Contacts of the strand formed by residues 14 - 28 (chain E) in PDB entry 2ZSU
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 TYR 14 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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9E TRP* 3.5 3.8 - - - -
10E TYR* 2.7 37.3 + + - +
11E PRO 4.0 1.8 - - - +
12E ARG 3.4 0.6 - - - -
13E GLY* 1.3 78.6 - - - +
15E GLY* 1.3 74.3 + - - +
16E VAL* 4.0 15.0 - - + -
200E LEU* 3.7 29.4 - - + -
230E ALA* 4.3 14.3 - - + -
231E SER 5.4 2.6 + - - -
14F TYR* 4.3 12.0 + - - -
16F VAL* 3.9 33.7 - - + +
17F ALA 3.6 4.3 - - - -
18F PHE* 3.7 24.9 - + - -
42F PHE* 3.7 21.8 - + + -
227F ILE* 6.1 1.1 - - + -
228F GLY 5.2 5.3 + - - -
229F TYR 4.5 6.9 + - - -
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Residues in contact with GLY 15 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7E ILE* 4.2 2.2 - - - -
8E GLU 3.3 9.0 - - - -
9E TRP* 3.7 14.1 - - - -
10E TYR* 5.0 0.2 - - - -
14E TYR* 1.3 84.7 - - - +
16E VAL* 1.3 64.8 + - - -
17E ALA 3.8 0.4 - - - -
15F GLY 3.7 3.3 - - - +
16F VAL* 3.9 2.3 - - - -
17F ALA* 2.7 42.5 + - - -
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Residues in contact with VAL 16 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6E PHE* 4.0 1.7 - - - +
7E ILE* 3.4 3.3 - - - -
8E GLU* 3.0 34.1 + - + +
10E TYR* 3.8 24.0 - - + +
14E TYR* 4.0 7.4 - - + -
15E GLY* 1.3 73.2 - - - -
17E ALA* 1.3 58.2 + - - +
18E PHE* 3.8 21.5 - - + -
52E VAL* 5.4 1.3 - - + -
228E GLY 3.8 14.8 - - - +
229E TYR 4.0 0.7 - - - +
230E ALA* 3.8 23.6 - - - +
14F TYR* 3.6 34.5 - - + +
15F GLY 3.9 2.7 - - - -
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Residues in contact with ALA 17 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6E PHE 3.4 4.0 - - - -
7E ILE* 3.7 21.8 - - + -
15E GLY 3.8 0.2 - - - -
16E VAL* 1.3 74.5 - - - +
18E PHE* 1.3 68.5 - - - +
7F ILE* 4.7 5.2 - - + -
9F TRP* 3.5 24.7 - - + -
14F TYR* 3.6 5.5 - - - -
15F GLY* 2.9 40.5 + - - +
17F ALA* 4.7 4.3 - - + -
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Residues in contact with PHE 18 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5E GLU* 3.2 3.1 - - - +
6E PHE* 2.8 48.4 + + + +
16E VAL* 3.8 21.3 - - + -
17E ALA* 1.3 79.7 - - - +
19E LYS* 1.3 64.4 + - - +
20E VAL* 3.6 9.4 + - + +
39E THR* 4.6 6.7 - - + -
42E PHE* 3.5 45.5 - + + -
45E LEU* 3.8 28.9 - - + -
52E VAL* 4.7 2.7 - - + -
55E VAL* 4.1 9.2 - - + -
228E GLY* 3.8 28.9 - - - -
9F TRP* 4.1 4.7 - - - -
13F GLY 3.5 4.3 - - - -
14F TYR* 3.6 21.5 - + - -
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Residues in contact with LYS 19 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3E ASP* 3.1 29.8 - - - +
4E MET 3.4 5.4 - - - +
5E GLU* 4.3 1.8 - - + +
18E PHE* 1.3 72.6 - - - +
20E VAL* 1.3 59.3 + - - +
39E THR* 3.6 6.2 - - - -
40E GLU* 2.9 35.7 + - + +
41E GLY 4.6 0.7 + - - -
42E PHE* 6.2 0.2 - - - -
9F TRP* 3.4 58.3 - - + +
10F TYR 5.4 0.8 + - - -
12F ARG 5.3 0.5 - - - +
13F GLY* 3.0 28.1 + - - +
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Residues in contact with VAL 20 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3E ASP* 5.4 1.0 - - - +
4E MET* 2.8 65.8 + - + +
5E GLU* 3.7 7.0 - - - +
6E PHE* 4.2 14.6 - - + -
18E PHE* 3.8 9.9 - - + +
19E LYS* 1.3 78.9 - - - +
21E LYS* 1.3 58.1 + - - +
22E ARG* 4.2 7.2 - - - +
37E TYR* 4.3 21.8 - - + -
38E GLU 3.3 9.6 - - - +
39E THR* 3.7 23.6 - - + +
40E GLU* 3.6 11.3 - - - +
45E LEU* 5.6 0.2 - - + -
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Residues in contact with LYS 21 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4E MET* 4.0 13.5 - - - +
20E VAL* 1.3 73.7 - - - +
22E ARG* 1.3 73.2 + - - +
38E GLU* 2.6 34.8 + - + +
39E THR 3.9 16.6 - - - +
40E GLU* 2.8 50.9 + - - +
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Residues in contact with ARG 22 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4E MET* 4.8 10.1 - - + -
20E VAL* 3.4 8.0 - - - +
21E LYS* 1.3 91.3 - - - +
23E LYS* 1.3 69.8 + - - +
24E ILE* 4.7 12.2 - - + +
37E TYR* 3.7 7.0 - - - +
38E GLU* 2.9 56.0 + - + +
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Residues in contact with LYS 23 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4E MET* 5.6 1.6 - - - +
22E ARG* 1.3 84.2 - - - +
24E ILE* 1.3 64.6 + - - +
25E LEU* 3.7 20.9 - - - +
26E GLU* 2.6 34.9 + - - -
35E GLU* 2.8 26.1 + - - -
36E VAL 3.7 10.5 - - - +
37E TYR* 3.8 30.5 + - + -
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Residues in contact with ILE 24 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22E ARG* 4.6 14.1 - - - +
23E LYS* 1.3 76.3 - - - +
25E LEU* 1.3 63.1 + - + +
36E VAL* 3.0 32.2 + - + +
37E TYR 4.1 2.9 - - - -
38E GLU* 3.9 30.1 - - + +
44E LYS* 3.8 30.5 - - + +
119E TYR* 3.7 33.0 - - + -
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Residues in contact with LEU 25 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23E LYS* 3.7 10.6 - - - +
24E ILE* 1.3 91.4 - - + +
26E GLU* 1.3 70.2 + - - +
27E GLU* 3.9 9.9 - - + +
34E ILE 3.7 16.2 - - - +
35E GLU* 3.4 3.3 - - - -
36E VAL* 3.1 41.4 + - + +
111E LYS* 6.0 1.1 - - - +
115E ILE* 4.0 23.3 - - + -
119E TYR* 3.3 42.0 - - + +
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Residues in contact with GLU 26 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23E LYS* 2.6 32.6 + - - -
25E LEU* 1.3 79.6 - - - +
27E GLU* 1.3 64.4 + - - +
33E LYS* 4.1 22.9 + - + +
34E ILE 3.4 4.3 - - - -
35E GLU* 3.5 22.0 - - + -
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Residues in contact with GLU 27 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25E LEU* 3.9 7.6 - - + +
26E GLU* 1.3 78.3 - - - +
28E GLN* 1.3 78.6 + - - +
29E SER* 4.0 1.8 + - - -
32E GLN 4.0 0.2 - - - +
33E LYS* 3.6 4.6 - - - +
34E ILE* 2.7 38.7 + - + +
111E LYS* 3.0 49.4 - - + +
115E ILE* 3.7 22.7 - - + -
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Residues in contact with GLN 28 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27E GLU* 1.3 87.5 + - - +
29E SER* 1.3 78.5 + - - +
30E GLU 5.1 1.0 - - - -
31E TYR 4.7 1.4 - - - -
32E GLN* 3.5 20.0 + - - +
33E LYS* 3.4 30.2 - - + +
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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