Contacts of the helix formed by residues 50 - 62 (chain K) in PDB entry 6IY6
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 50 (chain K).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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235I SER* 3.4 25.1 + - - +
238I ASP* 5.0 8.3 - - + +
239I ILE* 4.7 9.0 - - - +
243I GLN* 5.3 8.1 + - - -
48K PHE* 3.7 0.6 - - - +
49K THR* 1.3 85.8 + - - +
51K VAL* 1.3 65.0 + - - +
52K ASN* 4.5 3.4 - - + +
53K SER* 3.4 19.8 + - - +
54K ILE* 3.3 21.7 + - - +
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Residues in contact with VAL 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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14K PRO* 4.6 20.6 - - + -
16K GLY* 6.3 0.4 - - - -
17K ALA* 4.9 9.0 - - + +
38K ASN* 5.2 8.7 - - - +
49K THR 3.6 2.8 + - - -
50K ASP* 1.3 72.2 - - - +
52K ASN* 1.3 72.3 + - - +
54K ILE* 3.2 15.7 + - + +
55K LEU* 3.1 39.5 + - + +
86K ALA* 6.0 3.6 - - + -
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Residues in contact with ASN 52 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
238I ASP* 4.5 14.9 + - - +
50K ASP* 3.3 3.9 - - + +
51K VAL* 1.3 86.9 - - - +
53K SER* 1.3 55.4 + - - +
55K LEU* 3.2 20.4 + - - +
56K ARG* 2.8 60.2 + - - +
82K LEU* 3.6 41.4 + - + +
83K GLU* 4.5 1.8 - - - +
85K SER* 5.0 1.7 + - - -
86K ALA* 3.9 14.7 - - - +
123K CYS* 5.3 0.3 - - - +
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Residues in contact with SER 53 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
231I THR* 3.0 29.6 - - - +
235I SER* 3.0 31.6 + - - -
238I ASP* 5.2 1.2 + - - -
48K PHE* 3.9 27.1 - - - -
50K ASP* 3.4 23.0 + - - +
52K ASN* 1.3 77.7 - - - +
54K ILE* 1.3 60.2 + - - +
56K ARG* 3.5 8.0 + - - +
57K TYR* 3.1 11.6 + - - +
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Residues in contact with ILE 54 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6K LEU* 4.5 12.6 - - + -
14K PRO* 6.3 1.1 - - + -
17K ALA* 4.7 15.7 - - + -
38K ASN* 4.3 17.5 - - + -
40K LEU* 3.8 41.5 - - + +
48K PHE* 3.9 19.7 - - + +
49K THR 4.1 8.1 - - - +
50K ASP 3.4 15.0 - - - +
51K VAL* 3.2 13.9 + - + +
52K ASN 3.2 0.4 - - - -
53K SER* 1.3 73.5 - - - +
55K LEU* 1.3 66.0 + - - +
57K TYR* 3.3 4.7 + - - +
58K LEU* 3.1 45.1 + - + +
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Residues in contact with LEU 55 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16K GLY* 3.8 9.6 - - - +
17K ALA* 3.8 33.2 - - + +
20K ALA* 4.0 12.3 - - + -
51K VAL* 3.1 29.5 + - + +
52K ASN* 3.4 25.1 - - - +
54K ILE* 1.3 75.6 - - - +
56K ARG* 1.3 62.3 + - - +
58K LEU* 3.4 7.5 + - + +
59K ALA* 3.1 19.4 + - - +
82K LEU* 4.1 14.6 - - + -
119K LEU* 3.3 27.9 - - + +
122K LEU* 5.7 3.1 - - + -
123K CYS* 4.1 15.7 - - + -
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Residues in contact with ARG 56 (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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212I ASN* 4.9 0.4 + - - -
215I ARG* 3.5 22.6 - - - +
231I THR* 4.0 13.0 - - + +
234I ASP* 3.0 42.0 + - - +
238I ASP* 3.3 23.2 + - - -
52K ASN* 2.8 39.8 + - - +
53K SER* 3.7 10.6 + - - +
55K LEU* 1.3 73.3 - - - +
57K TYR* 1.3 61.4 + - - +
59K ALA* 3.5 2.6 + - - +
60K ARG* 3.1 30.6 + - - +
68K TYR* 3.6 16.1 - - + -
79K ASP* 3.0 26.7 + - - -
82K LEU* 3.7 30.7 - - + +
119K LEU* 4.0 6.3 - - - -
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Residues in contact with TYR 57 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
227I ALA* 3.8 34.4 - - + +
228I VAL* 3.9 20.4 - - + +
231I THR* 3.5 13.4 + - + +
4K LEU* 4.2 14.1 - - + -
40K LEU* 3.7 22.9 - - + -
42K VAL* 3.1 35.2 - - + +
48K PHE* 4.3 12.3 - + + -
53K SER 3.1 14.2 + - - +
54K ILE 3.6 7.2 - - - +
56K ARG* 1.3 74.3 - - - +
58K LEU* 1.3 54.4 + - - +
60K ARG* 3.1 5.5 + - - +
61K VAL* 2.9 61.6 + - + +
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Residues in contact with LEU 58 (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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4K LEU* 3.8 16.8 - - + -
17K ALA* 4.4 2.7 - - - +
20K ALA* 4.3 18.6 - - + -
21K VAL* 4.0 22.0 - - + +
24K VAL* 3.9 22.0 - - + +
30K ILE* 3.6 27.4 - - + -
40K LEU* 4.5 9.2 - - + -
54K ILE* 3.1 35.4 + - + +
55K LEU* 3.7 7.6 - - - +
57K TYR* 1.3 78.7 - - + +
59K ALA* 1.3 54.1 + - - +
61K VAL* 3.3 7.1 - - + +
62K ALA* 2.8 39.2 + - - +
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Residues in contact with ALA 59 (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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24K VAL* 5.0 0.2 - - - +
55K LEU 3.1 6.3 + - - +
56K ARG 3.8 2.5 - - - +
57K TYR 3.3 0.2 - - - -
58K LEU* 1.3 76.2 - - - +
60K ARG* 1.3 59.1 + - - +
62K ALA* 3.1 24.0 - - - +
63K THR* 5.0 0.2 - - - -
66K GLY* 5.4 0.5 - - - -
67K LEU* 3.8 28.0 + - + -
68K TYR* 4.0 16.9 + - + +
119K LEU* 3.4 40.3 - - + +
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Residues in contact with ARG 60 (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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225I HIS 5.4 3.4 + - - -
227I ALA* 4.2 19.1 - - + +
230I ALA* 3.5 34.8 - - - +
231I THR* 4.1 15.6 + - - +
234I ASP* 3.8 21.6 + - - -
56K ARG* 3.1 19.5 + - - +
57K TYR 3.5 4.3 - - - +
59K ALA* 1.3 77.3 - - - +
61K VAL* 1.3 61.2 + - - +
62K ALA 4.2 0.2 - - - -
63K THR* 3.9 14.9 + - - +
68K TYR* 4.3 21.1 + - + -
75K HIS* 3.3 33.1 + - - -
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Residues in contact with VAL 61 (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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227I ALA* 4.6 9.4 - - + +
4K LEU* 4.9 9.6 - - + -
24K VAL* 6.0 1.8 - - + -
27K ASP* 4.4 1.0 - - - +
28K VAL* 4.0 34.0 - - + +
57K TYR* 2.9 47.4 + - + +
58K LEU* 3.3 18.4 - - + +
60K ARG* 1.3 71.6 - - - +
62K ALA* 1.3 62.8 + - + +
63K THR* 3.1 17.7 + - - +
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Residues in contact with ALA 62 (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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24K VAL* 3.4 30.7 - - + -
27K ASP* 3.2 18.8 - - + +
28K VAL* 5.1 1.1 - - + -
58K LEU 2.8 19.2 + - - +
59K ALA* 3.1 17.3 - - - +
61K VAL* 1.3 73.7 - - + +
63K THR* 1.3 63.7 + - - +
64K THR 3.5 0.2 - - - -
65K ALA* 3.5 22.3 - - + +
66K GLY 3.7 2.4 + - - -
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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