + - - +
73A ILE* 1.3 64.6 + - - +
75A ASN* 3.2 28.1 + - - +
76A GLU* 4.4 1.0 + - - +
271A LEU* 4.8 11.4 - - + +
118B ASP 3.7 24.1 + - - +
119B GLU* 4.8 4.9 - - - +
122B PRO* 3.8 16.0 - - - +
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Residues in contact with ILE 73 (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 ILE* 4.2 17.5 - - + -
36A ILE* 3.7 7.1 - - + +
45A ILE* 3.7 35.0 - - + -
56A LEU* 4.8 1.3 - - + -
69A ILE 2.9 16.1 + - - +
70A ARG* 3.3 22.2 - - - +
72A GLN* 1.3 76.7 - - - +
74A LYS* 1.3 61.4 + - + +
75A ASN 3.0 0.9 - - - -
76A GLU* 3.0 31.1 + - + +
78A LEU* 4.4 19.1 - - + +
80A LEU* 4.1 34.1 - - + -
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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