Contacts of the strand formed by residues 16 - 21 (chain C) in PDB entry 2ZTC
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 16 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11C GLU* 3.6 23.4 + - - -
13C ALA* 2.9 37.9 + - + +
14C LEU 3.7 0.6 - - - -
15C ASP* 1.3 100.3 + - - +
17C VAL* 1.3 71.8 - - - +
18C VAL* 4.3 6.7 - - + +
27C ARG* 2.7 40.5 + - + +
28C VAL 3.3 15.9 - - - +
29C ASN* 3.4 15.5 - - - +
30C ALA 4.1 0.9 - - - +
35C LEU* 3.0 17.3 - - - +
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Residues in contact with VAL 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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9C VAL* 3.7 21.3 - - + -
11C GLU 3.3 15.3 - - - +
12C VAL* 4.7 2.2 - - - -
16C HIS* 1.3 79.9 - - - +
18C VAL* 1.3 74.3 + - - +
19C ILE* 3.9 13.0 - - + -
27C ARG* 3.5 4.7 - - - -
28C VAL* 2.9 57.3 + - + +
30C ALA* 5.2 0.7 - - + -
35C LEU* 4.0 11.0 - - + -
38C LEU* 3.8 15.5 - - + -
46C LEU* 3.9 15.7 - - + -
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Residues in contact with VAL 18 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9C VAL* 3.7 0.5 - - - -
10C LEU* 2.8 44.2 + - + +
11C GLU* 3.0 39.4 + - + +
16C HIS* 4.3 9.0 - - + +
17C VAL* 1.3 82.6 - - - +
19C ILE* 1.3 61.7 + - - +
25C GLY* 4.0 22.7 - - - +
26C TYR 3.3 10.1 - - - +
27C ARG* 4.6 3.1 - - + -
3D ALA* 4.4 18.4 - - + -
4D SER* 4.4 5.4 - - - +
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Residues in contact with ILE 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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5C VAL* 3.9 25.6 - - + +
6C ARG 3.8 4.9 - - - -
7C GLY* 3.2 35.0 - - - +
8C GLU 3.7 1.6 - - - -
9C VAL* 3.6 31.0 - - + +
17C VAL* 3.9 24.9 - - + -
18C VAL* 1.3 70.8 - - - +
20C GLU* 1.3 61.7 + - - +
21C ALA 3.6 1.2 + - - -
24C VAL 3.6 0.9 - - - +
25C GLY* 4.3 1.1 - - - -
26C TYR* 2.8 38.1 + - + +
28C VAL* 4.6 8.1 - - + -
38C LEU* 5.3 2.7 - - + -
44C ALA* 4.1 15.3 - - + +
46C LEU* 5.2 7.9 - - + -
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Residues in contact with GLU 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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7C GLY* 3.3 17.9 - - - -
8C GLU* 2.9 32.5 + - + +
10C LEU* 3.6 26.9 - - + +
18C VAL 3.8 0.4 + - - -
19C ILE* 1.3 70.4 - - - +
21C ALA* 1.3 59.2 + - - +
22C ALA 3.7 16.0 + - - +
23C GLY 3.4 13.7 - - - +
24C VAL 3.1 11.5 - - - +
25C GLY* 4.0 1.9 + - - -
4D SER* 5.0 0.7 + - - -
5D VAL 5.6 0.2 - - - -
6D ARG* 2.6 37.3 + - - +
45D ARG* 3.6 19.5 + - - -
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Residues in contact with ALA 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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23A GLY* 3.5 29.6 - - - +
24A VAL* 4.3 1.3 - - + +
5C VAL* 3.9 13.2 - - + -
6C ARG 3.5 11.7 - - - +
19C ILE 3.6 2.4 + - - -
20C GLU* 1.3 70.3 - - - +
22C ALA* 1.3 73.9 + - - +
24C VAL* 2.8 26.2 + - - +
26C TYR* 3.8 19.7 - - + -
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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