Contacts of the helix formed by residues 13 - 21 (chain G) 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 THR 13 (chain G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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12G ARG* 1.3 82.8 - - - +
14G GLY* 1.3 77.6 + - - +
15G ILE* 3.7 26.2 - - + +
16G GLU* 3.2 27.6 + - - +
17G LYS* 3.0 20.8 + - - +
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Residues in contact with GLY 14 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12G ARG 3.8 0.6 + - - -
13G THR* 1.3 74.9 - - - +
15G ILE* 1.3 55.9 + - - +
17G LYS* 3.0 13.5 + - - +
18G TRP* 2.7 36.7 + - - +
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Residues in contact with ILE 15 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13G THR* 4.2 16.4 - - + -
14G GLY* 1.3 74.4 - - - +
16G GLU* 1.3 53.8 + - + +
18G TRP* 3.4 14.3 - - + +
19G LEU* 2.8 47.0 + - + +
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Residues in contact with GLU 16 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9G TYR* 3.0 32.2 + - - +
10G GLU 4.1 1.2 - - - +
11G PRO* 3.7 4.9 - - + +
12G ARG* 3.1 30.1 + - - +
13G THR* 3.2 31.8 + - - +
14G GLY 3.0 0.6 - - - -
15G ILE* 1.3 77.7 - - + +
17G LYS* 1.3 57.1 + - - +
19G LEU* 3.0 8.6 + - + +
20G HIS* 2.7 36.6 + - - +
26G VAL* 5.6 7.2 - - + -
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Residues in contact with LYS 17 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11G PRO* 2.8 44.6 + - + +
12G ARG* 3.2 20.5 + - - +
13G THR 3.0 16.4 + - - +
14G GLY* 3.5 9.9 - - - +
16G GLU* 1.3 74.9 - - - +
18G TRP* 1.3 62.1 + - - +
20G HIS* 3.5 1.2 + - - +
21G SER* 3.1 25.3 + - - -
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Residues in contact with TRP 18 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14G GLY 2.7 20.4 + - - +
15G ILE* 3.4 16.2 - - + +
17G LYS* 1.3 71.9 - - - +
19G LEU* 1.3 82.6 + - + +
21G SER* 2.8 18.8 + - - -
22G ARG* 2.8 68.4 + - - +
126J GLU* 3.7 32.5 + - + -
127J VAL* 4.4 16.4 - - + -
130J ILE* 5.0 6.7 - - + -
348J TRP* 4.8 13.7 - + - -
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Residues in contact with LEU 19 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15G ILE* 2.8 30.8 + - + +
16G GLU* 3.4 7.4 - - + +
18G TRP* 1.3 87.3 - - + +
20G HIS* 1.3 53.5 + - - +
22G ARG* 2.9 6.7 + - - +
23G LEU* 2.8 50.5 + - + +
25G ILE* 4.8 7.6 - - + -
26G VAL* 3.7 27.6 - - + -
127J VAL* 4.4 22.9 - - + -
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Residues in contact with HIS 20 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9G TYR* 3.6 34.8 + + + +
11G PRO* 3.6 23.8 - - + +
16G GLU 2.7 19.8 + - - +
17G LYS 3.9 2.7 - - - +
19G LEU* 1.3 74.4 - - - +
21G SER* 1.3 63.9 + - - +
22G ARG 3.2 1.0 + - - -
23G LEU 4.0 0.4 + - - -
24G PRO* 3.9 35.2 - - + +
26G VAL* 6.6 0.2 - - + -
27G ALA* 4.2 12.5 - - + +
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Residues in contact with SER 21 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17G LYS 3.1 12.5 + - - -
18G TRP* 2.8 19.8 + - - -
20G HIS* 1.3 80.5 + - - +
22G ARG* 1.3 69.0 + - - +
124J PRO* 5.6 1.9 - - - +
218J SER 4.5 8.7 - - - +
219J THR* 4.6 3.1 - - - +
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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