Contacts of the strand formed by residues 23 - 32 (chain K) in PDB entry 1ZGL
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 ARG 23 (chain K).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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18K PHE* 3.1 53.8 + - + +
22K GLU* 1.3 81.4 + - + +
24K VAL* 1.3 67.8 + - - +
25K ARG* 6.4 0.7 - - + -
43K ASP* 5.9 0.8 + - - -
80K ARG* 4.4 0.7 - - - +
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Residues in contact with VAL 24 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15K CYS* 4.9 0.2 - - + -
16K HIS 3.6 4.3 - - - +
17K PHE* 3.4 34.5 - - + -
21K THR 3.7 7.4 - - - +
23K ARG* 1.3 80.8 - - - +
25K ARG* 1.3 61.8 + - - +
42K SER* 4.4 1.0 + - - -
75K VAL* 3.6 20.8 - - + +
79K CYS* 3.4 38.1 - - + -
80K ARG* 2.9 42.2 + - - +
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Residues in contact with ARG 25 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14K GLU 3.5 2.3 - - - +
15K CYS* 3.4 2.8 - - - -
16K HIS* 2.8 53.0 + - + +
18K PHE* 4.5 8.7 - - + -
23K ARG* 6.4 0.4 - - + -
24K VAL* 1.3 73.4 - - - +
26K PHE* 1.3 61.0 + - - +
27K LEU* 3.8 3.6 + - + +
41K ASP* 5.7 1.1 - - - +
42K SER* 3.7 8.5 - - - +
43K ASP* 4.5 15.9 - - - +
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Residues in contact with PHE 26 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13K TYR* 4.6 6.1 - + + -
14K GLU 3.2 12.1 - - - -
25K ARG* 1.3 72.1 - - - +
27K LEU* 1.3 70.9 + - - +
28K HIS* 4.5 8.1 - - + -
40K PHE* 3.7 30.0 - + - +
41K ASP* 4.1 0.3 - - - +
42K SER* 2.9 34.4 + - - -
71K ARG* 4.2 12.6 - - - -
74K ALA* 3.9 21.3 - - + -
75K VAL* 3.5 24.5 - - + +
78K TYR* 3.2 41.1 - + - -
79K CYS* 3.6 14.1 - - - -
7L ILE* 3.4 20.2 - - + -
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Residues in contact with LEU 27 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12K LYS 3.6 0.7 - - - +
13K TYR* 3.5 4.3 - - - -
14K GLU* 2.7 53.2 + - + +
16K HIS* 5.1 12.3 - - + +
25K ARG* 4.9 3.6 - - + +
26K PHE* 1.3 81.1 - - - +
28K HIS* 1.3 61.4 + - - +
29K ARG* 3.3 44.2 - - + +
39K ARG* 4.6 10.1 - - + +
40K PHE 3.5 2.0 - - - -
41K ASP* 3.4 45.5 - - + +
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Residues in contact with HIS 28 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11K ASP* 3.9 13.9 + - - -
12K LYS 3.6 2.5 - - - -
13K TYR* 3.4 26.8 - + + -
26K PHE* 4.5 11.7 - - + -
27K LEU* 1.3 73.1 - - - +
29K ARG* 1.3 75.4 + - - +
30K ASP* 4.4 5.2 + - - +
38K LEU* 4.9 6.5 - - + -
39K ARG* 3.1 8.0 - - - +
40K PHE* 2.8 45.8 + - + +
47K TYR* 2.8 36.8 + + - +
71K ARG* 3.7 5.3 + - - -
9L THR* 3.8 29.1 - - + +
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Residues in contact with ARG 29 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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141J GLU* 4.3 16.8 + - - +
143J HIS* 3.9 23.0 + - - -
11K ASP* 3.3 8.1 - - - +
12K LYS* 2.9 51.5 + - + +
14K GLU* 5.7 4.3 - - + -
16K HIS* 6.1 2.0 - - - -
27K LEU* 3.3 35.5 - - + +
28K HIS* 1.3 81.1 - - - +
30K ASP* 1.3 60.8 + - - +
31K ILE* 3.6 11.9 - - + +
36K GLU* 2.9 29.4 + - - +
38K LEU 3.7 2.5 - - - -
39K ARG* 4.9 8.0 - - + +
169M ARG* 5.7 4.4 - - - +
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Residues in contact with ASP 30 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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69J ASN* 3.9 9.9 + - - -
73J MET* 5.0 2.2 - - - +
9K GLN* 3.3 25.6 + - - +
11K ASP* 3.0 19.8 - - - +
28K HIS* 4.7 5.0 + - - +
29K ARG* 1.3 74.5 - - - +
31K ILE* 1.3 61.8 + - - +
36K GLU* 3.4 5.0 - - - +
37K ASP* 2.5 58.5 + - - +
38K LEU* 2.8 32.9 + - + +
57K ASP* 6.5 0.7 - - - -
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Residues in contact with ILE 31 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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143J HIS* 3.7 39.3 - - + +
9K GLN* 3.5 4.6 - - - +
10K GLN* 3.0 49.9 + - + +
12K LYS* 4.2 12.3 - - + -
29K ARG* 3.6 27.8 - - + +
30K ASP* 1.3 86.8 + - - +
32K TYR* 1.3 59.7 + - - +
33K ASN 3.9 3.8 + - - +
34K GLN* 3.9 10.1 - - - +
35K GLU 3.0 35.4 - - - +
36K GLU* 3.6 9.2 - - + +
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Residues in contact with TYR 32 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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70J LEU* 4.2 15.0 - - + -
73J MET* 3.6 20.0 - - + -
74J THR* 3.4 25.1 - - - -
77J SER* 3.3 26.6 + - - -
80J THR* 2.9 22.0 + - - -
7K PHE* 3.2 13.5 - + - -
8K LEU 3.7 8.3 - - - -
9K GLN* 4.2 5.4 - - - +
31K ILE* 1.3 70.5 - - - +
33K ASN* 1.3 87.7 + - - +
34K GLN 2.7 15.5 + - - -
35K GLU* 2.8 22.1 + - + +
37K ASP* 3.9 18.0 + - - +
53K LEU* 3.9 22.9 - - + -
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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