Contacts of the strand formed by residues 14 - 28 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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14A TYR* 4.5 7.8 + - - -
16A VAL* 3.8 39.1 - - + +
17A ALA 3.6 7.2 - - - -
18A PHE* 4.0 20.4 - + - -
42A PHE* 4.0 18.2 - + + -
227A ILE* 6.2 0.9 - - + -
228A GLY 5.0 7.0 - - - -
229A TYR 4.5 6.2 + - - -
231A SER* 5.6 4.3 + - - -
8B GLU 3.9 0.3 - - - +
9B TRP* 3.4 3.3 - - - -
10B TYR* 2.7 35.8 + + - +
11B PRO 4.2 0.4 - - - +
12B ARG 3.4 1.6 - - - -
13B GLY* 1.3 77.5 - - - +
15B GLY* 1.3 66.6 + - - +
16B VAL* 4.0 22.0 - - + -
200B LEU* 3.6 33.7 - - + -
230B ALA* 4.2 15.3 - - + -
231B SER 5.6 2.8 + - - -
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Residues in contact with GLY 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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15A GLY 3.6 4.3 - - - +
16A VAL* 3.8 1.9 - - - -
17A ALA* 2.8 43.2 + - - +
7B ILE* 4.3 2.0 - - - -
8B GLU 3.4 7.4 - - - -
9B TRP* 3.6 17.2 - - - -
14B TYR* 1.3 83.8 - - - +
16B VAL* 1.3 64.8 + - - -
17B ALA 3.9 0.4 - - - -
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Residues in contact with VAL 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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14A TYR* 3.9 26.9 - - + +
15A GLY 4.0 3.1 - - - -
6B PHE* 3.8 3.5 - - - +
7B ILE* 3.3 1.6 - - - -
8B GLU* 2.8 38.8 + - + +
10B TYR* 3.7 24.0 - - + -
14B TYR* 4.0 9.9 - - + -
15B GLY* 1.3 73.3 - - - -
17B ALA* 1.3 59.3 + - - +
18B PHE* 4.0 11.4 - - + -
52B VAL* 5.1 2.7 - - + -
228B GLY 3.8 21.5 - - - +
229B TYR 4.0 2.2 - - - +
230B ALA* 3.9 23.6 - - - +
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Residues in contact with ALA 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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7A ILE* 4.9 4.3 - - + -
9A TRP* 3.8 20.6 - - + -
14A TYR* 3.6 6.6 - - - -
15A GLY* 2.8 42.5 + - - +
17A ALA* 5.0 3.8 - - + -
6B PHE 3.1 3.4 - - - -
7B ILE* 3.5 28.7 - - + -
15B GLY 3.8 0.2 + - - -
16B VAL* 1.3 75.7 - - - +
18B PHE* 1.3 68.3 + - - +
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Residues in contact with PHE 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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9A TRP* 4.1 4.7 - - - -
13A GLY 3.4 4.7 - - - -
14A TYR* 3.5 26.9 - + - -
5B GLU* 3.6 1.4 - - - +
6B PHE* 2.7 46.8 + + + +
16B VAL* 4.0 20.4 - - + -
17B ALA* 1.3 78.3 - - - +
19B LYS* 1.3 67.0 + - - +
20B VAL* 3.5 10.0 - - + +
39B THR* 4.6 10.1 - - + -
42B PHE* 3.4 46.7 - + + -
45B LEU* 3.8 19.5 - - + -
52B VAL* 4.6 2.9 - - + -
55B VAL* 4.1 15.3 - - + -
228B GLY* 4.0 25.1 - - - -
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Residues in contact with LYS 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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9A TRP* 3.4 60.6 - - + +
12A ARG 5.4 0.2 - - - +
13A GLY* 2.9 25.2 + - - +
3B ASP* 5.3 7.9 - - + +
4B MET 3.6 6.7 - - - +
5B GLU* 3.7 20.9 - - + +
18B PHE* 1.3 73.8 - - - +
20B VAL* 1.3 61.1 + - - +
39B THR* 3.7 4.7 - - - -
40B GLU* 3.2 38.8 + - + +
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Residues in contact with VAL 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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3B ASP* 5.4 0.5 - - - -
4B MET* 2.9 59.9 + - + +
5B GLU* 4.4 2.0 - - - +
6B PHE* 3.8 20.0 - - + +
18B PHE* 3.5 14.1 - - + +
19B LYS* 1.3 80.2 - - - +
21B LYS* 1.3 63.0 + - - +
22B ARG 4.4 2.9 - - - +
37B TYR* 4.4 25.6 - - + -
38B GLU 3.8 9.6 - - - +
39B THR* 4.0 14.8 - - + +
40B GLU* 4.3 5.0 - - - +
45B LEU* 5.9 0.7 - - + -
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Residues in contact with LYS 21 (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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4B MET* 4.4 7.1 - - - +
20B VAL* 1.3 75.1 - - - +
22B ARG* 1.3 68.1 + - + +
38B GLU* 2.7 24.4 + - + +
39B THR* 3.8 18.0 + - - +
40B GLU* 3.0 40.6 + - - +
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Residues in contact with ARG 22 (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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4B MET* 4.2 10.8 - - - -
20B VAL* 3.6 1.8 - - - -
21B LYS* 1.3 84.9 - - + +
23B LYS* 1.3 66.1 + - - +
24B ILE* 3.8 25.4 - - - +
37B TYR* 3.5 6.4 - - - +
38B GLU* 2.9 65.1 + - + +
44B LYS* 4.3 4.6 - - - +
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Residues in contact with LYS 23 (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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4B MET* 4.4 15.6 - - + -
22B ARG* 1.3 81.3 + - - +
24B ILE* 1.3 63.9 + - - +
25B LEU 4.2 8.3 - - - +
26B GLU* 2.3 45.9 + - + +
35B GLU* 2.6 25.8 + - - -
36B VAL 4.0 5.2 - - - +
37B TYR* 3.6 33.2 + - + -
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Residues in contact with ILE 24 (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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22B ARG* 3.8 28.9 - - - +
23B LYS* 1.3 78.8 - - - +
25B LEU* 1.3 63.2 + - + +
36B VAL* 2.7 27.1 + - + +
37B TYR 4.3 2.9 - - - -
38B GLU* 3.8 28.7 - - + +
44B LYS* 3.4 31.2 - - + +
119B TYR* 3.8 29.8 - - + -
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Residues in contact with LEU 25 (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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23B LYS* 3.8 6.9 - - - +
24B ILE* 1.3 85.6 - - + +
26B GLU* 1.3 70.2 + - - +
27B GLU* 4.1 15.9 - - + +
34B ILE 4.9 1.3 - - - +
35B GLU* 3.0 6.8 - - - +
36B VAL* 2.8 41.3 + - + +
115B ILE* 3.5 47.3 - - + -
119B TYR* 4.0 35.2 - - + +
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Residues in contact with GLU 26 (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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23B LYS* 2.3 38.3 + - + +
25B LEU* 1.3 81.1 - - - +
27B GLU* 1.3 64.5 + - - +
33B LYS* 4.1 24.9 + - + -
34B ILE 3.5 2.9 - - - -
35B GLU* 3.6 20.9 - - + -
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Residues in contact with GLU 27 (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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25B LEU* 4.1 16.4 - - + +
26B GLU* 1.3 76.2 - - - +
28B GLN* 1.3 66.0 + - - +
29B SER 4.2 0.2 - - - -
33B LYS* 3.5 6.2 - - - +
34B ILE* 2.7 43.6 + - + +
111B LYS* 2.8 38.6 + - + +
115B ILE* 3.7 24.3 - - + +
119B TYR* 6.0 0.2 - - - -
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Residues in contact with GLN 28 (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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27B GLU* 1.3 84.6 - - - +
29B SER* 1.3 77.9 + - - +
31B TYR 4.9 0.4 - - - -
32B GLN* 3.4 23.4 + - - +
33B LYS* 3.5 27.8 - - + +
49B ASP* 5.3 0.4 + - - -
111B LYS* 5.2 2.2 - - - +
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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