Contacts of the strand formed by residues 12 - 22 (chain C) 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 MET 12 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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7C ILE 3.8 13.7 - - - +
8C ILE* 4.1 2.5 - - + -
9C LYS* 3.6 40.6 - - - +
11C PHE* 1.3 85.0 - - - +
13C ARG* 1.3 63.0 + - - +
34C GLU* 3.4 0.8 - - - -
35C GLY 3.0 26.2 + - - +
37C PRO* 3.7 13.5 - - + -
72C TYR* 2.8 22.7 + - - +
113C LEU* 3.4 32.5 - - + -
116C GLY* 3.6 19.3 - - - +
117C GLU* 4.7 1.1 - - - -
118C PHE* 3.7 22.7 - - + -
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Residues in contact with ARG 13 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11C PHE* 3.7 33.9 - - + -
12C MET* 1.3 75.2 - - - +
14C PHE* 1.3 64.8 + - - +
33C GLY 3.2 12.5 + - - +
34C GLU* 2.8 32.1 + - + +
72C TYR* 3.7 2.5 + - - -
116C GLY 5.1 1.8 + - - -
117C GLU* 3.7 32.9 - - + +
118C PHE* 3.2 21.0 + - - -
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Residues in contact with PHE 14 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13C ARG* 1.3 78.1 - - - +
15C LYS* 1.3 69.5 + - - +
16C VAL* 4.3 13.5 - - + -
32C GLU* 3.4 5.0 - - - +
33C GLY* 2.7 50.5 + - - +
34C GLU 4.1 1.1 - - - -
42C GLN* 3.1 28.5 - - + -
43C THR 4.0 4.7 - - - -
44C ALA* 3.7 26.0 - - + -
65C PHE 3.9 13.0 - - - -
66C CH6 4.3 0.2 - - + -
69C SER* 3.9 2.2 - - - -
72C TYR* 3.3 26.5 - + - +
117C GLU* 4.3 3.3 - - - +
118C PHE* 3.2 26.9 - - + +
120C TYR* 3.5 26.7 - + + -
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Residues in contact with LYS 15 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14C PHE* 1.3 79.3 - - - +
16C VAL* 1.3 62.6 + - - +
31C GLY 3.5 4.3 - - - +
32C GLU* 3.9 24.5 - - + -
117C GLU* 3.3 31.6 + - - +
118C PHE 2.9 6.9 + - - +
119C ILE* 3.6 21.5 - - + +
120C TYR* 2.8 28.8 + - - +
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Residues in contact with VAL 16 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14C PHE* 4.3 12.8 - - + -
15C LYS* 1.3 77.5 - - - +
17C HIS* 1.3 66.7 + - - +
29C ILE* 6.4 0.2 - - - -
30C GLU* 3.4 3.9 - - - +
31C GLY* 2.8 54.1 + - - +
46C LEU* 3.9 17.9 - - + -
65C PHE* 4.0 21.3 - - + -
120C TYR* 3.3 32.8 - - + +
122C VAL* 3.9 21.1 - - + -
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Residues in contact with HIS 17 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16C VAL* 1.3 76.7 - - - +
18C MET* 1.3 69.7 + - - +
19C GLU* 4.1 18.6 - - + +
28C GLU* 3.1 32.7 + - - +
29C ILE 3.4 15.7 - - - -
30C GLU* 3.8 21.9 + - + -
120C TYR 3.1 9.3 + - - +
121C LYS* 3.5 11.9 - - + +
122C VAL* 2.9 25.5 + - - +
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Residues in contact with MET 18 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17C HIS* 1.3 77.3 - - - +
19C GLU* 1.3 73.0 + - - +
20C GLY 4.4 0.2 + - - -
27C PHE* 3.7 28.3 - - + -
28C GLU* 3.3 6.9 - - - +
29C ILE* 2.9 39.7 + - + +
61C LEU* 4.3 9.2 - - + +
64C GLN* 3.6 35.0 - - + -
65C PHE* 3.5 40.6 - - + -
122C VAL* 3.2 23.6 - - + +
124C LEU* 4.2 9.2 - - + -
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Residues in contact with GLU 19 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17C HIS* 4.1 15.0 - - + +
18C MET* 1.3 76.6 - - - +
20C GLY* 1.3 58.9 + - - +
27C PHE 3.7 4.5 - - - +
28C GLU* 4.4 17.7 - - + +
122C VAL 3.0 11.3 + - - +
123C LYS* 3.3 38.1 - - + +
124C LEU 3.0 22.3 + - - +
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Residues in contact with GLY 20 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18C MET 4.2 0.2 - - - -
19C GLU* 1.3 76.3 - - - +
21C SER* 1.3 60.8 + - - -
26C GLU* 3.3 6.1 - - - +
27C PHE* 2.9 53.2 + - - +
124C LEU* 3.1 13.2 - - - -
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Residues in contact with SER 21 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20C GLY* 1.3 76.9 - - - -
22C VAL* 1.3 60.0 + - - +
24C GLY* 4.5 9.9 - - - -
25C HIS 3.1 12.6 - - - -
26C GLU* 3.8 19.3 - - - -
27C PHE* 3.7 0.8 - - - -
124C LEU* 3.0 7.6 + - - +
125C ARG* 3.5 14.9 - - - +
126C GLY 2.8 30.8 + - - +
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Residues in contact with VAL 22 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21C SER* 1.3 78.1 - - - +
23C ASN* 1.3 71.6 + - - +
25C HIS* 2.9 24.6 + - - +
27C PHE* 4.0 1.8 - - + -
56C PHE* 3.6 46.7 - - + -
60C ILE* 4.0 17.3 - - + -
61C LEU* 4.7 0.7 - - + -
124C LEU* 3.9 18.8 - - + -
126C GLY* 3.3 7.0 - - - -
129C PHE* 4.0 24.2 - - + -
136C MET* 4.3 11.7 - - - +
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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