Contacts of the helix formed by residues 8 - 18 (chain D) in PDB entry 3CUQ
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 8 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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6D GLU 3.5 6.3 - - - +
7D TRP* 1.3 88.4 - - + +
9D TRP* 1.3 57.6 + - + +
10D GLN* 3.5 20.2 - - + +
11D TYR* 2.7 41.0 + - + +
12D ARG* 3.8 4.8 + - - -
16D PHE* 6.3 1.6 - - + -
32D ALA 6.0 0.4 - - - +
36D LEU* 3.5 36.1 - - + -
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Residues in contact with TRP 9 (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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381B LEU* 3.6 39.9 - - + -
382B PHE* 3.9 11.2 - + - -
384B THR 4.6 0.7 - - - -
385B GLN* 3.0 50.6 + - + +
7D TRP 4.1 0.6 + - - -
8D PRO* 1.3 73.1 - - + +
10D GLN* 1.3 107.7 + - + +
12D ARG* 3.2 22.8 + - - +
13D PHE* 3.3 25.3 + + + +
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Residues in contact with GLN 10 (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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382B PHE* 3.9 19.3 - - + -
8D PRO* 2.9 22.9 + - + +
9D TRP* 1.3 119.1 + - + +
11D TYR* 1.3 54.3 + - - +
12D ARG 3.0 4.9 - - - -
13D PHE* 2.6 39.6 + - - +
16D PHE* 3.4 33.0 - - + +
17D PHE* 4.3 0.2 - - - -
32D ALA* 3.7 21.4 - - + +
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Residues in contact with TYR 11 (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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7D TRP* 3.4 48.9 - + + -
8D PRO* 2.7 32.6 + - + +
10D GLN* 1.3 72.7 - - - +
12D ARG* 1.3 60.6 + - + +
13D PHE 3.4 0.4 - - - -
16D PHE* 3.9 11.3 - + + -
17D PHE* 3.7 29.3 - + - -
36D LEU* 4.7 7.6 - - + -
58D PRO* 2.4 31.3 + - - +
59D LEU 4.0 13.0 - - - -
61D ASN 3.4 14.6 + - - -
62D ASN* 3.0 51.5 + - + -
65D LEU* 4.3 0.5 - - - +
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Residues in contact with ARG 12 (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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7D TRP* 3.6 38.2 + - - +
8D PRO 3.8 7.8 + - - -
9D TRP* 3.2 13.3 + - - +
10D GLN 3.0 1.0 - - - -
11D TYR* 1.3 83.0 - - + +
13D PHE* 1.3 58.6 + - - +
14D PRO* 3.3 11.4 - - - +
62D ASN* 5.2 3.1 - - - +
65D LEU* 3.7 21.5 - - + +
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Residues in contact with PHE 13 (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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367B CYS* 3.6 4.3 - - - -
378B TYR* 3.8 23.3 - + + -
379B PRO* 3.6 21.8 - - + -
381B LEU* 3.2 33.7 - - + -
382B PHE* 3.5 37.9 - + - -
9D TRP* 3.3 22.0 + + + +
10D GLN* 2.6 21.1 + - - +
11D TYR 3.4 0.4 - - - -
12D ARG* 1.3 72.9 - - - +
14D PRO* 1.3 71.9 - - + +
15D PRO* 3.4 31.4 - - + -
16D PHE* 2.9 20.6 + - - +
17D PHE* 3.9 4.0 - - - -
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Residues in contact with PRO 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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369B ASP* 3.1 29.6 - - - +
378B TYR* 3.5 23.1 - - + +
12D ARG 3.3 11.0 - - - +
13D PHE* 1.3 88.2 - - + +
15D PRO* 1.4 65.2 - - + +
16D PHE 3.0 5.5 + - - -
17D PHE* 3.1 19.3 + - + +
18D THR 4.2 1.4 + - - -
65D LEU* 4.2 24.9 - - + -
67D ARG* 3.7 17.8 - - - +
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Residues in contact with PRO 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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367B CYS* 3.7 10.8 - - - -
368B ARG 3.0 23.8 - - - +
369B ASP* 3.9 4.0 - - + -
378B TYR* 3.5 31.9 - - + -
382B PHE* 4.3 2.8 - - + -
13D PHE* 3.3 40.2 - - + -
14D PRO* 1.4 93.9 - - + +
16D PHE* 1.3 55.8 + - - +
17D PHE 3.1 0.7 - - - -
18D THR 2.8 27.4 + - - +
20D GLN* 3.0 10.4 + - - +
29D GLN* 3.7 1.2 + - - -
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Residues in contact with PHE 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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382B PHE* 3.7 25.4 - + + -
8D PRO* 6.3 2.0 - - + -
10D GLN* 3.4 44.6 - - + +
11D TYR* 3.9 6.7 - + + -
13D PHE* 2.9 17.6 + - + +
15D PRO* 1.3 78.6 - - - +
17D PHE* 1.3 67.1 + + + +
18D THR 3.3 0.4 - - - -
29D GLN* 3.2 14.6 + - + +
32D ALA* 3.9 22.0 - - + -
33D TRP* 3.0 93.0 + + - -
36D LEU* 4.9 8.5 - - + -
69D LEU* 5.3 0.2 - - - +
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Residues in contact with PHE 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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370B ASP 5.6 0.2 - - - +
11D TYR* 3.7 48.7 - + - -
13D PHE 3.9 11.7 - - - -
14D PRO* 3.1 16.7 + - + +
15D PRO 3.1 0.8 - - - -
16D PHE* 1.3 92.9 - + - +
18D THR* 1.3 58.8 + - - +
19D LEU 4.2 0.2 - - - -
33D TRP* 3.9 26.7 - + - -
60D PHE 4.2 11.0 - - - -
62D ASN* 4.1 13.7 - - + -
65D LEU* 4.1 10.8 - - + -
66D GLN 5.3 0.2 - - - -
67D ARG* 3.9 25.0 - - + +
68D LYS* 4.0 11.1 - - - +
69D LEU* 4.1 21.4 - - - +
70D PRO* 3.5 24.8 - - - +
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Residues in contact with THR 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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368B ARG* 4.0 22.0 - - - -
369B ASP* 3.8 6.1 + - - -
370B ASP* 2.9 53.3 + - + +
14D PRO 4.6 0.2 + - - -
15D PRO 2.8 13.3 + - - +
17D PHE* 1.3 80.0 + - - +
19D LEU* 1.3 71.7 + - - +
20D GLN* 3.0 5.7 + - - -
29D GLN* 2.6 23.3 + - - -
67D ARG* 5.6 1.0 - - - -
70D PRO* 5.5 2.0 - - - -
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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