Contacts of the helix formed by residues 46 - 51 (chain K) in PDB entry 2QJK
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 PRO 46 (chain K).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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85J ARG* 4.2 15.5 - - + +
86J ASN* 4.6 7.4 - - - +
44K PHE 3.3 11.2 - - - +
45K VAL* 1.3 83.0 - - + +
47K ILE* 1.3 61.7 + - - +
48K ARG* 3.2 36.6 - - + +
49K SER* 2.3 50.9 + - - +
52K GLU* 5.5 0.7 - - - +
85K PRO 5.1 0.4 - - - +
86K THR 5.7 1.8 - - - +
87K ASP 3.8 5.6 - - - +
88K HIS* 3.1 24.0 - - + +
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Residues in contact with ILE 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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45K VAL 3.3 1.6 + - - -
46K PRO* 1.3 68.6 - - - +
48K ARG* 1.3 53.1 + - - +
50K LEU* 2.5 61.3 + - + +
63K VAL* 4.2 9.8 - - + +
66K TYR* 4.3 7.2 - - + -
67K ALA* 4.1 20.9 - - + +
70K PHE* 3.9 30.7 - - + -
72K VAL* 6.5 0.2 - - + -
83K GLY* 5.7 0.7 - - - -
84K LYS 4.0 11.9 - - - +
85K PRO* 3.9 4.9 - - + +
87K ASP* 2.9 27.6 + - + +
88K HIS 4.3 7.2 - - - +
89K PHE* 3.8 28.3 - - + +
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Residues in contact with ARG 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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86J ASN* 3.0 28.7 + - - +
46K PRO* 4.0 23.1 - - + +
47K ILE* 1.3 71.0 - - - +
49K SER* 1.3 62.0 + - - +
50K LEU 3.1 0.9 - - - -
51K SER* 3.3 24.1 + - - +
52K GLU* 3.0 33.0 + - - +
63K VAL* 4.3 1.6 - - - -
85K PRO* 2.8 41.5 + - + +
86K THR* 4.1 14.5 + - + +
88K HIS* 5.8 0.6 - - - -
42L ALA* 3.5 24.1 + - - +
43L ASP* 3.4 28.5 + - - +
46L ALA* 4.6 12.2 - - - +
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Residues in contact with SER 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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85J ARG* 5.5 1.5 + - - -
45K VAL* 3.6 15.9 - - - +
46K PRO* 2.3 41.0 + - - +
47K ILE 2.5 4.4 + - - -
48K ARG* 1.3 72.4 - - - +
50K LEU* 1.3 63.7 + - - +
51K SER 2.9 7.0 + - - -
52K GLU* 3.2 40.9 + - - +
56K PRO* 4.6 0.2 - - - +
217K TRP* 3.5 26.8 - - - -
221K PRO* 5.7 4.3 - - - -
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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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29K LEU* 3.5 32.5 - - + -
47K ILE* 2.5 48.1 + - + +
49K SER* 1.3 73.2 + - - +
51K SER* 1.3 55.1 + - - +
56K PRO* 3.9 10.6 - - + +
57K GLU 3.1 13.5 + - - -
58K LEU* 2.9 26.7 + - + -
63K VAL* 3.9 17.5 - - + -
66K TYR* 4.2 15.5 - - + -
89K PHE* 3.9 24.2 - - + -
214K PHE* 4.6 2.0 - - + -
217K TRP* 4.2 22.4 - - + -
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Residues in contact with SER 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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48K ARG* 3.4 13.8 + - - -
49K SER 2.9 0.8 - - - -
50K LEU* 1.3 75.9 - - - +
52K GLU* 1.3 70.5 + - - +
53K PRO 3.6 0.2 - - - -
57K GLU* 3.5 13.3 - - - +
58K LEU 3.4 17.7 + - - +
60K GLU* 4.4 19.3 - - - +
63K VAL* 3.1 26.7 - - - +
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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