Contacts of the helix formed by residues 2 - 20 (chain B) in PDB entry 2Z9A
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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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3B VAL* 1.3 66.4 + - - +
4B TYR* 3.3 20.0 + - - +
5B CYS* 3.2 31.2 + - + +
6B GLU* 3.2 19.6 + - - +
77B LEU 3.7 8.7 - - - +
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Residues in contact with VAL 3 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43A LEU* 3.7 24.5 - - + -
46A GLU* 4.1 26.0 - - + +
2B ASP* 1.3 74.2 + - - +
4B TYR* 1.3 67.9 + - + +
6B GLU* 3.1 11.6 + - - +
7B VAL* 2.8 39.5 + - - +
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Residues in contact with TYR 4 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45A GLU* 5.8 0.2 + - - -
46A GLU* 3.5 38.4 + - + +
49A GLU* 3.9 24.7 + - + +
50A VAL* 3.5 21.7 - - + +
2B ASP* 3.3 16.5 + - - +
3B VAL* 1.3 90.1 - - + +
5B CYS* 1.3 56.9 + - - +
7B VAL* 4.0 3.3 - - - +
8B CYS* 3.0 28.4 + - - +
77B LEU* 4.1 25.3 - - + +
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Residues in contact with CYS 5 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2B ASP* 3.2 24.1 + - + +
3B VAL 3.2 0.4 - - - -
4B TYR* 1.3 74.9 - - - +
6B GLU* 1.3 63.4 + - - +
8B CYS* 3.9 0.8 - - - +
9B GLU* 3.1 45.1 + - - +
69B GLU* 4.5 1.1 - - - -
77B LEU 3.1 15.2 + - - +
78B CYS* 2.0 51.5 - - - -
79B SER 4.5 3.1 - - - +
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Residues in contact with GLU 6 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39A LEU* 5.4 0.5 - - - +
43A LEU* 3.9 26.1 - - + +
2B ASP 3.2 10.8 + - - +
3B VAL* 3.1 15.3 + - - +
5B CYS* 1.3 79.8 - - - +
7B VAL* 1.3 55.7 + - + +
9B GLU* 3.4 10.4 + - - +
10B PHE* 2.9 28.4 + - - +
87B GOL 3.7 34.3 - - - -
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Residues in contact with VAL 7 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39A LEU* 4.4 8.7 - - + -
43A LEU* 4.3 36.8 - - + +
46A GLU* 3.9 8.7 - - + +
47A CYS* 3.5 30.5 - - + -
50A VAL* 3.8 16.8 - - + -
3B VAL 2.8 24.9 + - - +
4B TYR* 4.0 5.6 - - - +
6B GLU* 1.3 70.0 - - - +
8B CYS* 1.3 60.5 + - - +
10B PHE* 3.4 7.9 - - - +
11B LEU* 3.0 36.1 + - + +
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Residues in contact with CYS 8 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50A VAL* 4.6 4.5 - - + -
58A ILE* 5.3 2.0 - - - -
4B TYR 3.0 19.9 + - - +
5B CYS 3.9 2.0 - - - +
7B VAL* 1.3 77.6 - - - +
9B GLU* 1.3 55.2 + - - +
11B LEU* 3.2 11.8 + - - +
12B VAL* 3.0 34.2 + - - +
72B CYS* 2.0 51.8 - - + -
75B LEU* 3.8 21.5 - - - -
77B LEU* 3.8 19.3 - - + -
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Residues in contact with GLU 9 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5B CYS* 3.1 36.1 + - - +
6B GLU* 3.7 9.1 - - - +
8B CYS* 1.3 70.8 - - - +
10B PHE* 1.3 65.3 + - - +
12B VAL* 3.4 3.4 + - - +
13B LYS* 3.1 31.3 + - - +
68B PRO* 3.9 19.9 - - + +
69B GLU* 3.1 35.5 - - - +
72B CYS* 3.8 8.3 - - - -
78B CYS* 3.9 8.7 - - - -
87B GOL 4.5 11.3 + - - +
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Residues in contact with PHE 10 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35A MET 3.3 30.1 - - - -
38A LYS* 3.7 22.0 - - + -
39A LEU* 3.8 32.1 - - + -
6B GLU 2.9 18.9 + - - +
7B VAL* 3.4 7.0 - - - +
9B GLU* 1.3 75.6 - - - +
11B LEU* 1.3 78.3 + - + +
13B LYS* 3.3 8.0 + - + +
14B GLU* 3.0 49.8 + - + +
87B GOL 3.7 38.2 + - - -
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Residues in contact with LEU 11 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32A PHE* 4.6 8.5 - - + -
35A MET* 4.4 17.3 - - + -
47A CYS* 3.9 16.6 - - - -
50A VAL* 3.9 21.8 - - + -
51A VAL* 4.1 21.5 - - + -
58A ILE* 4.2 14.4 - - + -
7B VAL* 3.0 37.1 + - + +
8B CYS* 3.2 7.2 + - - +
10B PHE* 1.3 96.7 - - + +
12B VAL* 1.3 63.8 + - - +
14B GLU* 3.3 4.2 + - - +
15B VAL* 3.0 30.3 + - - +
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Residues in contact with VAL 12 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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58A ILE* 4.6 11.7 - - + -
62A LEU* 4.9 7.4 - - + -
8B CYS* 3.0 17.1 + - - +
9B GLU 3.7 6.1 - - - +
10B PHE 3.3 0.2 - - - -
11B LEU* 1.3 76.5 - - - +
13B LYS* 1.3 56.3 + - - +
15B VAL* 3.5 6.5 + - - +
16B THR* 2.9 32.6 + - - +
66B VAL* 4.1 21.1 - - + -
68B PRO* 3.7 23.8 - - + +
71B VAL* 3.8 32.5 - - + -
72B CYS* 3.8 13.9 - - - -
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Residues in contact with LYS 13 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9B GLU* 3.1 18.9 + - - +
10B PHE* 3.7 8.7 - - + +
12B VAL* 1.3 75.7 - - - +
14B GLU* 1.3 57.1 + - + +
16B THR* 3.3 7.4 + - - +
17B LYS* 3.0 40.3 + - - +
68B PRO* 3.7 27.1 - - + -
87B GOL 2.7 39.7 + - - +
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Residues in contact with GLU 14 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35A MET* 3.6 28.2 - - + +
38A LYS* 3.4 31.2 + - - +
10B PHE* 3.0 50.0 + - + +
11B LEU 3.5 7.6 - - - +
13B LYS* 1.3 74.4 - - + +
15B VAL* 1.3 59.1 + - - +
17B LYS* 2.7 40.5 + - - +
18B LEU* 2.8 29.8 + - - +
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Residues in contact with VAL 15 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28A ILE* 3.7 32.8 - - + -
32A PHE* 4.1 18.8 - - + -
35A MET* 4.0 15.7 - - + -
58A ILE* 4.3 14.6 - - + -
62A LEU* 3.8 22.9 - - + -
11B LEU 3.0 22.0 + - - +
12B VAL* 3.7 6.1 - - - +
14B GLU* 1.3 75.0 - - - +
16B THR* 1.3 62.6 + - - +
18B LEU* 3.1 8.3 + - - +
19B ILE* 3.0 26.8 + - + +
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Residues in contact with THR 16 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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62A LEU* 4.2 7.1 - - - +
12B VAL 2.9 23.3 + - - -
13B LYS* 3.5 8.7 - - - -
14B GLU 3.3 0.2 - - - -
15B VAL* 1.3 78.4 - - - +
17B LYS* 1.3 62.9 + - + +
19B ILE* 3.6 6.0 + - - +
20B ASP* 3.5 19.1 + - - +
63B LEU* 3.5 45.9 - - + +
66B VAL* 3.6 22.3 - - + +
68B PRO* 6.0 0.5 - - - +
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Residues in contact with LYS 17 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38A LYS* 5.5 2.8 - - - +
13B LYS* 3.0 23.3 + - - +
14B GLU* 2.7 36.0 + - - +
16B THR* 1.3 76.1 - - + +
18B LEU* 1.3 64.2 - - - +
20B ASP* 3.2 24.6 + - - +
21B ASN* 5.4 0.2 - - - +
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Residues in contact with LEU 18 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27A GLU* 3.4 53.3 - - + +
28A ILE* 4.2 14.4 - - + -
31A ALA* 4.4 10.1 - - + -
35A MET* 4.2 12.3 - - + -
14B GLU 2.8 18.2 + - - +
15B VAL* 3.1 9.8 + - - +
17B LYS* 1.3 78.6 - - - +
19B ILE* 1.3 51.2 + - - +
20B ASP 3.5 0.2 + - - -
21B ASN* 2.7 36.1 + - - +
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Residues in contact with ILE 19 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19A ILE* 5.4 9.6 - - + -
24A THR* 3.8 21.5 - - + -
27A GLU* 3.4 20.0 - - - +
28A ILE* 4.0 15.5 - - + -
59A LEU* 3.9 23.6 - - + -
62A LEU* 4.7 8.7 - - + -
63A LEU* 5.4 0.4 - - + -
15B VAL* 3.0 24.5 + - + +
16B THR 3.9 1.1 - - - +
17B LYS 3.3 0.2 - - - -
18B LEU* 1.3 74.9 - - + +
20B ASP* 1.3 60.5 + - - +
21B ASN* 3.1 3.9 + - - +
24B THR* 2.6 39.5 + - + +
59B LEU* 4.4 2.1 - - + +
63B LEU* 3.8 28.2 - - + +
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Residues in contact with ASP 20 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16B THR 3.5 7.0 + - - +
17B LYS* 3.2 20.0 + - - +
19B ILE* 1.3 74.4 - - - +
21B ASN* 1.3 59.8 + - - +
59B LEU* 3.7 17.6 - - - +
60B SER* 4.2 19.8 + - - -
63B LEU* 3.3 23.0 - - + +
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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