Contacts of the helix formed by residues 9 - 22 (chain C) 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 C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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8A PRO 6.1 1.1 - - - +
9A THR* 5.8 13.0 - - + -
7C PRO 4.7 3.8 - - - +
8C PRO* 1.3 77.7 - - - +
10C ASN* 1.3 65.8 + - - +
11C ALA 3.6 1.2 + - - -
12C GLU* 2.9 36.1 + - - +
13C ARG* 2.9 23.1 + - - +
99C ASP* 2.7 35.0 + - - +
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Residues in contact with ASN 10 (chain C).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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88A TYR* 2.9 24.2 + - - +
99A ASP* 3.0 26.6 + - - +
102A PHE* 3.1 50.4 - - + +
9C THR* 1.3 73.8 - - - +
11C ALA* 1.3 61.5 + - - +
13C ARG* 3.1 28.5 + - - +
14C LEU* 3.2 21.1 + - - +
88C TYR* 3.5 20.6 + - + -
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Residues in contact with ALA 11 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9C THR* 3.2 0.8 + - - -
10C ASN* 1.3 78.0 - - - +
12C GLU* 1.3 63.7 + - + +
14C LEU* 3.1 16.1 + - - +
15C HIS* 3.3 9.9 + - - +
88C TYR* 3.7 27.5 - - + -
92C ASP* 4.5 4.2 - - - +
97C ASP* 5.2 1.3 - - - +
98C ALA* 4.0 13.5 - - + +
99C ASP* 3.6 31.0 - - - +
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Residues in contact with GLU 12 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7C PRO 4.5 1.0 - - - +
8C PRO* 3.4 16.1 - - + +
9C THR* 2.9 43.2 + - - +
11C ALA* 1.3 75.3 - - + +
13C ARG* 1.3 62.3 + - - +
15C HIS* 3.2 12.4 + - - +
16C GLU* 3.1 20.4 + - - +
99C ASP* 4.7 4.1 - - - +
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Residues in contact with ARG 13 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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99A ASP* 5.4 4.6 + - - +
102A PHE* 3.9 14.1 - - + -
103A ALA* 4.2 22.8 - - - +
106A HIS* 3.1 49.1 - - + +
7C PRO* 5.1 4.6 - - - +
8C PRO* 2.8 52.2 + - + +
9C THR 2.9 14.1 + - - +
10C ASN* 3.1 36.4 + - - +
11C ALA 3.1 0.2 - - - -
12C GLU* 1.3 78.4 - - - +
14C LEU* 1.3 62.4 + - - +
16C GLU* 3.2 7.4 + - - +
17C PHE* 2.9 18.5 + - - +
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Residues in contact with LEU 14 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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102A PHE* 3.6 30.3 - - + -
10C ASN 3.2 8.5 + - - +
11C ALA* 3.1 11.6 + - - +
13C ARG* 1.3 75.2 - - - +
15C HIS* 1.3 58.2 + - - +
17C PHE* 3.2 5.9 + - + +
18C HIS* 2.9 51.2 + - + +
85C TYR* 3.6 43.3 - - + +
88C TYR* 3.8 9.6 - - + -
89C GLY* 3.6 31.9 - - - +
92C ASP* 4.1 15.7 - - + -
201C UMP 4.8 1.3 - - - +
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Residues in contact with HIS 15 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11C ALA 3.3 5.2 + - - +
12C GLU* 3.2 14.9 + - - +
14C LEU* 1.3 78.8 - - - +
16C GLU* 1.3 64.2 + - - +
18C HIS* 3.4 0.7 + - - +
19C ARG* 2.9 72.9 + - + +
25C THR* 2.7 29.2 + - + -
26C PRO 5.7 0.9 + - - -
27C GLU* 5.6 9.1 + - + -
92C ASP* 3.5 18.3 + - - +
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Residues in contact with GLU 16 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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106A HIS* 2.9 24.8 + - - -
110A LEU* 3.8 22.5 - - + +
8C PRO* 6.0 1.4 - - - +
12C GLU 3.1 12.6 + - - +
13C ARG* 3.4 11.7 - - - +
15C HIS* 1.3 80.6 - - - +
17C PHE* 1.3 56.6 + - - +
19C ARG* 3.4 6.6 + - - +
20C ALA* 2.9 28.3 + - + +
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Residues in contact with PHE 17 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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106A HIS* 4.1 2.7 - - + -
109A ASN* 3.3 39.3 - - + -
110A LEU* 3.7 13.6 - - + +
112A LYS* 5.1 1.3 - - + -
123A GLN* 4.5 7.6 - - + -
13C ARG 2.9 9.8 + - - +
14C LEU* 3.6 7.6 - - + +
16C GLU* 1.3 77.0 - - - +
18C HIS* 1.3 79.2 + + - +
20C ALA* 3.1 4.5 + - - +
21C ILE* 3.0 57.0 + - + +
85C TYR* 3.2 33.4 - + + +
201C UMP 3.6 44.0 - + - -
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Residues in contact with HIS 18 (chain C).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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14C LEU* 2.9 23.6 + - + +
15C HIS 4.0 0.4 - - - +
17C PHE* 1.3 96.9 - + - +
19C ARG* 1.3 61.4 + - - +
21C ILE* 3.4 4.9 + - + -
22C GLY* 3.0 4.0 + - - -
23C ALA* 2.9 52.7 + - + +
24C ALA 4.4 0.9 - - - -
25C THR* 3.8 12.6 - - - -
40C ARG* 3.9 12.9 + - - -
89C GLY* 3.5 25.5 - - - -
92C ASP* 2.7 25.8 + - - +
93C GLN* 3.4 25.1 - - + +
201C UMP 5.0 3.8 + - - -
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Residues in contact with ARG 19 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15C HIS* 2.9 49.0 + - + +
16C GLU* 3.6 6.3 - - - +
18C HIS* 1.3 76.6 - - - +
20C ALA* 1.3 63.1 + - - +
22C GLY* 3.3 11.7 + - - -
23C ALA 5.0 2.2 + - - -
25C THR* 3.3 42.1 + - + +
26C PRO* 5.4 0.6 - - - +
27C GLU* 5.1 9.3 - - - +
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Residues in contact with ALA 20 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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110A LEU* 4.3 17.3 - - + +
113A ALA* 3.8 24.6 - - + +
16C GLU* 2.9 19.4 + - + +
17C PHE 3.1 6.3 + - - +
19C ARG* 1.3 77.6 - - - +
21C ILE* 1.3 61.7 + - + +
22C GLY 3.6 0.5 + - - -
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Residues in contact with ILE 21 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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109A ASN 5.1 0.2 - - - +
110A LEU 5.7 0.2 - - - +
113A ALA* 4.1 21.3 - - + +
117A ARG* 3.6 24.7 + - + +
121A GLY 5.6 3.4 - - - +
123A GLN* 3.5 33.2 - - + +
17C PHE* 3.0 61.5 + - + +
18C HIS* 3.7 10.5 - - + +
19C ARG 3.3 0.2 - - - -
20C ALA* 1.3 79.3 - - + +
22C GLY* 1.3 60.5 + - - +
23C ALA* 3.8 20.4 - - + -
201C UMP 4.8 4.3 - - - +
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Residues in contact with GLY 22 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18C HIS 3.0 5.4 + - - -
19C ARG* 3.3 9.7 + - - -
20C ALA 3.4 1.0 + - - -
21C ILE* 1.3 78.8 - - - +
23C ALA* 1.3 62.3 + - - +
24C ALA 4.2 0.3 + - - -
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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