Contacts of the helix formed by residues 53 - 64 (chain A) in PDB entry 1KXJ
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 HIS 53 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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10A PRO* 5.3 0.2 - - - +
52A GLY* 1.3 76.8 - - - -
54A PHE* 1.3 66.5 + - - +
55A GLY 4.6 2.7 - - - +
56A GLU* 3.1 23.0 + - + +
57A GLY 3.1 17.8 + - - -
85A LEU* 3.6 6.0 - - - +
96A GLU* 2.8 28.5 + - + +
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Residues in contact with PHE 54 (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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52A GLY 3.9 0.8 + - - -
53A HIS* 1.3 70.7 - - - +
55A GLY* 1.3 61.4 + - - +
57A GLY 3.3 1.6 + - - -
58A MET* 3.2 23.3 + - + +
85A LEU* 4.1 11.1 - - + +
88A GLN* 3.6 35.9 - - + +
89A LEU* 3.6 20.0 - - + +
91A PHE 4.9 0.7 - - - -
93A GLU 4.3 6.3 - - - -
94A SER* 3.3 38.8 - - - +
96A GLU* 3.0 26.4 + - + +
97A ALA* 3.4 17.3 - - + -
100A VAL* 3.8 31.2 - - + -
102A GLY* 3.8 24.0 - - - -
110A VAL* 4.7 1.1 - - + -
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Residues in contact with GLY 55 (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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53A HIS* 3.3 2.8 - - - +
54A PHE* 1.3 75.3 - - - +
56A GLU* 1.3 54.9 + - - +
58A MET* 3.2 3.8 + - - +
59A ARG* 2.8 34.3 + - - +
62A ARG* 5.0 1.6 + - - -
96A GLU* 5.8 0.4 - - - +
97A ALA* 3.6 21.8 - - - +
100A VAL* 4.2 17.0 - - - +
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Residues in contact with GLU 56 (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 PRO* 3.9 13.2 - - + -
53A HIS* 3.1 25.4 + - + +
55A GLY* 1.3 76.3 - - - +
57A GLY* 1.3 58.1 + - - +
59A ARG* 3.1 39.8 + - - +
60A ARG* 2.7 73.7 + - - +
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Residues in contact with GLY 57 (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 GLY* 5.5 0.5 - - - -
10A PRO* 3.9 18.5 - - - +
53A HIS 3.1 12.1 + - - -
54A PHE 3.3 4.0 + - - -
55A GLY 3.2 0.2 - - - -
56A GLU* 1.3 78.2 - - - +
58A MET* 1.3 61.1 + - - +
60A ARG* 3.4 2.4 + - - +
61A LEU* 3.2 27.9 + - - +
85A LEU* 4.3 4.9 - - - -
89A LEU* 4.1 19.0 - - - +
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Residues in contact with MET 58 (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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54A PHE* 3.2 16.6 + - + +
55A GLY 3.2 6.8 + - - +
57A GLY* 1.3 76.8 - - - +
59A ARG* 1.3 62.2 + - - +
61A LEU* 3.6 4.9 + - + +
62A ARG* 3.0 38.8 + - + +
67A ILE* 3.9 26.2 - - + -
89A LEU* 3.6 30.0 - - + +
100A VAL* 4.0 11.4 - - + -
101A LYS 3.5 23.8 - - - +
102A GLY* 3.5 25.1 - - - +
103A LEU* 3.5 18.4 - - + +
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Residues in contact with ARG 59 (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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55A GLY 2.8 14.6 + - - +
56A GLU* 3.1 43.0 + - - +
58A MET* 1.3 74.0 - - - +
60A ARG* 1.3 71.7 + - - +
62A ARG* 3.1 25.8 + - - +
63A GLU* 2.7 52.1 + - + +
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Residues in contact with ARG 60 (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 VAL* 3.2 40.2 + - + +
9A GLY* 4.0 9.4 - - - +
10A PRO* 3.5 25.7 - - + +
56A GLU* 2.7 44.6 + - - +
57A GLY 3.4 4.2 + - - +
59A ARG* 1.3 91.4 - - - +
61A LEU* 1.3 62.1 + - + +
63A GLU* 4.3 5.6 - - - -
64A ASN* 3.0 31.6 + - - +
205A PO4 3.3 40.4 + - - -
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Residues in contact with LEU 61 (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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6A ILE* 3.9 30.1 - - + -
8A VAL* 4.4 5.2 - - + -
9A GLY* 5.6 2.2 - - - +
48A ILE* 4.4 11.0 - - + -
57A GLY 3.2 13.6 + - - +
58A MET* 3.8 7.9 - - - +
60A ARG* 1.3 81.5 - - + +
62A ARG* 1.3 59.4 + - - +
64A ASN 3.6 0.9 + - - -
65A ASP 3.3 2.6 + - - -
66A LEU* 2.9 42.8 + - + +
67A ILE* 3.9 16.1 + - + +
70A VAL* 5.6 5.8 - - + -
89A LEU* 4.1 24.0 - - + -
103A LEU* 4.0 31.4 - - + -
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Residues in contact with ARG 62 (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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55A GLY 5.0 1.2 + - - -
58A MET* 3.0 44.8 + - + +
59A ARG* 3.6 27.4 - - - +
61A LEU* 1.3 72.1 - - - +
63A GLU* 1.3 56.2 + - - +
64A ASN 2.9 3.6 - - - -
65A ASP* 2.6 28.2 + - - +
67A ILE* 4.0 24.2 - - + -
100A VAL* 4.7 13.7 - - - +
101A LYS 5.3 1.4 + - - -
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Residues in contact with GLU 63 (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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59A ARG* 2.7 40.0 + - + +
60A ARG* 3.9 6.1 - - - +
62A ARG* 1.3 72.9 - - - +
64A ASN* 1.3 73.9 + - - +
65A ASP* 3.8 0.9 + - - +
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Residues in contact with ASN 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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8A VAL* 3.2 29.4 - - + +
36A GLU* 3.0 23.8 - - - +
37A SER* 4.2 1.9 - - - -
38A PRO* 3.5 14.2 - - - +
60A ARG* 3.0 18.3 + - - +
61A LEU 4.3 1.1 - - - +
62A ARG 2.8 1.0 + - - -
63A GLU* 1.3 102.1 + - - +
65A ASP* 1.3 70.7 + - - +
66A LEU* 3.2 14.2 + - + +
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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