Contacts of the helix formed by residues 58 - 71 (chain A) in PDB entry 3KHE
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 58 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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52A ASN* 4.9 7.8 + - - -
54A ASP* 5.6 0.7 - - - +
56A GLN 4.1 0.8 + - - -
57A LEU* 1.3 76.9 - - - +
59A ARG* 1.3 66.6 + - - +
60A LYS* 3.4 13.4 + - - +
61A GLU* 3.1 34.9 + - - +
62A LEU* 3.0 23.2 + - - +
93A LEU* 5.3 0.4 - - - -
102A GLY 4.6 2.9 - - - +
103A TYR* 3.3 33.2 - - + -
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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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58A ASP* 1.3 75.9 - - - +
60A LYS* 1.3 60.6 + - + +
62A LEU* 3.2 4.0 + - - +
63A ILE* 2.9 41.0 + - + +
86A GLU* 2.2 41.1 + - - +
89A VAL* 3.9 26.3 - - + +
90A ASP* 2.6 33.3 + - - +
93A LEU* 4.0 23.3 - - + +
102A GLY 4.9 2.1 + - - +
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Residues in contact with LYS 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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58A ASP* 3.3 11.2 + - - +
59A ARG* 1.3 78.6 - - + +
61A GLU* 1.3 54.1 + - + +
63A ILE* 3.3 12.8 + - + +
64A GLU* 2.7 41.4 + - + +
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Residues in contact with GLU 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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49A LEU* 3.7 25.7 - - - +
50A ASP* 3.7 1.3 - - - +
51A ASN* 3.7 19.0 - - + +
52A ASN* 3.0 26.7 + - - +
56A GLN 3.0 10.0 - - - +
57A LEU* 3.0 17.3 - - + +
58A ASP* 3.1 26.2 + - - +
60A LYS* 1.3 78.9 - - + +
62A LEU* 1.3 63.1 + - - +
64A GLU* 3.4 6.0 + - - +
65A GLY* 3.0 19.2 + - - -
195A CA 2.3 31.6 - - - -
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Residues in contact with LEU 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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9A LEU* 5.4 3.3 - - + +
12A MET* 3.9 24.0 - - + -
49A LEU* 4.9 5.8 - - + +
57A LEU* 3.5 33.9 - - + +
58A ASP 3.0 16.2 + - - +
59A ARG 3.2 4.7 + - - +
61A GLU* 1.3 73.6 - - - +
63A ILE* 1.3 67.4 + - - +
65A GLY* 3.2 10.5 + - - +
66A TYR* 3.3 19.6 + - + -
89A VAL* 3.9 28.5 - - + -
92A ILE* 4.0 13.9 - - + -
93A LEU* 4.0 12.6 - - + -
104A ILE* 4.0 24.0 - - + -
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Residues in contact with ILE 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* 2.9 39.6 + - + +
60A LYS* 3.6 13.5 - - + +
62A LEU* 1.3 78.3 - - - +
64A GLU* 1.3 65.6 + - - +
66A TYR* 3.2 3.6 + - - +
67A ARG* 3.1 43.4 + - + +
85A ILE* 4.0 11.8 - - + +
86A GLU* 3.8 33.4 - - - +
89A VAL* 3.8 19.5 - - + +
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Residues in contact with GLU 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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60A LYS* 2.7 22.6 + - + +
61A GLU* 3.8 6.7 - - - +
63A ILE* 1.3 76.1 - - + +
65A GLY* 1.3 51.5 + - - +
67A ARG* 3.7 30.4 + - - +
68A LYS* 2.6 53.4 + - + +
71A GLN* 5.6 1.4 - - - +
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Residues in contact with GLY 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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5A LEU* 4.2 4.6 - - - +
9A LEU* 4.0 10.4 - - - +
49A LEU* 3.9 26.0 - - - -
61A GLU 3.0 11.3 + - - -
62A LEU 3.2 5.5 + - - -
64A GLU* 1.3 75.1 - - - +
66A TYR* 1.3 57.6 + - - +
68A LYS* 3.7 5.1 - - - +
69A LEU* 3.0 27.7 + - - +
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Residues in contact with TYR 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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9A LEU* 3.1 55.7 + - + +
13A LYS* 3.6 36.8 - - - +
62A LEU* 3.3 19.0 + - + -
63A ILE 3.2 2.2 + - - -
65A GLY* 1.3 70.7 - - - +
67A ARG* 1.3 66.8 + - - +
69A LEU* 3.2 13.2 + - + +
70A MET* 3.1 27.5 + - + +
85A ILE* 3.5 40.8 - - + -
88A GLU* 4.2 16.6 - - + -
89A VAL* 4.5 4.9 - - + -
92A ILE* 4.1 20.8 - - + +
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Residues in contact with ARG 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 ILE* 3.1 40.3 + - + +
64A GLU* 3.7 24.8 + - - +
66A TYR* 1.3 75.1 - - - +
68A LYS* 1.3 61.3 + - - +
70A MET* 3.7 1.4 + - - +
71A GLN* 3.2 50.2 + - - +
77A VAL* 3.6 22.5 + - + +
82A SER* 2.8 29.3 + - - +
85A ILE* 3.9 18.4 - - + -
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Residues in contact with LYS 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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5A LEU* 5.5 6.7 - - + -
64A GLU* 2.6 36.4 + - - +
65A GLY* 3.7 6.1 - - - +
67A ARG* 1.3 70.4 - - - +
69A LEU* 1.3 65.8 + - - +
71A GLN* 3.3 32.7 + - + -
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Residues in contact with LEU 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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3A HIS 5.6 3.1 - - - +
5A LEU* 4.0 24.1 - - + +
6A THR* 3.5 38.1 - - + +
9A LEU* 3.6 24.2 - - + -
65A GLY 3.0 9.7 + - - +
66A TYR* 3.2 17.2 + - + +
68A LYS* 1.3 78.4 - - - +
70A MET* 1.3 66.9 + - + +
71A GLN 3.5 6.4 - - - +
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Residues in contact with MET 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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66A TYR* 3.1 12.4 + - + +
67A ARG 4.3 0.2 - - - +
69A LEU* 1.3 80.9 - - + +
71A GLN* 1.3 61.8 + - - +
77A VAL* 3.8 26.2 - - + -
81A ASP* 4.2 37.7 - - + +
85A ILE* 4.5 14.1 - - + -
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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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64A GLU* 5.6 1.2 - - - +
67A ARG* 3.2 41.5 + - - +
68A LYS* 3.3 29.1 - - + +
69A LEU 3.2 7.1 - - - +
70A MET* 1.3 82.4 - - - +
77A VAL* 4.0 24.5 - - + +
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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