Contacts of the helix formed by residues 60 - 74 (chain K) in PDB entry 6ALH
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 ASN 60 (chain K).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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13K ILE* 4.2 18.4 - - + -
22K VAL* 3.8 16.4 - - - +
57K GLY 5.4 3.4 + - - +
58K LEU 4.3 0.4 - - - -
59K ILE* 1.3 75.3 - - - +
61K ASN* 1.3 64.5 + - - +
62K GLN* 2.9 28.5 + - - +
63K ILE* 3.1 26.0 + - - +
64K LEU* 3.6 23.9 + - - +
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Residues in contact with ASN 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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13K ILE* 5.4 0.2 - - - +
18K ASP* 6.2 2.5 - - + -
22K VAL* 3.7 22.7 - - + +
25K ARG* 3.7 18.1 + - - +
60K ASN* 1.3 77.3 - - - +
62K GLN* 1.3 57.4 + - - +
64K LEU* 3.5 5.0 + - - +
65K ASP* 2.9 44.1 + - - +
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Residues in contact with GLN 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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60K ASN* 2.9 18.1 + - - +
61K ASN* 1.3 76.9 - - - +
63K ILE* 1.3 64.9 + - + +
65K ASP* 3.1 15.3 + - - +
66K VAL* 2.9 44.6 + - + +
69K ARG* 5.2 3.5 + - - -
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Residues in contact with ILE 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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57K GLY 5.1 2.5 - - - +
58K LEU* 3.8 29.8 - - - +
59K ILE* 4.6 12.1 - - + -
60K ASN* 3.1 38.3 + - - +
62K GLN* 1.3 80.5 - - + +
64K LEU* 1.3 61.4 + - + +
66K VAL* 3.3 5.5 + - - +
67K ARG* 2.9 51.6 + - + +
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Residues in contact with LEU 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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22K VAL* 3.9 29.2 - - + +
25K ARG* 4.0 26.9 - - + +
26K ARG* 4.1 32.8 - - + +
29K GLN* 3.9 21.3 - - - +
59K ILE* 4.9 4.9 - - + -
60K ASN 3.6 14.4 + - - +
61K ASN* 3.5 10.9 + - - +
62K GLN 3.3 0.4 - - - -
63K ILE* 1.3 82.5 - - + +
65K ASP* 1.3 56.6 + - - +
67K ARG* 4.7 6.5 - - + -
68K GLU* 2.9 46.2 + - + +
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Residues in contact with ASP 65 (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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25K ARG* 4.3 13.3 + - - -
61K ASN* 2.9 44.7 + - - +
62K GLN* 3.1 21.5 + - - +
64K LEU* 1.3 74.8 - - - +
66K VAL* 1.3 58.6 + - + +
68K GLU* 4.1 2.8 - - - +
69K ARG* 3.0 39.0 + - - +
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Residues in contact with VAL 66 (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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62K GLN* 2.9 39.1 + - + +
63K ILE* 3.9 5.8 - - - +
65K ASP* 1.3 76.3 - - - +
67K ARG* 1.3 61.5 + - + +
69K ARG* 3.4 32.0 + - - +
70K GLN* 2.9 38.5 + - + +
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Residues in contact with ARG 67 (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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26K ARG* 3.1 40.8 - - - +
35K LYS* 4.3 25.0 - - - +
36K ASP* 5.5 1.6 + - - -
38K LEU* 4.3 13.2 - - - +
59K ILE* 5.5 1.8 - - - +
63K ILE* 2.9 38.2 + - + +
64K LEU* 4.2 7.2 - - + +
66K VAL* 1.3 80.2 - - + +
68K GLU* 1.3 61.7 + - + +
70K GLN* 3.3 8.0 + - - +
71K GLU* 2.9 44.9 + - + +
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Residues in contact with GLU 68 (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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25K ARG* 2.4 46.9 + - - +
29K GLN* 2.7 39.6 + - - +
64K LEU* 2.9 26.5 + - + +
65K ASP* 4.2 2.5 - - - +
67K ARG* 1.3 76.6 - - + +
69K ARG* 1.3 59.2 + - - +
71K GLU* 3.4 13.3 + - - +
72K GLN* 2.9 28.9 + - - +
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Residues in contact with ARG 69 (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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62K GLN* 5.2 3.6 + - - -
65K ASP* 3.0 21.4 + - - +
66K VAL* 3.4 44.7 + - - +
68K GLU* 1.3 77.7 - - - +
70K GLN* 1.3 55.4 + - - +
72K GLN* 3.2 16.6 + - - +
73K GLN* 2.9 50.5 + - + +
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Residues in contact with GLN 70 (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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66K VAL* 2.9 29.0 + - + +
67K ARG* 3.8 6.7 - - - +
68K GLU 3.3 0.2 - - - -
69K ARG* 1.3 73.9 - - - +
71K GLU* 1.3 61.4 + - + +
73K GLN* 3.1 18.3 + - + +
74K GLU* 2.9 30.5 + - + +
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Residues in contact with GLU 71 (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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29K GLN* 5.6 1.0 - - - +
35K LYS* 3.3 39.0 + - - +
67K ARG* 2.9 33.1 + - + +
68K GLU* 3.8 13.4 - - - +
70K GLN* 1.3 74.1 - - + +
72K GLN* 1.3 64.6 + - - +
74K GLU* 3.6 24.7 + - - +
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Residues in contact with GLN 72 (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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68K GLU 2.9 13.0 + - - +
69K ARG* 3.3 20.9 - - - +
70K GLN 3.2 0.2 - - - -
71K GLU* 1.3 78.7 - - - +
73K GLN* 1.3 63.0 + - + +
74K GLU 3.4 3.8 + - - -
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Residues in contact with GLN 73 (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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69K ARG* 2.9 40.5 + - + +
70K GLN* 3.1 21.5 + - + +
72K GLN* 1.3 78.9 - - + +
74K GLU* 1.3 62.7 + - - +
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Residues in contact with GLU 74 (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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70K GLN* 2.9 17.4 + - + +
71K GLU* 4.1 21.6 - - - +
72K GLN 3.2 4.8 - - - -
73K GLN* 1.3 82.0 - - - +
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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