Contacts of the helix formed by residues 15 - 23 (chain D) in PDB entry 4QYP
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 ASN 15 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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13D ASN 3.9 1.6 + - - -
14D GLU* 1.3 75.6 - - + +
16D PHE* 1.4 65.4 + - - +
17D GLU* 3.1 2.9 - - - +
18D GLY* 3.0 21.7 + - - -
19D TYR 3.2 11.2 + - - +
124D GLN* 3.0 23.9 + - - +
125D VAL 3.0 28.5 + - - +
126D CYS* 3.7 7.3 - - - +
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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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13D ASN* 3.3 33.1 + - - +
14D GLU 3.2 4.0 - - - -
15D ASN* 1.4 76.4 - - - +
17D GLU* 1.3 57.1 - - - +
19D TYR* 3.4 25.2 + + - +
20D MET* 2.9 67.6 + - + +
33D ALA* 3.8 24.2 - - + -
34D VAL* 4.1 12.2 - - + +
38D GLN* 3.7 21.8 - - - -
77D LEU* 4.6 11.2 - - + -
119D LEU* 5.3 2.0 - - + -
126D CYS* 3.6 18.4 - - - -
128D GLN* 3.9 9.6 - - - -
201D ACT 4.8 7.4 - - + -
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Residues in contact with GLU 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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15D ASN* 3.1 2.5 - - - +
16D PHE* 1.3 76.7 - - - +
18D GLY* 1.3 58.8 + - - +
20D MET* 3.8 8.5 - - + +
21D LYS* 2.9 35.1 + - + +
30D ARG* 3.0 40.1 + - + +
31D LYS* 3.3 29.4 + - - +
34D VAL* 4.5 24.6 - - + +
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Residues in contact with GLY 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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15D ASN* 3.0 24.0 + - - -
17D GLU* 1.3 77.5 - - - +
19D TYR* 1.3 63.7 + - - +
21D LYS* 3.2 11.7 + - - +
22D ALA 3.0 18.5 + - - -
124D GLN* 3.5 24.5 - - - +
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Residues in contact with TYR 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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15D ASN* 3.2 13.1 + - - +
16D PHE* 3.7 32.1 - + - +
18D GLY* 1.3 79.3 - - - +
20D MET* 1.3 64.5 + - + +
22D ALA* 3.3 5.1 + - - +
23D LEU* 3.1 48.9 + - + +
77D LEU* 4.3 16.0 - - + +
97D GLN* 4.9 8.8 + - - -
104D ARG* 4.8 6.5 + - + +
105D GLY 5.0 1.2 + - - -
106D TRP* 5.9 0.7 - - - -
119D LEU* 3.7 47.0 - - + +
120D THR 3.7 21.7 + - - -
121D CYS* 3.9 16.8 - - + -
124D GLN* 4.1 12.8 - - + +
126D CYS* 3.8 14.1 - - + +
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Residues in contact with MET 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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16D PHE* 2.9 62.9 + - + +
17D GLU* 4.0 4.5 - - - +
18D GLY 3.3 0.4 - - - -
19D TYR* 1.3 79.6 - - + +
21D LYS* 1.3 61.7 + - - +
23D LEU* 3.1 16.6 + - - +
25D ILE* 3.1 41.7 + - + -
29D THR* 6.0 0.2 - - - -
30D ARG* 3.7 50.9 - - + +
33D ALA* 3.6 21.3 - - + -
34D VAL* 4.1 4.9 - - + +
77D LEU* 4.6 4.9 - - + -
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Residues in contact with LYS 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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17D GLU* 2.9 28.6 + - + +
18D GLY* 3.9 9.0 - - - +
19D TYR 3.2 0.2 - - - -
20D MET* 1.3 77.0 - - - +
22D ALA* 1.3 61.2 + - - +
24D ASP* 3.0 19.5 + - - +
25D ILE 4.8 1.6 - - - +
30D ARG* 3.3 43.5 - - - +
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Residues in contact with ALA 22 (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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18D GLY 3.0 13.1 + - - +
19D TYR 3.3 8.9 + - - +
21D LYS* 1.3 76.9 - - - +
23D LEU* 1.3 57.9 + - - +
24D ASP* 3.4 3.1 + - - +
101D LYS* 3.3 23.7 + - - +
121D CYS* 3.8 33.9 - - + +
122D GLY* 5.8 0.2 - - - -
124D GLN* 3.9 13.4 - - + +
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Residues in contact with LEU 23 (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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19D TYR* 3.1 45.4 + - + +
20D MET* 3.1 10.3 + - - +
22D ALA* 1.3 74.6 - - - +
24D ASP* 1.3 72.0 + - - +
25D ILE* 3.4 18.1 + - + -
77D LEU* 4.2 12.6 - - + -
78D ASP* 3.4 17.1 - - + +
80D ARG* 2.9 18.4 + - - +
101D LYS* 4.5 2.9 - - + -
104D ARG* 3.6 39.5 - - - +
121D CYS* 3.6 23.6 - - + -
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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