Contacts of the helix formed by residues 52 - 67 (chain A) in PDB entry 1KPI
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 THR 52 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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46A PHE* 4.3 2.0 - - - -
50A ASP 4.9 3.4 - - - +
51A MET* 1.3 76.4 - - - +
53A LEU* 1.3 66.0 + - - +
54A GLU* 3.5 8.5 + - - +
55A GLU* 2.9 37.6 + - - +
56A ALA* 2.8 20.3 + - - +
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Residues in contact with LEU 53 (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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34A TRP 4.8 1.8 - - - +
35A LEU 4.8 0.9 - - - -
36A ASP* 3.9 24.9 - - + +
44A ALA* 4.1 21.8 - - + -
46A PHE* 4.4 8.6 - - + -
52A THR* 1.3 72.5 - - - +
54A GLU* 1.3 58.9 + - - +
56A ALA* 3.0 7.1 + - - +
57A GLN* 2.8 38.7 + - + +
250A THR* 4.3 24.7 - - + -
253A ALA* 3.9 20.9 - - + -
254A TRP* 3.6 29.6 - - + +
257A ALA* 6.5 0.2 - - + -
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Residues in contact with GLU 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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36A ASP* 3.7 16.9 - - - +
37A PRO* 3.2 48.8 - - + +
38A SER* 4.5 4.4 + - - -
52A THR* 3.2 9.5 + - - +
53A LEU* 1.3 80.1 - - - +
55A GLU* 1.3 62.9 + - + +
57A GLN* 3.6 2.9 + - - +
58A TYR* 3.2 20.6 + - - +
61A ARG* 4.4 4.3 + - - +
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Residues in contact with GLU 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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48A ARG* 5.1 6.7 + - - +
50A ASP 3.9 3.6 - - - +
51A MET* 3.3 23.9 - - + +
52A THR* 2.9 41.2 + - - +
54A GLU* 1.3 78.1 - - + +
56A ALA* 1.3 61.4 + - - +
58A TYR* 3.5 8.2 + - - +
59A ALA* 2.9 27.0 + - - +
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Residues in contact with ALA 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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44A ALA* 3.9 6.5 - - + -
45A TYR 3.1 33.8 + - - +
46A PHE* 3.6 32.5 - - + -
51A MET* 4.0 4.2 - - + +
52A THR 2.8 12.0 + - - +
53A LEU 3.0 7.8 + - - +
55A GLU* 1.3 75.7 - - - +
57A GLN* 1.3 55.2 + - - +
59A ALA* 3.2 1.0 + - - -
60A LYS 2.7 28.8 + - - -
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Residues in contact with GLN 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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36A ASP* 3.7 20.3 + - - +
40A THR* 3.1 44.2 + - - +
42A SER 3.3 14.5 + - - -
44A ALA* 3.4 17.6 - - - +
53A LEU* 2.8 29.0 + - + +
54A GLU 3.8 5.4 - - - +
56A ALA* 1.3 73.2 - - - +
58A TYR* 1.3 66.3 + - - +
60A LYS* 3.0 27.1 + - - +
61A ARG* 2.9 31.6 + - - +
254A TRP* 3.9 10.7 - - - +
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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
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54A GLU 3.2 10.5 + - - +
55A GLU* 3.6 10.8 - - - +
57A GLN* 1.3 77.9 - - - +
59A ALA* 1.3 62.0 + - - +
61A ARG* 3.1 29.4 + - - +
62A LYS* 2.9 33.3 + - + +
89A HIS* 3.3 28.1 - + - -
93A GLU* 3.5 24.6 - - - +
904A SO4 2.8 35.1 + - - -
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Residues in contact with ALA 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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45A TYR* 3.3 32.2 - - + +
47A GLU* 4.3 2.7 - - + -
51A MET* 3.8 20.4 - - + -
55A GLU 2.9 15.0 + - - +
56A ALA 3.3 2.5 - - - +
58A TYR* 1.3 82.9 - - - +
60A LYS* 1.3 56.3 + - - +
62A LYS* 3.8 7.1 - - - +
63A LEU* 2.9 29.1 + - - +
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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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40A THR* 3.6 12.1 - - - +
42A SER* 2.7 29.9 + - - -
43A CYS 2.9 31.5 + - - +
44A ALA 4.1 0.2 - - - -
45A TYR* 3.5 22.9 - - + +
56A ALA 2.7 17.0 + - - +
57A GLN* 3.1 25.2 + - - +
59A ALA* 1.3 72.0 - - - +
61A ARG* 1.3 72.6 + - - +
63A LEU* 3.3 6.0 + - + +
64A ALA* 3.1 19.9 + - - +
144A LEU* 3.9 21.5 - - + -
182A HIS* 4.0 20.9 - - + +
243A ILE* 5.2 1.6 - - + -
297A GLN* 4.3 6.3 + - - +
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Residues in contact with ARG 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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38A SER* 2.9 18.6 + - - -
40A THR* 2.7 30.4 + - + +
54A GLU* 4.4 5.3 + - - +
57A GLN* 2.9 15.7 + - - +
58A TYR* 3.1 43.4 - - - +
60A LYS* 1.3 89.2 - - - +
62A LYS* 1.3 58.1 + - - +
64A ALA* 3.3 4.9 + - - +
65A LEU* 2.9 37.8 + - + +
85A SER* 3.5 36.2 - - - +
86A THR* 3.9 14.8 - - + +
89A HIS* 2.9 34.4 + - + +
144A LEU* 5.0 3.4 - - + -
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Residues in contact with LYS 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* 2.9 24.5 + - + +
59A ALA* 3.8 7.4 - - - +
61A ARG* 1.3 75.4 - - - +
63A LEU* 1.3 60.8 + - - +
66A ASP* 2.8 62.9 + - - +
89A HIS* 3.9 11.1 - - + +
94A TYR* 4.0 11.9 - - - +
904A SO4 2.9 44.4 + - - +
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Residues in contact with LEU 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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45A TYR* 3.6 48.5 - - + +
59A ALA 2.9 17.9 + - - +
60A LYS* 3.4 5.4 - - - +
62A LYS* 1.3 77.7 - - - +
64A ALA* 1.3 61.0 + - - +
66A ASP* 3.8 4.9 + - - +
67A LYS* 3.1 46.0 + - - +
239A ARG* 5.0 2.9 - - - +
241A HIS* 3.8 21.3 - - + -
243A ILE* 4.7 4.9 - - + -
297A GLN* 3.5 26.0 - - - +
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Residues in contact with ALA 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 3.1 9.3 + - - +
61A ARG* 3.7 8.3 - - - +
63A LEU* 1.3 80.3 - - - +
65A LEU* 1.3 63.3 + - + +
67A LYS* 3.2 20.1 + - - +
68A LEU* 3.9 5.4 + - - +
86A THR* 6.3 0.2 - - + -
142A VAL* 4.4 7.4 - - + -
144A LEU* 3.9 19.3 - - + -
180A LEU* 3.8 36.1 - - + +
297A GLN* 4.0 7.9 - - - +
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Residues in contact with LEU 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 ARG* 2.9 20.3 + - + +
64A ALA* 1.3 73.3 - - + +
66A ASP* 1.3 62.1 + - - +
67A LYS 3.0 5.9 + - - -
68A LEU* 3.0 29.1 + - + +
69A ASN 4.1 2.4 + - - -
70A LEU* 4.1 17.0 + - + +
76A LEU* 3.9 26.7 - - + -
86A THR* 4.3 20.2 - - + +
89A HIS* 3.9 11.7 - - + -
90A ALA* 3.8 23.6 - - + +
94A TYR* 3.4 40.0 - - + +
142A VAL* 4.7 6.5 - - + -
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Residues in contact with ASP 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 LYS* 2.8 55.7 + - - +
63A LEU* 4.2 5.2 - - - +
64A ALA 3.4 0.2 - - - -
65A LEU* 1.3 71.0 - - - +
67A LYS* 1.3 57.2 + - + +
68A LEU 3.3 0.2 - - - -
69A ASN* 3.2 22.1 + - - -
94A TYR* 2.6 32.5 + - - -
904A SO4 5.6 0.5 + - - -
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Residues in contact with LYS 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 LEU* 3.1 35.4 - - - +
64A ALA 3.4 7.4 - - - +
65A LEU 3.0 1.0 - - - -
66A ASP* 1.3 77.5 - - + +
68A LEU* 1.3 56.5 + - + +
69A ASN* 3.2 7.0 - - - +
178A ARG* 2.7 32.4 + - - +
180A LEU* 3.7 16.4 - - + -
239A ARG* 4.1 15.3 - - - +
241A HIS* 3.2 32.3 + - - +
297A GLN* 2.9 25.9 + - - +
299A THR* 3.4 31.9 + - + +
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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