Contacts of the helix formed by residues 2 - 20 (chain C) in PDB entry 1Z6T
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 ASP 2 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1C MET* 1.3 76.8 - - - +
3C ALA* 1.3 65.2 + - - +
4C LYS* 4.3 11.2 - - + +
5C ALA* 3.3 9.7 + - + +
6C ARG* 3.0 19.6 + - - +
65C ASN* 2.8 35.9 + - - +
92C PRO* 3.7 16.3 - - + +
93C VAL 5.5 0.3 + - - -
94C VAL* 6.0 2.4 - - - +
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Residues in contact with ALA 3 (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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1C MET 3.6 1.4 + - - -
2C ASP* 1.3 68.2 - - - +
4C LYS* 1.3 58.0 + - + +
6C ARG* 3.0 31.1 + - - +
7C ASN* 2.7 50.1 + - - +
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Residues in contact with LYS 4 (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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2C ASP* 3.3 9.1 - - + +
3C ALA* 1.3 77.5 - - - +
5C ALA* 1.3 56.2 + - - +
7C ASN* 3.4 6.9 + - - +
8C CYS* 3.0 30.2 + - - +
89C ASP 5.9 2.9 - - - +
90C GLY* 4.5 10.7 - - - +
92C PRO* 6.5 0.4 - - + -
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Residues in contact with ALA 5 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1C MET* 3.7 9.6 - - + -
2C ASP* 3.3 9.7 + - + +
3C ALA 3.2 0.4 - - - -
4C LYS* 1.3 76.0 - - - +
6C ARG* 1.3 68.0 + - - +
8C CYS* 3.3 1.5 + - - +
9C LEU* 2.9 20.3 + - - +
68C TYR* 3.2 32.3 - - + -
90C GLY 3.3 23.7 + - - +
92C PRO* 4.0 17.3 - - + -
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Residues in contact with ARG 6 (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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1C MET* 3.1 44.0 + - + +
2C ASP 3.0 10.3 + - - +
3C ALA* 3.4 31.9 - - - +
5C ALA* 1.3 78.1 - - - +
7C ASN* 1.3 61.2 + - - +
9C LEU* 3.2 4.5 + - - +
10C LEU* 2.8 53.3 + - + +
61C LEU* 3.8 15.3 + - + +
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Residues in contact with ASN 7 (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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3C ALA* 2.7 35.5 + - - +
4C LYS* 3.8 5.8 - - - +
6C ARG* 1.3 77.2 + - - +
8C CYS* 1.3 60.4 + - - +
10C LEU* 3.3 18.4 + - - +
11C GLN* 2.9 32.7 + - - +
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Residues in contact with CYS 8 (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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4C LYS 3.0 19.0 + - - +
5C ALA 3.6 4.3 - - - +
7C ASN* 1.3 74.5 - - - +
9C LEU* 1.3 65.6 + - - +
11C GLN* 3.5 7.5 + - - +
12C HIS* 3.2 39.0 + - - +
68C TYR* 3.2 20.6 - - - +
86C LEU 3.3 26.0 - - - -
87C LEU* 3.9 3.1 - - - -
89C ASP* 5.1 1.6 - - - -
90C GLY* 3.8 20.0 - - - -
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Residues in contact with LEU 9 (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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1C MET* 4.6 4.0 - - + -
5C ALA 2.9 17.5 + - - +
6C ARG 3.5 4.0 - - - +
8C CYS* 1.3 75.3 - - - +
10C LEU* 1.3 62.0 + - - +
12C HIS 3.5 1.0 + - - -
13C ARG* 3.1 24.4 + - - +
16C LEU* 3.7 24.7 - - + -
57C ILE* 3.9 14.8 - - + -
60C ILE* 4.1 25.8 - - + -
61C LEU* 3.7 33.9 - - + +
68C TYR* 4.0 16.6 - - + -
71C PHE* 4.2 12.8 - - + -
87C LEU* 3.8 14.8 - - + +
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Residues in contact with LEU 10 (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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6C ARG* 2.8 38.9 + - + +
7C ASN* 3.6 17.3 - - - +
8C CYS 3.3 0.2 - - - -
9C LEU* 1.3 77.6 - - - +
11C GLN* 1.3 62.8 + - - +
12C HIS 3.4 0.9 + - - -
13C ARG* 3.6 23.8 + - - +
14C GLU* 5.1 0.9 + - - +
61C LEU* 3.4 31.0 - - + -
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Residues in contact with GLN 11 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7C ASN 2.9 20.4 + - - +
8C CYS* 3.9 7.5 - - - +
9C LEU 3.4 0.2 - - - -
10C LEU* 1.3 75.6 - - - +
12C HIS* 1.3 91.1 + - + +
13C ARG 3.8 0.2 + - - -
14C GLU* 4.6 9.4 + - - +
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Residues in contact with HIS 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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8C CYS* 3.2 26.8 + - - +
9C LEU 3.9 1.6 - - - +
10C LEU 3.3 0.2 - - - -
11C GLN* 1.3 108.1 + - + +
13C ARG* 1.3 64.0 + - - +
14C GLU* 3.1 3.4 - - - -
15C ALA* 3.0 18.7 + - + +
16C LEU* 3.1 17.6 + - + +
86C LEU* 3.3 68.7 + - + +
87C LEU* 4.8 8.3 - - + -
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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
----------------------------------------------------------
9C LEU 3.1 16.8 + - - +
10C LEU* 3.7 19.8 - - - +
11C GLN 3.5 0.8 - - - -
12C HIS* 1.3 74.5 - - - +
14C GLU* 1.3 61.0 + - + +
16C LEU* 3.8 10.1 - - - -
17C GLU* 2.9 58.8 + - - +
54C ALA* 3.2 23.0 + - - +
57C ILE* 3.6 28.9 - - + +
58C LYS* 3.3 35.6 - - - +
61C LEU* 4.5 10.8 - - - +
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Residues in contact with GLU 14 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10C LEU 5.1 0.9 + - - +
11C GLN 4.6 8.5 + - - +
12C HIS* 3.1 1.8 - - - +
13C ARG* 1.3 78.2 - - + +
15C ALA* 1.3 63.5 + - - +
17C GLU* 3.4 17.4 + - - +
18C LYS* 3.2 26.0 + - - +
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Residues in contact with ALA 15 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12C HIS* 3.0 11.3 + - + +
14C GLU* 1.3 79.8 - - - +
16C LEU* 1.3 60.5 + - - +
18C LYS* 3.9 3.8 - - - +
19C ASP* 3.2 34.6 + - - +
83C LEU* 3.6 22.7 - - + +
86C LEU* 4.2 16.6 - - + -
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Residues in contact with LEU 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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9C LEU* 3.7 29.8 - - + -
12C HIS* 3.1 22.0 + - + +
13C ARG* 3.9 4.0 - - - +
15C ALA* 1.3 75.6 - - - +
17C GLU* 1.3 64.0 + - - +
20C ILE* 3.3 43.7 + - + +
53C ALA* 3.4 1.7 - - - +
57C ILE* 3.4 21.8 - - + -
71C PHE* 4.3 9.6 - - + -
75C LEU* 4.1 22.2 - - + -
83C LEU* 4.0 29.4 - - + +
87C LEU* 4.3 12.6 - - + -
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Residues in contact with GLU 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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13C ARG* 2.9 51.4 + - + +
14C GLU* 3.4 24.3 - - - +
16C LEU* 1.3 76.4 - - - +
18C LYS* 1.3 69.6 + - - +
20C ILE 4.3 0.3 - - - +
49C GLN 3.7 5.0 - - - +
50C GLN* 3.0 31.1 - - + +
53C ALA* 3.6 7.8 - - - +
54C ALA* 3.1 40.6 - - + +
57C ILE* 4.3 1.8 - - + -
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Residues in contact with LYS 18 (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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14C GLU 3.2 14.5 + - - +
15C ALA* 3.9 4.3 - - - +
17C GLU* 1.3 84.2 - - - +
19C ASP* 1.3 91.5 + - - +
20C ILE 3.4 1.6 + - - +
49C GLN* 3.6 14.2 + - - +
50C GLN* 3.7 32.0 - - - +
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Residues in contact with ASP 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 ALA* 3.2 25.1 + - - +
18C LYS* 1.3 109.7 + - - +
20C ILE* 1.3 60.7 + - - +
21C LYS 3.8 1.0 + - - -
49C GLN* 3.5 11.4 + - - +
80C TYR* 4.1 8.9 - - + -
83C LEU* 4.0 20.2 - - + +
431C LYS* 4.1 26.4 + - + +
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Residues in contact with ILE 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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16C LEU* 3.3 31.6 + - + +
18C LYS 3.4 1.4 + - - +
19C ASP* 1.3 77.6 - - - +
21C LYS* 1.3 65.4 + - - +
22C THR* 4.5 1.9 + - - +
25C ILE* 3.9 22.0 - - + -
49C GLN* 3.2 26.4 - - - +
53C ALA* 3.6 19.1 - - + +
56C LEU* 5.0 7.4 - - + -
57C ILE* 5.3 1.6 - - + -
71C PHE* 4.6 13.7 - - + -
75C LEU* 4.2 10.3 - - + -
80C TYR* 3.7 17.9 - - + -
83C LEU* 3.0 32.5 - - + -
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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
------------------------------------------------------------
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