Contacts of the strand formed by residues 20 - 30 (chain C) in PDB entry 3AB0
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 VAL 20 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12C MET* 4.9 13.5 - - - -
14C ALA* 4.7 7.0 - - + -
18C GLU* 4.1 13.5 - - + +
19C LYS* 1.3 80.6 - - - +
21C THR* 1.3 64.7 + - - +
22C ILE* 4.7 15.7 - - + +
73C LEU* 3.4 2.2 - - + +
74C THR* 3.0 9.2 - - - +
75C ILE* 2.7 69.4 + - + -
78C MET* 4.3 20.0 - - + -
104C LEU* 4.3 15.5 - - + -
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Residues in contact with THR 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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9C PRO* 5.4 0.2 - - - +
12C MET* 4.9 10.7 - - - +
19C LYS* 3.8 29.4 + - - +
20C VAL* 1.3 78.7 + - - +
22C ILE* 1.3 68.1 + - - +
72C SER* 4.0 25.4 - - - +
73C LEU 3.4 3.8 - - - +
74C THR* 4.0 13.6 - - + +
101D ILE* 4.5 15.3 - - + -
196D LEU* 3.3 22.4 - - + +
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Residues in contact with ILE 22 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7C GLN* 5.2 0.4 - - - +
8C SER 4.0 6.3 - - - +
9C PRO* 4.8 3.8 - - + -
12C MET* 5.4 4.9 - - - -
20C VAL* 4.7 14.1 - - + -
21C THR* 1.3 79.2 - - - +
23C SER* 1.3 62.9 + - - +
35C TRP* 3.7 23.5 - - + -
71C TYR 3.6 0.2 - - - +
72C SER* 3.3 10.1 - - - -
73C LEU* 3.1 52.6 + - + +
86C TYR* 3.8 30.1 - - + +
102C THR* 3.6 33.2 - - + +
104C LEU* 5.3 4.7 - - + -
196D LEU* 4.2 2.2 - - - -
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Residues in contact with SER 23 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6C THR 4.2 1.6 + - - -
7C GLN* 3.2 21.7 + - - +
8C SER* 3.0 38.6 + - - +
22C ILE* 1.3 74.8 - - - +
24C CYS* 1.3 64.6 + - - +
25C SER* 3.4 7.6 + - - -
35C TRP* 4.3 1.9 - - - -
71C TYR 3.7 3.6 - - - -
72C SER* 5.1 0.7 - - - +
195D GLY* 3.3 30.1 - - - -
196D LEU* 3.7 19.8 - - - +
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Residues in contact with CYS 24 (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 LEU* 3.9 14.1 - - - -
6C THR 3.4 5.4 - - - -
7C GLN* 4.2 0.7 - - - -
23C SER* 1.3 75.7 + - - +
25C SER* 1.3 59.5 + - - +
33C MET* 3.7 21.0 - - - +
35C TRP* 3.5 18.8 - - + -
70C SER* 3.6 0.5 - - - -
71C TYR* 2.8 41.7 + - + +
88C CYS* 2.0 47.1 - - - -
195D GLY* 5.5 0.2 - - - -
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Residues in contact with SER 25 (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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4C VAL 4.0 0.5 - - - +
5C LEU* 3.3 4.5 - - - -
6C THR* 2.8 45.1 + - - -
23C SER* 3.4 3.0 + - - -
24C CYS* 1.3 75.1 + - - +
26C ALA* 1.3 64.1 + - - +
33C MET* 6.1 0.2 - - - -
69C THR 3.2 11.9 + - - -
70C SER* 4.0 0.9 - - - -
166D SER* 4.0 20.9 - - - -
194D THR* 4.1 4.9 - - - -
195D GLY* 3.2 35.4 + - - -
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Residues in contact with ALA 26 (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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3C ILE* 3.6 11.4 - - + -
4C VAL 3.9 7.0 - - - -
5C LEU* 3.9 11.9 - - + -
24C CYS 4.4 0.2 + - - -
25C SER* 1.3 77.4 - - - +
27C ARG* 1.3 61.3 + - - +
28C SER 3.2 22.4 - - - +
30C VAL* 4.3 9.2 - - + -
33C MET* 5.6 1.1 - - + -
69C THR* 2.9 25.3 + - - +
164D GLY* 3.5 20.8 - - - +
166D SER* 5.6 0.5 + - - -
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Residues in contact with ARG 27 (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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3C ILE* 3.5 10.4 - - + +
4C VAL* 3.7 16.6 + - + +
26C ALA* 1.3 74.9 - - - +
28C SER* 1.3 67.1 + - - +
69C THR* 4.4 1.7 - - - +
160D VAL 4.8 0.7 - - - +
162D GLY* 3.3 48.8 + - - -
163D THR 3.8 0.2 + - - -
164D GLY* 3.4 33.5 + - - -
165D SER* 5.3 5.8 + - - +
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Residues in contact with SER 28 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3C ILE* 3.5 18.7 - - - +
26C ALA* 3.2 21.5 - - - +
27C ARG* 1.3 85.6 + - - +
29C SER* 1.3 68.5 + - - +
30C VAL* 3.2 4.5 + - - +
69C THR* 3.3 11.5 - - - +
159D PRO* 5.2 1.8 - - - -
160D VAL 5.6 0.2 - - - -
161D PRO* 4.1 13.4 - - - +
162D GLY* 3.7 13.2 + - - +
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Residues in contact with SER 29 (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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3C ILE* 5.7 0.5 - - - +
28C SER* 1.3 73.9 - - - +
30C VAL* 1.3 64.2 + - - +
31C SER* 4.4 1.0 + - - -
68C GLY* 3.4 14.5 - - - -
69C THR* 4.0 1.6 - - - +
93C SER* 5.8 3.5 - - - -
158D VAL* 4.1 15.0 - - - +
159D PRO* 3.8 35.0 + - - +
161D PRO* 5.9 0.4 - - - +
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Residues in contact with VAL 30 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3C ILE* 3.8 22.4 - - + -
5C LEU* 4.4 1.1 - - + -
26C ALA* 4.3 7.4 - - + -
28C SER 3.8 7.4 - - - +
29C SER* 1.3 80.5 + - - +
31C SER* 1.3 57.6 + - - +
32C TYR 5.1 1.1 - - - +
33C MET* 3.8 17.0 - - + -
68C GLY* 3.0 15.3 + - - +
71C TYR* 2.6 49.5 + - + -
90C GLN* 3.7 37.2 - - + +
93C SER* 5.6 2.0 - - - -
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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