Contacts of the helix formed by residues 39 - 53 (chain K) in PDB entry 5IYB
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 39 (chain K).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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950B ARG* 4.3 16.6 + - - +
36C ARG* 4.6 6.9 + - - +
41C GLU* 4.4 0.9 - - - +
171C LYS* 3.5 34.6 + - - +
255C LYS* 4.7 1.2 + - - -
9K SER 5.9 1.8 - - - -
38K GLU* 1.3 92.0 - - - +
40K HIS* 1.3 68.8 + - + +
41K THR* 3.0 22.6 + - - +
42K LEU* 3.5 2.8 + - - +
43K GLY* 3.4 14.7 + - - -
63K VAL* 6.1 1.6 - - - -
69K HIS* 5.5 6.7 - - + -
71K ILE* 4.0 16.5 - - - +
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Residues in contact with HIS 40 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
566A PHE* 6.5 0.7 - + - -
681A LEU* 6.3 0.9 - - + -
953B ASP* 4.4 5.6 - - - -
1032B PHE* 3.3 55.0 - + + +
36C ARG* 4.1 19.0 - - - +
39K ASP* 1.3 79.6 - - + +
41K THR* 1.3 58.6 + - - +
43K GLY 3.9 0.4 - - - +
44K ASN* 2.8 38.7 + - - +
61K TYR* 3.3 29.4 + + - +
62K LYS* 6.1 0.2 - - - -
63K VAL* 3.5 32.1 - - + +
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Residues in contact with THR 41 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33C SER* 3.8 15.2 - - - +
36C ARG* 2.9 42.9 + - + +
37C VAL* 4.2 25.6 - - + +
41C GLU* 5.0 13.2 + - + +
252C LEU* 5.1 9.4 - - + +
255C LYS* 5.4 4.7 - - - -
39K ASP* 4.0 16.0 + - - -
40K HIS* 1.3 79.9 - - - +
42K LEU* 1.3 60.0 + - - +
45K ILE* 3.5 15.9 + - - +
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Residues in contact with LEU 42 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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252C LEU* 6.2 1.1 - - - -
255C LYS* 3.9 29.8 - - + +
256C LEU* 4.8 16.4 - - + -
259C LEU* 3.6 42.0 - - + -
18K LYS* 6.4 0.2 - - - -
35K ILE* 3.9 18.6 - - + -
38K GLU* 4.1 24.7 - - + +
39K ASP* 3.5 5.8 + - - +
41K THR* 1.3 78.9 - - - +
43K GLY* 1.3 68.4 + - - +
45K ILE* 3.1 21.7 - - + +
46K ILE* 3.3 18.9 + - + +
71K ILE* 4.6 2.2 - - + -
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Residues in contact with GLY 43 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39K ASP 3.4 13.0 + - - -
40K HIS 4.0 0.9 - - - -
42K LEU* 1.3 80.2 - - - +
44K ASN* 1.3 61.0 + - - +
46K ILE* 3.2 10.3 - - - +
47K LYS* 3.1 26.3 + - - +
61K TYR* 3.9 23.8 - - - -
71K ILE* 4.1 12.1 - - - +
73K ILE* 5.2 0.9 - - - -
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Residues in contact with ASN 44 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1032B PHE 3.3 22.1 + - - +
1033B THR* 3.6 24.1 + - - +
29C ALA* 3.9 23.6 + - - +
32C ASN* 3.7 9.9 - - - +
33C SER* 5.5 2.3 - - - +
36C ARG* 6.6 0.2 - - - -
40K HIS 2.8 23.7 + - - +
41K THR 5.2 0.4 - - - +
43K GLY* 1.3 71.3 - - - +
45K ILE* 1.3 61.5 + - - +
47K LYS* 3.8 8.7 + - - +
48K SER* 3.3 20.4 + - - -
61K TYR* 3.5 27.7 + - - +
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Residues in contact with ILE 45 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27C ASP* 4.9 1.1 - - - +
29C ALA* 3.7 9.9 - - + +
30C VAL* 3.4 46.0 - - + +
33C SER* 3.9 16.5 - - - +
252C LEU* 6.2 4.7 - - + -
256C LEU* 5.5 7.2 - - + -
41K THR 3.5 14.4 + - - +
42K LEU* 3.1 16.8 - - + +
44K ASN* 1.3 78.8 - - - +
46K ILE* 1.3 60.8 + - + +
48K SER* 3.1 5.0 + - - -
49K GLN* 3.0 28.2 + - + +
94K LEU* 3.5 32.1 - - + -
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Residues in contact with ILE 46 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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259C LEU* 4.6 7.4 - - + -
42K LEU* 3.4 17.5 - - + +
43K GLY* 3.2 17.7 - - - +
45K ILE* 1.3 80.1 - - + +
47K LYS* 1.3 68.2 - - - +
49K GLN* 3.3 7.0 + - + +
50K LEU* 3.1 32.0 + - + +
73K ILE* 3.9 18.4 - - + -
87K PHE* 3.4 40.8 - - + +
90K ALA* 5.2 5.2 - - + -
91K ILE* 3.6 28.0 - - + -
94K LEU* 5.0 5.8 - - + -
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Residues in contact with LYS 47 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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558A GLY* 3.7 23.2 + - - -
559A GLU* 4.9 6.1 + - - -
561A MET* 5.5 0.2 - - - -
562A ASN* 4.9 15.0 - - - +
43K GLY 3.1 19.4 + - - +
44K ASN* 3.8 10.9 + - - +
46K ILE* 1.3 78.7 - - + +
48K SER* 1.3 69.2 + - - +
50K LEU* 3.5 9.6 + - - +
51K LEU* 3.2 43.4 + - + +
59K ALA* 3.9 9.9 - - - +
60K GLY* 3.8 21.3 - - - +
61K TYR* 3.7 31.4 - - + +
73K ILE* 5.6 2.2 - - + -
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Residues in contact with SER 48 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27C ASP* 2.8 30.2 + - - +
29C ALA* 3.8 16.6 - - - +
44K ASN* 3.3 4.9 + - - -
45K ILE* 3.1 11.0 + - - -
47K LYS* 1.3 85.4 + - - +
49K GLN* 1.3 65.5 + - - +
51K LEU* 3.3 10.6 + - - +
52K LYS* 3.2 23.7 + - - +
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Residues in contact with GLN 49 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3C TYR* 3.7 30.5 - - - -
27C ASP* 5.5 2.4 - - - +
30C VAL* 5.2 2.3 - - - +
45K ILE* 3.0 20.6 + - + +
46K ILE* 3.3 9.1 + - + +
48K SER* 1.3 76.3 - - - +
50K LEU* 1.3 62.0 + - - +
52K LYS* 2.5 49.4 + - - +
53K ASP* 3.6 5.4 + - - +
90K ALA* 3.6 29.6 + - + +
93K ASP* 4.0 4.4 + - - -
94K LEU* 3.9 44.5 - - + +
97K GLU* 3.8 7.5 + - - +
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Residues in contact with LEU 50 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46K ILE* 3.1 24.0 + - + +
47K LYS* 3.8 2.0 - - - +
48K SER 3.3 0.2 - - - -
49K GLN* 1.3 75.6 - - - +
51K LEU* 1.3 63.9 + - - +
53K ASP* 3.4 9.2 + - + +
56K VAL* 3.2 32.6 - - + +
59K ALA* 3.8 25.1 - - + -
73K ILE* 4.2 22.2 - - + -
75K VAL* 4.3 12.8 - - + -
86K ALA* 3.5 40.4 - - + +
87K PHE* 3.9 18.2 - - + +
90K ALA* 3.8 9.6 - - + -
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Residues in contact with LEU 51 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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557A ARG* 2.7 44.7 + - - +
558A GLY* 4.3 15.9 - - - -
561A MET* 3.3 31.2 - - + -
47K LYS* 3.2 48.4 + - + +
48K SER* 3.3 12.5 + - - +
50K LEU* 1.3 76.9 - - - +
52K LYS* 1.3 60.6 + - - +
53K ASP 3.4 5.9 + - - +
56K VAL* 5.0 3.3 - - + +
58K PHE 5.1 0.4 - - - -
59K ALA* 3.7 17.3 - - + +
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Residues in contact with LYS 52 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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557A ARG* 5.0 1.3 + - - +
3C TYR* 3.1 42.4 + - + +
4C ALA* 4.4 4.6 - - - +
5C ASN* 4.7 7.8 - - - +
27C ASP* 5.1 15.9 - - - +
30C VAL* 6.1 0.2 - - - +
225C LYS* 6.1 3.1 - - - +
48K SER 3.2 11.3 + - - +
49K GLN* 2.5 45.2 + - - +
50K LEU 3.3 0.2 - - - -
51K LEU* 1.3 79.5 - - - +
53K ASP* 1.3 61.3 + - - +
54K PRO* 3.5 8.5 - - - +
97K GLU* 3.9 14.5 + - - -
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Residues in contact with ASP 53 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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557A ARG* 5.0 1.1 + - - -
1C MET* 4.8 5.5 - - - +
3C TYR* 4.0 29.4 - - + +
49K GLN 3.6 4.2 + - - +
50K LEU* 3.4 17.2 + - + +
51K LEU 3.2 10.9 - - - +
52K LYS* 1.3 76.9 - - - +
54K PRO* 1.3 79.5 - - - +
55K GLN* 3.2 27.1 + - - +
56K VAL* 3.5 24.2 + - + +
81K TYR* 3.9 17.5 + - - -
86K ALA* 4.3 3.6 - - - +
90K ALA* 6.3 0.7 - - + -
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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