Contacts of the helix formed by residues 59 - 67 (chain E) 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 59 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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57E GLU 4.2 4.3 - - - +
58E LEU* 1.3 87.8 - - + +
60E GLU* 1.3 67.4 + - - +
61E ASP* 3.0 20.9 - - - +
62E GLN* 2.8 50.1 + - - +
63E VAL* 3.1 9.4 + - - +
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Residues in contact with GLU 60 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51E SER* 4.0 26.6 - - - +
58E LEU 3.5 2.2 + - - -
59E PRO* 1.3 70.1 - - - +
61E ASP* 1.3 59.7 + - - +
63E VAL* 3.5 2.5 - - - +
64E ARG* 2.8 50.8 + - - +
85E PRO* 5.1 0.7 - - - +
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Residues in contact with ASP 61 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59E PRO* 2.8 19.2 + - - +
60E GLU* 1.3 80.5 + - - +
62E GLN* 1.3 65.4 + - - +
64E ARG* 3.1 23.3 + - - +
65E ALA* 2.8 29.9 + - - +
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Residues in contact with GLN 62 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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58E LEU* 4.6 18.7 - - + +
59E PRO* 2.8 51.0 + - + +
61E ASP* 1.3 75.0 + - - +
63E VAL* 1.3 55.5 + - - +
65E ALA* 2.9 8.6 + - - +
66E TYR* 2.6 37.4 + - - +
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Residues in contact with VAL 63 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47E ILE* 4.2 22.2 - - + +
48E ARG* 4.3 0.7 - - - -
50E LEU* 3.9 15.0 - - + -
51E SER* 3.2 28.5 - - - +
58E LEU* 3.8 23.8 - - + +
59E PRO 3.1 9.6 + - - +
60E GLU 3.5 7.4 - - - +
62E GLN* 1.3 78.4 - - - +
64E ARG* 1.3 65.8 + - - +
66E TYR* 2.8 9.8 + - - +
67E ALA* 2.8 23.6 + - - +
85E PRO* 3.8 24.7 - - + -
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Residues in contact with ARG 64 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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60E GLU* 2.8 47.4 + - - +
61E ASP* 3.1 34.2 + - - +
63E VAL* 1.3 73.7 - - - +
65E ALA* 1.3 59.0 + - - +
67E ALA* 3.6 5.2 + - - +
68E THR* 3.0 21.0 + - - -
83E GLY 4.2 2.6 - - - +
85E PRO* 3.5 28.5 - - + +
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Residues in contact with ALA 65 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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61E ASP 2.8 13.7 + - - +
62E GLN* 3.1 12.6 - - - +
64E ARG* 1.3 75.3 - - - +
66E TYR* 1.3 64.9 + - - +
68E THR* 2.8 27.9 + - - -
69E GLN 4.0 0.9 + - - -
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Residues in contact with TYR 66 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29E LEU* 3.2 32.5 - - + +
32E TYR* 4.6 2.4 - - - -
33E THR* 2.8 31.7 + - + +
47E ILE* 4.3 3.1 - - + -
50E LEU* 4.2 14.8 - - + -
58E LEU* 5.9 4.5 - - + -
62E GLN 2.6 17.0 + - - +
63E VAL* 2.8 13.7 + - - +
65E ALA* 1.3 66.5 - - - +
67E ALA* 1.3 57.5 + - - +
68E THR 2.6 16.1 + - - -
69E GLN* 2.9 47.0 + - - +
70E PHE* 3.0 32.1 - + - -
89E PHE* 3.5 18.8 - + - -
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Residues in contact with ALA 67 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47E ILE* 4.1 12.3 - - + -
63E VAL 2.8 18.8 + - - +
64E ARG 3.7 5.4 - - - +
66E TYR* 1.3 74.6 - - - +
68E THR* 1.3 59.9 + - - +
69E GLN 3.3 0.8 + - - -
70E PHE* 3.4 21.4 + - - -
83E GLY* 3.0 42.2 + - - +
84E LYS 3.7 16.8 - - - +
85E PRO* 3.7 7.2 - - + -
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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