Contacts of the helix formed by residues 13 - 21 (chain D) in PDB entry 3QI6
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 GLY 13 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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375B ASP* 3.0 24.5 - - - -
378B ASP* 2.8 19.3 + - - -
12D ALA* 1.3 73.9 - - - +
14D LEU* 1.3 62.6 + - - -
16D THR* 3.5 1.1 + - - -
17D ARG* 3.1 27.3 + - - +
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Residues in contact with LEU 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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375B ASP* 3.2 3.2 + - - -
13D GLY* 1.3 70.0 - - - -
15D ALA* 1.3 61.0 + - - +
17D ARG* 3.3 29.0 + - + +
18D ALA* 2.9 30.6 + - + +
74D VAL* 3.5 36.6 - - + +
189D PRO* 3.4 28.9 - - + +
190D ALA* 3.7 21.1 - - + +
193D GLN* 4.5 3.4 - - - +
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Residues in contact with ALA 15 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
264B ARG* 6.1 2.0 - - - +
373B ILE* 3.9 22.9 - - + +
374B GLU* 4.5 3.1 - - - -
375B ASP* 3.0 20.3 + - - +
14D LEU* 1.3 77.5 - - - +
16D THR* 1.3 63.1 + - - +
18D ALA* 3.4 6.3 + - - +
19D ILE* 3.4 28.1 + - + +
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Residues in contact with THR 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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330B ILE* 3.8 19.7 - - + -
374B GLU* 3.5 15.8 - - + +
375B ASP* 3.0 21.0 + - - -
378B ASP* 2.6 27.4 + - + +
11D PHE 3.4 26.9 - - - +
13D GLY 3.7 4.0 - - - -
14D LEU 3.2 0.2 - - - -
15D ALA* 1.3 75.8 - - - +
17D ARG* 1.3 55.4 + - - +
19D ILE 3.2 1.7 + - - -
20D HIS* 3.0 50.0 + - + +
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Residues in contact with ARG 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 PHE* 3.1 27.1 + - - +
12D ALA 3.0 24.4 + - - -
13D GLY* 3.1 9.8 + - - +
14D LEU* 3.6 40.6 - - + +
16D THR* 1.3 71.3 - - - +
18D ALA* 1.3 65.4 + - - +
19D ILE 3.1 2.2 - - - -
21D SER* 2.8 50.2 + - - +
22D GLY 4.3 0.7 + - - -
70D ALA* 5.6 1.6 - - - +
73D ALA* 3.2 31.7 + - + +
74D VAL* 4.3 5.2 + - + +
76D ASP* 4.6 14.1 + - - +
193D GLN* 5.2 2.4 + - - -
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Residues in contact with ALA 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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14D LEU* 2.9 18.9 + - + +
15D ALA* 3.6 9.4 - - - +
16D THR 3.4 0.2 - - - -
17D ARG* 1.3 76.3 - - - +
19D ILE* 1.3 61.2 + - + +
22D GLY 5.6 0.7 + - - -
70D ALA* 5.0 12.1 - - - +
74D VAL* 3.7 22.8 - - + +
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Residues in contact with ILE 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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340B VAL* 3.7 30.3 - - + +
341B GLU* 3.4 47.6 - - + +
373B ILE* 3.8 22.9 - - + +
374B GLU* 4.3 11.4 - - + +
15D ALA* 3.4 15.5 + - + +
16D THR 3.2 7.0 + - - +
17D ARG 3.1 0.4 - - - -
18D ALA* 1.3 81.7 - - + +
20D HIS* 1.3 68.7 + - + +
21D SER 3.8 0.4 - - - -
22D GLY 5.2 2.0 + - - -
23D TYR 5.0 3.8 + - - +
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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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329B ASN 5.1 3.2 + - - +
330B ILE* 3.1 35.7 + - + +
332B ILE* 4.1 12.3 - - + +
341B GLU* 3.9 16.6 - - + -
374B GLU* 2.5 35.8 + - + -
11D PHE* 5.4 5.6 - - - +
16D THR* 3.0 33.5 + - + +
17D ARG* 5.1 0.4 - - - -
19D ILE* 1.3 85.8 + - + +
21D SER* 1.3 65.7 + - - +
22D GLY 3.4 3.6 + - - -
23D TYR 3.5 15.8 + - - +
24D ARG* 5.2 1.6 - - - -
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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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11D PHE* 4.7 10.4 - - - +
17D ARG* 2.8 46.5 + - - +
20D HIS* 1.3 73.0 - - - +
22D GLY* 1.3 59.1 + - - +
23D TYR 3.6 0.7 - - - -
69D ALA* 4.3 8.0 - - - +
73D ALA* 3.4 26.2 - - - +
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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