Contacts of the strand formed by residues 19 - 23 (chain C) in PDB entry 1C3Q
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 LEU 19 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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-11C MET* 5.4 1.4 - - - +
17C SER 3.6 1.2 + - - -
18C PRO* 1.3 72.4 - - - +
20C VAL* 1.3 59.5 + - - +
21C HIS 4.0 0.2 - - - -
42C SER* 3.2 28.0 - - - +
43C PRO 5.0 0.9 - - - +
44C VAL* 4.3 24.2 - - + -
55C MET* 5.1 4.5 - - - +
58C ILE* 4.1 39.7 - - + +
59C ALA* 3.7 8.2 - - + +
60C GLY* 2.7 39.2 + - - +
61C ALA 3.4 1.7 + - - -
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Residues in contact with VAL 20 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18C PRO* 3.9 12.1 - - + +
19C LEU* 1.3 74.6 - - - +
21C HIS* 1.3 61.6 + - - +
22C SER* 3.6 17.5 + - - +
36C LEU* 4.1 14.9 - - + +
41C ALA* 4.4 6.1 - - + -
42C SER 2.8 9.9 + - - +
43C PRO* 3.6 3.3 - - - +
44C VAL* 3.1 24.2 + - - +
45C MET* 5.6 0.2 - - - +
61C ALA* 3.7 8.7 - - + +
63C VAL* 4.2 15.9 - - + -
202C SER 4.0 16.4 - - - +
205C GLY 4.4 2.9 - - - -
206C ALA* 3.6 38.4 - - + +
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Residues in contact with HIS 21 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19C LEU 4.0 1.0 + - - -
20C VAL* 1.3 71.3 - - - +
22C SER* 1.3 70.5 + - - +
23C ILE* 3.7 17.5 - - + +
44C VAL* 3.4 27.6 - - + -
46C ALA* 3.1 30.2 + - - +
52C VAL* 3.9 17.0 - - + -
55C MET* 3.7 20.6 - - + +
56C ALA* 3.5 24.3 + - + +
59C ALA* 3.8 17.0 - - + -
61C ALA 3.0 8.7 + - - +
62C LEU* 3.2 11.3 - - + +
63C VAL* 2.9 25.3 + - - +
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Residues in contact with SER 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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20C VAL* 3.6 9.4 + - - +
21C HIS* 1.3 80.0 + - - +
23C ILE* 1.3 63.1 + - - +
24C THR* 3.6 13.0 + - - -
32C THR* 4.1 4.6 - - - +
36C LEU* 4.5 1.6 - - - +
44C VAL 3.1 14.1 + - - +
45C MET* 3.8 35.6 - - - +
46C ALA 4.2 0.2 + - - -
47C TYR* 4.0 5.5 - - - -
63C VAL* 3.4 11.6 - - - +
202C SER* 3.3 25.1 + - - -
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Residues in contact with ILE 23 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21C HIS* 3.7 14.6 - - + +
22C SER* 1.3 75.2 - - - +
24C THR* 1.3 59.9 + - - +
46C ALA 3.7 11.9 - - - +
47C TYR* 4.3 22.4 - - + -
52C VAL* 4.1 10.1 - - + -
62C LEU* 4.4 2.2 - - + -
63C VAL 2.9 7.8 + - - -
64C LEU* 3.5 21.1 - - + -
65C ASN 2.9 26.6 + - - +
73C SER* 4.7 10.1 - - - +
76C ALA* 4.1 11.7 - - + +
77C MET* 3.9 20.2 - - + +
80C ALA* 3.6 31.0 - - + -
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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