Contacts of the helix formed by residues 51 - 64 (chain K) in PDB entry 5O6I
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 HIS 51 (chain K).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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46K ASN* 3.4 31.9 + - - -
47K LEU* 3.3 34.0 + - + +
49K LYS 3.5 0.2 - - - -
50K GLN* 1.3 88.7 + - + +
52K PHE* 1.3 74.7 + - + +
53K ALA 3.5 0.4 - - - -
54K PRO* 3.6 7.1 - - - +
55K LEU* 3.6 24.5 - - + +
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Residues in contact with PHE 52 (chain K).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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13K TYR* 4.0 16.6 - + - -
14K LEU* 4.5 3.3 - - - +
17K LEU* 3.5 39.3 - - + -
40K ILE* 3.9 26.2 - - + -
42K GLN* 4.1 24.2 - - + -
47K LEU* 3.0 36.5 + - + -
48K ILE* 3.5 27.6 - - + +
51K HIS* 1.3 83.7 - - + +
53K ALA* 1.3 65.6 + - - +
55K LEU* 3.2 7.5 + - - +
56K MET* 3.0 22.3 + - - +
80K LEU* 3.9 13.0 - - + -
115K VAL* 4.1 11.9 - - + -
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Residues in contact with ALA 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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48K ILE 2.8 22.1 + - - +
49K LYS* 3.7 11.0 - - - +
52K PHE* 1.3 73.0 - - - +
54K PRO* 1.3 61.8 - - + +
56K MET 3.2 0.7 + - - -
57K GLN* 2.8 31.0 + - - +
69K ILE* 3.4 18.9 - - + +
71K ILE* 4.6 8.1 - - + -
80K LEU* 3.7 15.7 - - + +
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Residues in contact with PRO 54 (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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49K LYS 3.3 20.0 - - - +
50K GLN* 3.7 17.5 - - - +
51K HIS 3.6 15.3 - - - +
53K ALA* 1.3 88.6 - - + +
55K LEU* 1.3 57.9 + - + +
57K GLN* 3.4 7.8 + - + +
58K PHE* 3.0 26.9 + - - +
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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
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10K ILE* 3.8 36.7 - - + +
13K TYR* 3.7 35.7 - - + -
14K LEU* 4.0 14.4 - - + +
51K HIS* 3.6 16.5 + - + +
52K PHE* 3.2 9.5 + - + +
53K ALA 3.2 0.6 - - - -
54K PRO* 1.3 75.3 - - + +
56K MET* 1.3 66.8 + - - +
58K PHE* 3.3 7.5 + - + +
59K LEU* 3.2 19.8 + - - +
183K ASN* 5.5 7.6 - - - +
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Residues in contact with MET 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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14K LEU* 4.0 24.3 - - + +
18K ILE* 4.4 5.6 - - + -
38K VAL* 4.3 19.5 - - + -
40K ILE* 4.2 25.8 - - + -
52K PHE 3.0 14.0 + - - +
53K ALA* 3.7 7.6 - - - +
55K LEU* 1.3 76.0 - - - +
57K GLN* 1.3 57.7 + - - +
59K LEU* 3.2 6.4 + - - +
60K ILE* 2.9 34.1 + - + +
69K ILE* 3.8 15.3 - - + -
80K LEU* 4.2 15.0 - - + -
82K VAL* 4.0 14.6 - - + -
87K LEU* 3.9 24.2 - - - -
91K PHE* 4.4 5.4 - - + -
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Residues in contact with GLN 57 (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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53K ALA 2.8 20.4 + - - +
54K PRO* 3.7 8.5 - - + +
55K LEU 3.2 0.2 - - - -
56K MET* 1.3 73.9 - - - +
58K PHE* 1.3 56.5 + - - +
60K ILE* 4.0 15.9 - - - +
61K ASP* 2.9 66.3 + - - +
69K ILE* 3.5 26.2 + - + +
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Residues in contact with PHE 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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6K ASN* 4.2 16.8 - - - -
7K VAL* 4.5 18.6 - - + -
10K ILE* 3.6 34.8 - - + -
54K PRO 3.0 13.7 + - - +
55K LEU* 3.6 11.0 - - + +
56K MET 3.3 0.2 - - - -
57K GLN* 1.3 77.7 - - - +
59K LEU* 1.3 61.9 + - + +
61K ASP* 3.3 11.2 + - + +
62K GLU* 2.9 57.1 + - + +
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Residues in contact with LEU 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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7K VAL* 4.2 16.8 - - + +
10K ILE* 5.5 2.9 - - + -
11K SER* 3.6 22.4 - - - +
14K LEU* 3.9 14.8 - - + -
55K LEU 3.2 9.1 + - - +
56K MET* 3.2 12.8 + - - +
58K PHE* 1.3 81.9 - - + +
60K ILE* 1.3 65.8 + - - +
62K GLU* 3.2 3.2 + - + +
63K LEU* 2.9 46.1 + - + +
87K LEU* 4.2 6.7 - - + -
90K TYR* 4.0 14.6 - - + +
91K PHE* 3.4 35.4 - - + -
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Residues in contact with ILE 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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56K MET* 2.9 29.3 + - + +
57K GLN* 3.6 20.9 - - - +
59K LEU* 1.3 77.6 - - - +
61K ASP* 1.3 64.4 + - - +
64K ASN* 3.1 4.0 + - - -
65K VAL* 3.1 72.4 + - + +
67K SER 3.9 14.1 - - - +
69K ILE* 4.7 9.6 - - + -
82K VAL* 4.1 7.6 - - + -
87K LEU* 3.6 34.1 - - + -
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Residues in contact with ASP 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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57K GLN* 2.9 47.1 + - - +
58K PHE* 3.6 10.5 - - + +
60K ILE* 1.3 76.6 - - - +
62K GLU* 1.3 63.2 + - - +
64K ASN* 3.4 17.4 + - - +
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Residues in contact with GLU 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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7K VAL* 4.1 31.1 - - + +
58K PHE* 2.9 46.9 + - + +
59K LEU* 3.2 8.2 + - - +
61K ASP* 1.3 79.0 - - + +
63K LEU* 1.3 64.2 + - + +
64K ASN* 3.3 5.8 + - - -
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Residues in contact with LEU 63 (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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7K VAL* 5.2 5.2 - - + -
59K LEU* 2.9 30.7 + - + +
62K GLU* 1.3 83.6 - - + +
64K ASN* 1.3 59.6 + - - +
65K VAL* 3.1 12.7 + - + -
86K LYS* 2.7 39.5 + - + -
87K LEU* 3.8 21.5 - - + -
90K TYR* 3.8 50.0 - - + +
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Residues in contact with ASN 64 (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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60K ILE 3.1 6.3 + - - -
61K ASP* 3.4 11.0 + - - +
62K GLU 3.3 6.1 + - - -
63K LEU* 1.3 80.0 - - - +
65K VAL* 1.3 65.3 + - - +
66K LYS* 3.3 29.1 + - - +
86K LYS* 4.1 10.4 + - - +
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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