Contacts of the strand formed by residues 25 - 36 (chain A) in PDB entry 4ZIN
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 HIS 25 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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21A SER* 3.1 4.0 - - - -
22A VAL 2.9 34.1 + - - +
23A ASN 3.3 2.1 + - - +
24A GLY* 1.3 75.3 - - - +
26A GLU* 1.3 75.3 + - - +
27A PHE* 3.4 5.9 - - - -
51A GLY* 2.7 33.6 + - - -
53A PRO 4.6 2.2 + - - -
54A LEU* 4.6 2.2 - - + -
55A PRO* 3.5 41.2 - - + +
56A PHE* 4.4 6.9 - - + -
136A MET* 6.1 0.7 - - + -
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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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20A GLY 3.4 6.3 - - - +
21A SER* 3.9 15.5 - - - -
24A GLY 3.4 9.2 + - - +
25A HIS* 1.3 86.6 - - - +
27A PHE* 1.3 63.9 + - - +
50A LYS 4.7 0.2 - - - -
51A GLY* 3.6 9.2 - - - -
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Residues in contact with PHE 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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18A MET* 3.7 25.6 - - + -
19A GLU* 3.7 1.7 - - - +
20A GLY* 2.9 58.0 + - - +
21A SER* 3.6 7.2 - - - -
22A VAL* 4.0 5.2 - - + -
25A HIS* 3.4 14.4 - - - +
26A GLU* 1.3 75.7 - - - +
28A GLU* 1.3 71.5 + - - +
29A ILE* 4.0 16.8 - - + -
50A LYS* 3.2 17.5 - - - +
51A GLY* 4.4 1.3 - - - +
54A LEU* 3.6 20.9 - - + -
56A PHE* 3.5 23.3 - + - -
61A LEU* 3.7 31.6 - - + -
124A LEU* 4.4 2.2 - - + -
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Residues in contact with GLU 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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17A HIS* 3.1 26.8 + - - +
18A MET 3.2 11.4 - - - +
19A GLU* 4.4 14.7 - - + +
27A PHE* 1.3 80.5 - - - +
29A ILE* 1.3 69.9 + - - +
30A GLU* 5.3 1.9 - - - +
48A VAL* 3.5 1.2 - - - +
49A THR* 3.0 35.2 + - - +
50A LYS* 3.0 41.7 + - + +
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Residues in contact with ILE 29 (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 VAL* 4.7 0.7 - - + -
17A HIS* 3.5 4.3 - - - -
18A MET* 2.8 38.6 + - + +
27A PHE* 4.0 14.1 - - + -
28A GLU* 1.3 80.8 - - - +
30A GLU* 1.3 74.4 + - - +
46A LEU* 4.1 14.4 - - + -
47A LYS 3.3 9.9 - - - +
48A VAL* 4.0 17.9 - - + -
49A THR* 4.2 0.2 - - - -
54A LEU* 4.4 0.7 - - + -
58A TRP* 3.6 18.6 - - + -
61A LEU* 3.5 32.3 - - + -
65A PHE* 3.8 26.2 - - + -
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Residues in contact with GLU 30 (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 VAL 3.4 7.4 - - - +
17A HIS* 3.9 20.1 + - + -
28A GLU* 5.3 1.9 - - - +
29A ILE* 1.3 82.1 - - - +
31A GLY* 1.3 58.9 + - - +
46A LEU* 3.4 1.3 - - - -
47A LYS* 2.7 53.6 + - - +
49A THR* 3.7 30.7 + - + +
141B MET* 5.3 10.6 - - + +
168B LYS* 3.0 45.7 + - - +
208B TYR* 5.6 0.9 + - - -
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Residues in contact with GLY 31 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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15A LYS* 3.5 4.2 - - - -
16A VAL* 2.9 43.8 + - - +
30A GLU* 1.3 77.8 - - - +
32A GLU* 1.3 64.3 + - - +
45A LYS 3.2 13.0 - - - -
46A LEU* 3.9 3.6 - - - -
141B MET* 4.0 9.1 - - - +
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Residues in contact with GLU 32 (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 ARG* 5.8 3.5 - - - -
14A PHE* 3.3 16.4 - - - +
15A LYS* 4.4 9.5 + - + +
16A VAL* 4.5 0.2 - - - +
31A GLY* 1.3 72.6 - - - +
33A GLY* 1.3 58.7 + - - +
44A ALA* 3.5 1.0 - - - -
45A LYS* 2.9 38.5 + - + +
46A LEU* 4.9 0.4 - - - +
117A GLU* 5.3 1.0 - - - +
141B MET* 3.4 32.7 - - + +
166B LYS* 3.0 40.3 + - - +
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Residues in contact with GLY 33 (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 ARG* 3.3 7.7 + - - +
14A PHE* 2.8 47.1 + - - +
32A GLU* 1.3 77.5 - - - +
34A GLU* 1.3 65.9 + - - +
43A THR 3.1 14.6 - - - -
44A ALA* 4.0 0.2 - - - -
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Residues in contact with GLU 34 (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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11A PHE* 3.8 23.0 - - + -
12A MET 3.3 8.5 - - - +
13A ARG* 2.2 43.0 + - + +
14A PHE* 3.8 3.0 - - - -
33A GLY* 1.3 75.9 - - - +
35A GLY* 1.3 60.8 + - - +
42A GLN* 3.3 5.1 - - - -
43A THR* 2.8 44.5 + - - +
45A LYS* 6.2 2.6 - - - -
72A TYR* 4.3 1.6 - - - -
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Residues in contact with GLY 35 (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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11A PHE* 3.4 11.0 - - - -
12A MET 3.0 31.1 + - - +
34A GLU* 1.3 79.3 - - - +
36A ARG* 1.3 67.5 - - - -
37A PRO* 3.4 0.7 - - - +
41A THR 3.2 12.8 - - - -
42A GLN* 3.9 1.3 - - - -
72A TYR* 3.5 9.7 - - - -
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Residues in contact with ARG 36 (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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10A GLU* 3.3 37.8 + - - +
11A PHE* 3.9 23.3 - - - +
35A GLY* 1.3 76.7 - - - -
37A PRO* 1.3 70.9 - - - +
38A TYR 3.2 2.5 - - - -
39A GLU* 3.0 53.6 + - + +
40A GLY 3.0 10.0 + - - -
41A THR* 2.9 29.1 + - - +
72A TYR* 4.1 0.2 - - - -
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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