Contacts of the helix formed by residues 45 - 56 (chain K) in PDB entry 6C6S
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 LYS 45 (chain K).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1313I HIS* 5.7 5.3 + - - -
414J GLU 4.4 6.1 + - - +
415J VAL* 3.4 37.2 + - - +
416J ILE 4.6 0.2 - - - -
417J ARG* 4.6 3.5 - - + +
418J GLU* 3.9 39.0 - - + +
419J HIS* 3.7 22.4 + - + +
477J GLN* 4.9 12.5 - - - +
44K ASP* 1.3 80.4 - - - +
46K THR* 1.3 67.6 + - - +
47K THR* 3.2 10.3 + - - +
48K VAL* 3.4 3.1 + - - +
49K ILE* 3.2 21.2 + - - +
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Residues in contact with THR 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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1313I HIS* 6.1 0.2 - - - -
474J LEU* 4.0 10.7 - - - +
27K ALA* 3.6 28.1 + - - +
30K MET* 3.7 28.0 - - + +
31K GLN* 4.1 18.0 + - + +
44K ASP 5.6 0.4 - - - +
45K LYS* 1.3 73.4 - - - +
47K THR* 1.3 61.5 + - - +
49K ILE* 4.2 11.0 - - + -
50K ALA* 2.9 30.1 + - - +
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Residues in contact with THR 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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418J GLU 5.6 2.9 - - - +
474J LEU* 3.3 24.4 - - - +
477J GLN* 3.4 18.5 + - + +
478J LEU* 3.7 34.4 - - + +
481J ARG* 4.0 24.9 - - - +
27K ALA* 4.4 7.6 - - - -
45K LYS* 3.2 6.9 - - - +
46K THR* 1.3 79.2 + - - +
48K VAL* 1.3 60.4 + - - +
50K ALA* 3.2 4.4 + - - +
51K LEU* 3.0 28.2 + - - +
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Residues in contact with VAL 48 (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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418J GLU* 3.4 41.5 - - + +
481J ARG* 4.1 15.5 - - - +
2K ALA 4.8 7.0 - - - +
3K ARG* 3.7 32.2 + - + +
44K ASP* 3.9 23.8 - - + +
45K LYS* 3.4 8.1 + - + +
46K THR 3.4 0.2 - - - -
47K THR* 1.3 75.9 - - + +
49K ILE* 1.3 61.4 + - - +
51K LEU* 3.4 6.0 + - - +
52K ARG* 2.8 34.2 + - + +
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Residues in contact with ILE 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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30K MET* 3.7 24.9 - - + -
37K PRO* 3.8 11.7 - - + -
39K VAL* 3.7 21.5 - - + +
41K GLU* 3.3 39.5 - - + +
44K ASP* 4.0 20.2 - - + +
45K LYS 3.2 19.0 + - - +
46K THR* 3.8 12.8 - - + +
47K THR 3.3 0.4 - - - -
48K VAL* 1.3 77.5 - - - +
50K ALA* 1.3 57.9 + - - +
52K ARG* 3.3 8.4 + - - +
53K GLU* 2.9 30.0 + - - +
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Residues in contact with ALA 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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23K ALA* 3.5 31.6 - - + +
26K ARG* 4.2 10.1 - - + +
27K ALA* 3.9 8.5 - - + +
30K MET* 3.6 11.4 - - + +
46K THR 2.9 18.1 + - - +
47K THR* 3.4 6.1 - - - +
49K ILE* 1.3 76.6 - - - +
51K LEU* 1.3 56.7 + - - +
53K GLU* 3.2 5.2 + - - +
54K ILE* 3.0 33.3 + - - +
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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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478J LEU* 3.8 20.2 - - + -
481J ARG* 3.7 31.2 - - + -
482J ALA* 5.8 1.1 - - + -
3K ARG* 3.6 20.0 - - - +
6K VAL* 4.0 17.5 - - + -
9K ALA* 4.4 7.4 - - + +
19K LEU* 4.0 33.0 - - + -
23K ALA* 4.0 17.9 - - + -
47K THR 3.0 17.7 + - - +
48K VAL* 4.0 1.6 - - - +
50K ALA* 1.3 75.9 - - - +
52K ARG* 1.3 56.9 + - - +
54K ILE* 3.3 5.4 + - + +
55K GLU* 2.9 31.2 + - - +
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Residues in contact with ARG 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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2K ALA 5.1 11.1 - - - +
3K ARG* 3.5 10.9 - - - +
39K VAL* 3.6 29.6 - - + +
40K PRO* 2.7 34.2 + - - +
41K GLU* 3.9 2.4 - - - +
42K GLU* 3.6 38.0 + - - +
44K ASP* 3.9 11.9 + - - -
48K VAL* 2.8 20.2 + - + +
49K ILE* 3.5 8.8 - - - +
50K ALA 3.2 0.2 - - - -
51K LEU* 1.3 76.5 - - - +
53K GLU* 1.3 63.9 + - - +
55K GLU* 3.3 10.6 + - - +
56K GLU* 3.2 28.0 + - + +
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Residues in contact with GLU 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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26K ARG* 2.6 44.5 + - - +
30K MET* 3.7 5.6 - - - +
37K PRO* 3.6 5.5 - - - +
38K LEU* 2.7 34.4 + - - -
39K VAL* 3.7 18.6 + - + +
49K ILE* 2.9 19.4 + - - +
50K ALA 3.6 4.0 - - - +
52K ARG* 1.3 74.8 - - - +
54K ILE* 1.3 65.3 + - - +
56K GLU* 3.5 9.7 + - - +
58K LEU* 3.6 30.6 + - + +
59K ILE* 3.8 18.6 + - + +
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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
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9K ALA* 3.7 26.2 - - + +
12K LYS* 3.5 9.3 - - + +
13K ILE* 3.8 23.8 - - + -
19K LEU* 4.0 11.0 - - + -
22K VAL* 3.7 25.6 - - + -
23K ALA* 4.8 7.9 - - + +
26K ARG* 5.8 0.9 - - + -
50K ALA 3.0 18.6 + - - +
51K LEU* 3.6 9.0 - - - +
52K ARG 3.3 0.2 - - - -
53K GLU* 1.3 76.3 - - - +
55K GLU* 1.3 53.4 + - - +
57K GLY* 2.8 25.6 + - - -
59K ILE* 3.3 36.6 - - + +
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Residues in contact with GLU 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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2K ALA 5.5 0.9 - - - +
3K ARG* 2.4 42.4 + - - -
5K THR 3.8 4.0 - - - +
6K VAL* 4.5 7.6 - - - -
7K GLN 4.9 0.2 + - - -
8K ASP* 4.2 18.0 + - + +
9K ALA* 3.9 23.4 + - + +
12K LYS* 3.4 18.8 - - - +
51K LEU 2.9 16.3 + - - +
52K ARG* 3.3 11.7 + - + +
54K ILE* 1.3 74.8 - - - +
56K GLU* 1.3 63.4 + - + +
57K GLY 3.2 0.2 - - - -
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Residues in contact with GLU 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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12K LYS* 4.4 3.4 + - - -
39K VAL* 4.9 16.7 - - + +
52K ARG* 3.2 17.7 + - + +
53K GLU* 3.9 6.1 - - - +
54K ILE 3.2 0.8 - - - -
55K GLU* 1.3 78.2 - - - +
57K GLY* 1.3 62.4 + - - +
58K LEU* 3.5 27.9 + - + +
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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