Contacts of the helix formed by residues 57 - 68 (chain A) in PDB entry 1KLC
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 GLN 57 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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56A THR* 1.3 69.4 - - - +
58A TYR* 1.3 57.5 + - - +
59A SER 2.9 9.6 + - - -
60A LYS* 3.1 47.5 + - + +
61A VAL* 3.4 4.0 + - + +
30B TRP* 5.7 0.2 - - + -
101B LEU* 3.0 24.1 - - + +
102B SER* 2.3 58.2 + - - +
103B ASN* 3.1 12.3 - - + +
104B MET* 3.8 13.6 - - + +
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Residues in contact with TYR 58 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56A THR* 3.2 3.0 + - - +
57A GLN* 1.3 75.9 - - - +
59A SER* 1.3 62.3 + - - +
60A LYS 3.3 0.2 - - - -
61A VAL* 4.0 7.0 - - - -
62A LEU* 2.7 64.9 + - + +
74A ALA 4.0 0.3 + - - -
75A ALA 4.4 0.5 + - - -
76A PRO* 5.0 1.7 - - + +
112A SER* 4.0 9.0 - - - -
20B LEU* 4.2 2.5 - - + -
39B TYR* 4.7 3.4 - - - -
41B ALA* 4.2 18.2 - - + -
42B ASN 3.4 19.5 - - - -
43B PHE* 2.8 27.3 - - + +
44B CYS 4.5 0.7 + - - -
80B PRO* 3.3 36.8 - - + -
83B LEU* 3.7 14.4 - - + -
103B ASN 2.8 15.7 + - - +
104B MET* 4.7 2.9 - - - +
105B ILE 4.6 5.8 - - - +
106B VAL* 4.2 3.1 - - + -
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Residues in contact with SER 59 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54A LEU* 2.9 29.5 - - - +
55A ASP 3.9 1.6 - - - -
56A THR* 2.7 38.4 + - - +
57A GLN 2.9 0.6 - - - -
58A TYR* 1.3 84.0 - - - +
60A LYS* 1.3 56.7 + - - +
62A LEU* 5.3 0.7 - - - -
63A ALA* 2.9 20.3 + - - +
76A PRO* 5.1 10.0 - - - +
111A CYS* 3.3 24.3 + - - -
112A SER* 4.1 3.5 + - - -
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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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50A TYR* 4.8 2.9 - - + +
54A LEU* 3.0 40.8 - - + +
56A THR 3.9 1.0 + - - +
57A GLN* 3.1 39.4 + - + +
59A SER* 1.3 80.3 - - - +
61A VAL* 1.3 75.7 + - + +
63A ALA* 3.6 3.6 - - - +
64A LEU* 3.3 26.9 + - + +
30B TRP* 4.4 15.7 - - + -
32B TRP* 6.3 1.8 - - - -
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Residues in contact with VAL 61 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57A GLN 3.4 12.9 + - - +
58A TYR* 4.3 5.8 - - + +
60A LYS* 1.3 81.4 - - + +
62A LEU* 1.3 68.5 + - + +
64A LEU 2.9 11.4 + - - -
65A TYR 2.9 8.3 + - - -
22B ILE* 3.5 12.1 - - + -
28B LEU* 3.0 31.1 - - + +
30B TRP* 2.9 36.1 - - + -
39B TYR* 3.2 24.2 - - + +
104B MET* 3.2 22.2 - - + -
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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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58A TYR* 2.7 44.9 + - + +
61A VAL* 1.3 82.1 - - - +
63A ALA* 1.3 65.4 + - - +
65A TYR* 2.6 31.8 + - + -
66A ASN* 3.0 12.0 + - - +
74A ALA 2.7 21.5 - - - +
75A ALA* 3.0 32.8 - - - +
76A PRO* 3.0 17.9 - - + -
20B LEU* 3.1 29.6 - - + -
22B ILE* 4.5 0.4 - - - -
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Residues in contact with ALA 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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48A CYS 3.9 8.6 - - - +
49A PRO 3.0 31.6 - - - +
50A TYR* 3.7 8.5 - - - -
59A SER 2.9 24.1 + - - +
60A LYS 3.6 7.6 - - - +
61A VAL 3.2 0.2 - - - -
62A LEU* 1.3 79.8 - - - +
64A LEU* 1.3 57.0 + - - +
66A ASN* 4.0 1.7 + - - +
67A GLN* 3.2 29.6 + - - +
76A PRO* 4.6 10.3 - - + +
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Residues in contact with LEU 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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50A TYR* 2.8 53.6 - - + -
60A LYS* 3.3 19.1 - - + +
61A VAL 2.9 1.4 + - - -
62A LEU 2.7 1.0 + - - -
63A ALA* 1.3 73.7 - - - +
65A TYR* 1.3 61.7 + - - +
66A ASN 3.0 2.2 - - - -
67A GLN* 4.0 0.4 - - - -
68A HIS* 2.7 61.0 + - + +
28B LEU* 3.3 13.5 - - + -
30B TRP* 3.6 28.3 - - + +
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Residues in contact with TYR 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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61A VAL 2.9 0.2 + - - -
62A LEU* 2.6 42.1 + - + +
64A LEU* 1.3 72.6 - - - +
66A ASN* 1.3 62.0 + - - +
69A ASN* 3.4 28.6 + - - +
72A ALA* 4.7 11.9 - - + +
74A ALA* 4.0 12.3 - - + -
20B LEU* 3.1 30.8 - - + +
21B TYR 4.0 5.2 + - - -
22B ILE* 3.5 23.6 - - + -
27B ASP* 2.7 50.7 + - + -
28B LEU* 2.9 19.0 - - + +
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Residues in contact with ASN 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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62A LEU 3.0 7.4 + - - +
63A ALA 4.4 2.2 - - - +
64A LEU 3.0 0.2 - - - -
65A TYR* 1.3 79.3 - - + +
67A GLN* 1.3 61.8 + - + +
68A HIS 2.7 10.7 + - - -
69A ASN 2.8 25.4 + - - +
70A PRO* 5.0 0.2 - - - +
72A ALA* 2.3 36.4 + - - +
73A SER* 4.9 0.2 - - - +
74A ALA* 3.1 5.5 + - - +
75A ALA* 2.8 48.1 + - + +
76A PRO* 5.2 0.2 - - + -
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Residues in contact with GLN 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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14A ASN* 5.8 3.8 - - - +
48A CYS 5.3 1.8 - - - +
49A PRO* 4.7 16.1 - - + +
50A TYR* 2.6 44.3 + - + +
63A ALA 3.2 20.3 + - - +
64A LEU* 3.3 3.0 + - - -
66A ASN* 1.3 79.8 - - + +
68A HIS* 1.3 61.5 + - - +
69A ASN 5.1 0.2 - - - -
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Residues in contact with HIS 68 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50A TYR* 5.2 2.7 - - - -
64A LEU* 2.7 55.1 + - + +
66A ASN 2.7 1.0 + - - -
67A GLN* 1.3 83.5 - - - +
69A ASN* 1.3 61.6 + - - +
70A PRO* 3.1 12.5 - - - +
26B LYS 5.6 0.2 - - - +
27B ASP 2.9 27.5 + - - +
28B LEU 3.4 21.3 + - - -
29B GLY* 4.9 2.8 - - - -
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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