Contacts of the helix formed by residues 9 - 22 (chain D) in PDB entry 5HZZ
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 9 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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8B PRO 6.2 0.2 - - - +
9B THR* 5.9 13.2 - - + -
7D PRO 4.7 4.5 - - - +
8D PRO* 1.3 77.3 - - - +
10D ASN* 1.3 60.1 + - - +
11D ALA 3.5 1.3 + - - -
12D GLU* 2.8 37.4 + - - +
13D ARG* 2.9 28.8 + - - +
99D ASP* 2.7 34.0 + - - +
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Residues in contact with ASN 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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88B TYR* 2.9 24.6 + - - +
98B ALA 4.8 0.2 + - - -
99B ASP* 3.1 24.3 + - - +
102B PHE* 3.2 41.6 - - + +
9D THR* 1.3 74.5 - - - +
11D ALA* 1.3 62.1 + - - +
13D ARG* 2.8 38.3 + - - +
14D LEU* 3.3 19.4 + - - +
88D TYR* 3.5 23.3 + - + +
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Residues in contact with ALA 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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9D THR* 3.2 1.6 + - - -
10D ASN* 1.3 79.2 - - - +
12D GLU* 1.3 60.8 + - + +
14D LEU* 3.2 14.6 + - - +
15D HIS* 3.4 9.9 + - - +
88D TYR* 3.7 28.3 - - + -
92D ASP* 4.5 4.7 - - - +
97D ASP* 5.0 1.8 - - - +
98D ALA* 3.9 14.4 - - + +
99D ASP* 3.6 30.9 + - - +
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Residues in contact with GLU 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 PRO 4.6 0.3 - - - +
8D PRO* 3.3 16.7 - - + +
9D THR* 2.8 46.0 + - - +
11D ALA* 1.3 72.4 - - + +
13D ARG* 1.3 65.7 + - - +
15D HIS* 3.2 11.3 + - - +
16D GLU* 3.2 18.5 + - - +
99D ASP* 4.7 3.5 - - - +
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Residues in contact with ARG 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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99B ASP* 4.5 10.3 + - - +
102B PHE* 3.9 14.6 - - + -
103B ALA* 3.6 29.7 - - - +
106B HIS* 3.0 48.6 - - + +
7D PRO* 4.5 8.9 - - - +
8D PRO* 3.5 46.2 + - + +
9D THR 2.9 13.9 + - - +
10D ASN* 2.8 42.9 + - - +
11D ALA 3.2 0.4 - - - -
12D GLU* 1.3 77.5 - - - +
14D LEU* 1.3 57.4 + - - +
16D GLU* 3.1 7.0 + - - +
17D PHE 2.9 23.9 + - - -
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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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102B PHE* 3.6 31.9 - - + -
10D ASN 3.3 7.1 + - - +
11D ALA 3.2 11.6 + - - +
13D ARG* 1.3 74.9 - - - +
15D HIS* 1.3 61.3 + - - +
17D PHE* 3.3 4.6 + - + +
18D HIS* 2.9 50.1 + - + +
85D TYR* 3.6 38.1 - - + +
88D TYR* 3.7 12.6 - - + +
89D GLY* 3.5 32.8 - - - +
92D ASP* 4.1 14.6 - - + -
201D UMP 4.8 1.6 - - - +
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Residues in contact with HIS 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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11D ALA 3.4 5.4 + - - +
12D GLU* 3.2 15.5 + - - +
14D LEU* 1.3 78.8 - - - +
16D GLU* 1.3 59.8 + - - +
18D HIS* 3.5 1.0 + - - +
19D ARG* 3.0 36.1 + - + +
25D THR* 2.7 45.2 + - + -
26D PRO 5.3 3.7 + - - -
27D GLU* 5.9 2.5 - - - -
92D ASP* 3.5 17.4 + - - +
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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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106B HIS* 2.8 28.3 + - - -
110B LEU* 3.8 22.1 - - + +
8D PRO* 5.7 3.3 - - - +
12D GLU 3.2 10.7 + - - +
13D ARG* 3.1 12.0 + - - +
15D HIS* 1.3 81.2 - - - +
17D PHE* 1.3 57.7 + - - +
19D ARG* 3.4 19.3 + - - +
20D ALA* 3.0 26.9 + - - +
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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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106B HIS* 4.0 2.9 - - + -
109B ASN* 3.4 37.9 - - + -
110B LEU* 3.9 11.8 - - + +
112B LYS* 5.0 1.6 - - + -
123B GLN* 4.5 7.9 - - + -
13D ARG 2.9 9.6 + - - +
14D LEU* 3.7 7.2 - - + +
16D GLU* 1.3 77.1 - - - +
18D HIS* 1.3 78.8 + + - +
20D ALA* 3.0 3.8 + - - +
21D ILE* 3.0 58.2 + - + +
85D TYR* 3.2 33.9 - + + +
201D UMP 3.6 45.3 - + - -
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Residues in contact with HIS 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 20.2 + - + +
15D HIS 4.1 0.4 - - - +
17D PHE* 1.3 101.4 - + - +
19D ARG* 1.3 62.7 + - - +
21D ILE* 3.4 5.5 + - + -
22D GLY* 3.0 4.7 + - - -
23D ALA* 2.9 50.7 + - + +
24D ALA 4.1 1.3 + - - -
25D THR* 3.8 12.8 - - - -
40D ARG* 3.9 13.5 + - - -
89D GLY* 3.4 37.4 - - - -
92D ASP* 2.8 25.4 + - - +
93D GLN* 3.5 15.3 - - + +
201D UMP 4.9 2.6 + - - -
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Residues in contact with ARG 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 HIS* 3.0 26.0 + - + +
16D GLU* 3.6 35.3 + - - +
18D HIS* 1.3 76.1 - - - +
20D ALA* 1.3 90.4 + - - +
21D ILE 3.3 0.7 + - - -
22D GLY* 3.3 10.3 + - - -
23D ALA 5.1 0.2 - - - -
25D THR* 4.2 11.0 - - + +
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Residues in contact with ALA 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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110B LEU* 4.0 19.7 - - + +
113B ALA* 3.7 25.0 - - + +
117B ARG* 5.1 0.2 + - - -
16D GLU 3.0 15.4 + - - +
17D PHE* 3.0 8.5 + - + +
19D ARG* 1.3 99.8 + - - +
21D ILE* 1.3 62.5 + - + +
22D GLY 3.7 0.3 + - - -
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Residues in contact with ILE 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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110B LEU 5.7 0.2 - - - +
113B ALA* 4.0 19.3 - - + +
117B ARG* 3.1 27.2 + - - +
121B GLY 5.7 2.5 - - - +
123B GLN* 3.4 34.1 - - + +
17D PHE* 3.0 61.1 + - + +
18D HIS* 3.6 9.6 - - + +
20D ALA* 1.3 79.1 - - + +
22D GLY* 1.3 60.8 + - - +
23D ALA* 3.9 20.6 - - + +
201D UMP 4.7 4.7 - - - +
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Residues in contact with GLY 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 HIS 3.0 5.4 + - - -
19D ARG* 3.3 10.2 + - - -
20D ALA 3.4 0.6 + - - -
21D ILE* 1.3 79.2 - - - +
23D ALA* 1.3 60.4 + - - +
24D ALA 4.2 0.5 + - - -
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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