Contacts of the helix formed by residues 12 - 28 (chain A) in PDB entry 2Z4U
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 12 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10A ASN 3.6 8.0 + - - +
11A ALA* 1.3 79.5 - - - +
13A ILE* 1.3 65.2 + - - +
14A ASN* 3.5 7.8 + - - +
15A LYS* 3.0 30.8 + - + +
16A TYR 2.9 18.5 + - - -
190A PHE* 3.3 16.3 - - - -
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Residues in contact with ILE 13 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12A THR* 1.3 73.9 - - - +
14A ASN* 1.3 66.7 + - - +
16A TYR* 3.2 3.6 + - - +
17A ALA* 2.9 27.0 + - + +
187A LYS* 3.7 44.6 - - + +
190A PHE* 3.5 36.8 - - + -
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Residues in contact with ASN 14 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12A THR* 3.2 6.6 + - - +
13A ILE* 1.3 85.4 - - - +
15A LYS* 1.3 59.0 + - + +
17A ALA* 3.3 8.4 + - - +
18A THR* 2.9 33.8 + - - +
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Residues in contact with LYS 15 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6A PHE* 4.1 13.2 - - + -
7A ASP* 5.8 1.1 - - + +
10A ASN 5.1 4.7 - - - +
11A ALA* 4.8 1.8 - - - -
12A THR* 3.0 34.9 + - + +
14A ASN* 1.3 76.8 - - + +
16A TYR* 1.4 57.8 + - - +
18A THR* 3.4 9.1 + - + -
19A PHE* 2.9 27.5 + - - +
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Residues in contact with TYR 16 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6A PHE* 3.6 28.8 - + + -
12A THR 2.9 6.4 + - - +
13A ILE 3.6 7.0 - - - +
15A LYS* 1.4 73.2 - - - +
17A ALA* 1.3 67.0 + - - +
19A PHE* 3.2 19.0 + + - +
20A MET* 2.9 30.5 + - + +
141A ILE* 4.8 0.7 - - + -
172A MET* 2.7 35.1 + - + -
176A ALA* 3.1 16.5 - - - +
183A GLU* 3.8 20.6 - - + -
186A VAL* 3.6 41.5 - - + +
187A LYS* 4.1 18.2 - - + -
190A PHE* 3.6 22.4 - + + -
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Residues in contact with ALA 17 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13A ILE* 2.9 11.8 + - + +
14A ASN* 3.6 13.7 - - - +
16A TYR* 1.3 78.0 - - - +
18A THR* 1.3 58.0 + - - +
20A MET* 3.3 3.5 + - - +
21A GLU* 3.0 28.2 + - - +
24A ARG* 5.6 0.2 + - - -
183A GLU* 3.8 12.9 - - - +
187A LYS* 3.6 25.4 - - - +
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Residues in contact with THR 18 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14A ASN* 2.9 17.4 + - - +
15A LYS* 3.6 11.3 - - + -
16A TYR 3.3 0.2 - - - -
17A ALA* 1.3 73.7 - - - +
19A PHE* 1.3 61.8 + - - +
21A GLU* 3.3 18.8 + - - +
22A SER* 2.8 41.2 + - - +
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Residues in contact with PHE 19 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4A ILE* 3.7 26.5 - - + -
5A THR 4.5 3.8 - - - +
6A PHE* 3.7 46.4 - + + -
15A LYS 2.9 13.9 + - - +
16A TYR* 3.2 21.1 + + - +
18A THR* 1.3 77.0 - - - +
20A MET* 1.3 84.8 + - + +
22A SER* 3.2 5.8 + - - -
23A LEU* 2.9 31.8 + - + +
52A VAL* 3.6 32.3 - - + -
54A LEU* 4.5 0.4 - - + -
173A VAL* 4.1 23.1 - - + -
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Residues in contact with MET 20 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16A TYR* 2.9 25.9 + - + +
17A ALA 3.6 4.7 - - - +
19A PHE* 1.3 108.4 - - + +
21A GLU* 1.3 58.3 + - - +
23A LEU* 3.4 7.2 + - + +
24A ARG* 2.9 47.6 + - - +
172A MET 3.7 12.1 - - - +
173A VAL 3.6 20.4 - - - +
176A ALA* 3.5 15.5 - - + +
177A ALA* 3.4 27.6 - - - -
183A GLU* 3.8 28.0 - - + +
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Residues in contact with GLU 21 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17A ALA 3.0 13.8 + - - +
18A THR* 3.6 24.3 + - - +
20A MET* 1.3 77.6 - - - +
22A SER* 1.3 58.1 + - - +
24A ARG* 3.8 9.7 - - - +
25A ASN* 2.8 52.3 + - - +
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Residues in contact with SER 22 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4A ILE* 3.5 21.5 - - - +
18A THR* 2.8 30.5 + - - +
19A PHE* 3.5 5.6 - - - -
21A GLU* 1.3 77.5 + - - +
23A LEU* 1.3 57.0 + - - +
25A ASN* 3.8 5.1 - - - +
26A GLU* 2.9 31.0 + - - +
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Residues in contact with LEU 23 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4A ILE* 3.3 22.8 - - + +
19A PHE* 2.9 21.7 + - + +
20A MET* 3.9 10.1 - - + +
22A SER* 1.3 74.3 - - - +
24A ARG* 1.3 64.7 + - - +
26A GLU* 3.3 0.7 + - - +
27A ALA* 3.0 23.1 + - + +
50A VAL* 4.1 17.7 - - + -
52A VAL* 4.2 11.9 - - + -
66A LEU* 4.3 13.7 - - + -
71A LEU* 4.7 10.8 - - + -
173A VAL* 3.8 31.9 - - + +
177A ALA* 3.8 24.9 - - + -
250A LEU* 5.6 0.2 - - - -
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Residues in contact with ARG 24 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17A ALA 5.6 0.2 + - - -
20A MET* 2.9 31.7 + - - +
21A GLU* 3.8 7.7 - - - +
23A LEU* 1.3 76.2 - - - +
25A ASN* 1.4 61.6 + - - +
28A LYS* 2.9 36.9 + - + +
38A PRO* 5.6 3.6 - - + -
176A ALA 2.9 26.7 + - - -
177A ALA* 2.9 27.1 + - + +
180A LYS* 3.8 34.5 - - - +
183A GLU* 2.8 33.7 + - - +
249A GLY* 3.7 15.4 - - - +
250A LEU* 4.0 24.2 - - + +
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Residues in contact with ASN 25 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21A GLU* 2.8 42.0 + - - +
22A SER* 3.9 5.5 - - - +
24A ARG* 1.4 78.9 - - - +
26A GLU* 1.3 63.2 + - - +
28A LYS* 3.0 45.2 + - - +
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Residues in contact with GLU 26 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2A ASN* 3.0 41.4 + - + +
4A ILE* 3.7 14.5 - - + +
22A SER 2.9 18.5 + - - +
23A LEU 3.8 1.1 - - - +
25A ASN* 1.3 79.7 - - - +
27A ALA* 1.3 63.5 + - - +
28A LYS 3.7 0.3 + - - +
47A PRO* 3.9 19.2 - - - +
49A TYR 5.1 0.2 - - - +
50A VAL* 3.9 29.3 - - + +
68A ARG* 3.7 17.0 + - - -
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Residues in contact with ALA 27 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23A LEU* 3.0 18.4 + - + +
24A ARG 4.2 1.1 - - - +
26A GLU* 1.3 76.7 - - - +
28A LYS* 1.3 63.0 + - - +
40A LEU* 3.6 17.7 - - + +
41A PRO* 3.2 12.3 - - - +
50A VAL* 4.4 7.9 - - + -
68A ARG* 2.8 33.5 + - + +
71A LEU* 3.8 22.4 - - + -
250A LEU* 4.9 3.1 - - + -
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Residues in contact with LYS 28 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24A ARG 2.9 21.5 + - - +
25A ASN* 3.0 39.9 + - - +
26A GLU 3.9 1.9 - - - +
27A ALA* 1.3 76.5 - - - +
29A ASP* 1.3 75.0 + - - +
30A PRO* 3.5 9.7 - - + +
38A PRO* 3.9 30.6 - - + +
39A MET 3.7 10.3 - - - +
40A LEU* 4.0 7.5 - - - +
68A ARG* 2.9 17.9 + - - -
250A LEU* 4.1 4.7 - - + -
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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