Contacts of the helix formed by residues 13 - 21 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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12D ARG* 1.3 82.8 - - - +
14D GLY* 1.3 75.6 + - - +
15D ILE* 3.7 26.9 - - + +
16D GLU* 3.1 27.6 + - - -
17D LYS* 3.0 21.1 + - - +
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Residues in contact with GLY 14 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12D ARG 3.9 0.6 + - - -
13D THR* 1.3 75.7 - - - +
15D ILE* 1.3 67.4 + - - +
17D LYS* 3.0 15.7 + - - +
18D TRP* 2.8 25.6 + - - +
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Residues in contact with ILE 15 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13D THR* 3.7 17.0 - - + +
14D GLY* 1.3 73.8 - - - +
16D GLU* 1.3 59.5 + - + +
18D TRP* 3.4 14.9 + - + +
19D LEU* 2.8 42.4 + - + +
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Residues in contact with GLU 16 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9D TYR* 3.1 31.7 + - - +
10D GLU 4.4 1.4 - - - +
11D PRO* 3.8 4.9 - - + +
12D ARG* 3.1 24.2 + - - +
13D THR* 3.1 36.8 + - - +
14D GLY 3.0 0.4 - - - -
15D ILE* 1.3 77.9 - - + +
17D LYS* 1.3 57.1 + - - +
19D LEU* 3.1 8.4 + - + +
20D HIS* 2.7 36.6 + - - +
26D VAL* 5.6 7.0 - - + -
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Residues in contact with LYS 17 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11D PRO* 3.6 32.6 + - + +
12D ARG* 2.6 31.0 + - - +
13D THR 3.0 12.3 + - - +
14D GLY* 3.0 10.2 + - - +
16D GLU* 1.3 75.2 - - - +
18D TRP* 1.3 62.8 + - - +
20D HIS* 3.4 0.9 + - - +
21D SER* 2.9 26.2 + - - -
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Residues in contact with TRP 18 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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126A GLU* 3.8 30.3 + - + -
127A VAL* 4.5 15.7 - - + -
130A ILE* 4.9 7.2 - - + -
348A TRP* 4.7 15.7 - + - -
14D GLY 2.8 17.1 + - - +
15D ILE* 3.5 14.8 - - + +
17D LYS* 1.3 76.2 - - - +
19D LEU* 1.3 83.5 + - + +
21D SER* 2.9 19.5 + - - -
22D ARG* 2.9 64.3 + - - +
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Residues in contact with LEU 19 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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127A VAL* 4.5 21.5 - - + -
15D ILE* 2.8 27.0 + - + +
16D GLU* 3.5 7.2 - - + +
18D TRP* 1.3 91.6 - - + +
20D HIS* 1.3 56.6 + - - +
22D ARG* 2.9 7.1 + - - +
23D LEU* 2.8 45.5 + - + +
25D ILE* 4.9 8.1 - - + -
26D VAL* 3.8 28.0 - - + -
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Residues in contact with HIS 20 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9D TYR* 3.5 41.3 + + + +
11D PRO* 3.8 22.5 - - + +
16D GLU 2.7 19.7 + - - +
17D LYS 3.9 2.2 - - - +
19D LEU* 1.3 73.3 - - - +
21D SER* 1.3 64.0 + - - +
22D ARG 3.1 1.0 + - - -
23D LEU 3.9 0.4 + - - -
24D PRO* 3.8 35.9 - - + +
26D VAL* 6.6 0.4 - - + -
27D ALA* 4.2 10.9 - - + +
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Residues in contact with SER 21 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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124A PRO* 5.7 2.1 - - - +
218A SER* 4.7 6.1 - - - +
219A THR* 4.6 6.2 - - - +
17D LYS 2.9 13.6 + - - -
18D TRP* 2.9 19.8 + - - -
20D HIS* 1.3 78.6 + - - +
22D ARG* 1.3 68.0 + - - +
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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