Contacts of the strand formed by residues 19 - 26 (chain C) in PDB entry 6BA5
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 THR 19 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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17C GLY 4.9 0.7 + - - -
18C GLY* 1.3 74.3 + - - -
20C VAL* 1.3 66.4 + - - +
21C THR* 4.2 12.3 + - + +
75C THR* 3.8 22.9 - - + -
76C ILE 3.3 11.1 + - - +
77C SER* 4.2 10.7 + - - +
78C GLY 4.2 1.4 + - - -
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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
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12C THR* 4.0 17.0 - - - +
14C GLY* 5.4 11.4 - - - +
19C THR* 1.3 77.3 - - - +
21C THR* 1.3 66.1 + - - +
22C ILE* 4.2 12.3 - - + -
74C LEU 3.8 0.6 - - - +
75C THR* 3.3 5.5 - - - +
76C ILE* 2.9 49.2 + - + +
79C VAL* 4.2 28.7 - - + -
108C VAL* 3.9 34.8 - - + -
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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* 4.0 12.6 - - - +
12C THR* 4.6 7.4 - - - +
19C THR* 4.2 16.2 - - + +
20C VAL* 1.3 80.4 - - - +
22C ILE* 1.3 66.9 + - - +
23C ASN* 4.7 10.7 + - - -
73C THR* 4.4 10.8 - - + -
74C LEU 3.4 5.2 - - - -
75C THR* 4.3 11.7 - - + +
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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
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7C GLN* 3.5 17.0 - - + +
8C THR 3.9 6.3 - - - +
9C PRO* 4.5 0.2 - - - -
12C THR* 4.9 0.4 - - - +
20C VAL* 4.2 11.2 - - + -
21C THR* 1.3 78.3 - - - +
23C ASN* 1.3 65.1 + - - +
36C TRP* 3.7 16.0 - - + -
73C THR* 3.3 4.9 - - - +
74C LEU* 2.9 47.1 + - + +
76C ILE* 5.2 1.8 - - + -
87C TYR* 3.8 28.5 - - + -
106C THR* 3.4 34.8 - - + +
108C VAL* 3.9 23.1 - - + -
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Residues in contact with ASN 23 (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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6C THR 4.5 0.4 - - - -
7C GLN* 3.4 5.5 - - - +
8C THR* 2.8 49.4 + - - +
9C PRO* 5.4 1.6 - - - +
21C THR* 4.7 12.4 + - - -
22C ILE* 1.3 75.2 - - - +
24C CYS* 1.3 65.6 + - - +
36C TRP* 4.3 0.4 - - - -
71C GLU* 3.6 27.2 + - - +
72C TYR 3.4 2.7 - - - -
73C THR* 2.8 34.2 + - - +
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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 MET* 4.1 9.6 - - + -
6C THR 3.4 4.0 - - - +
7C GLN* 3.5 22.9 - - - -
23C ASN* 1.3 81.2 - - - +
25C GLN* 1.3 60.3 + - - +
36C TRP* 3.6 13.7 - - + -
70C THR 3.7 1.4 - - - +
71C GLU* 3.4 6.7 - - - -
72C TYR* 2.8 42.6 + - + +
89C CYS* 2.3 49.1 - - + -
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Residues in contact with GLN 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 3.6 1.2 - - - +
5C MET* 3.5 5.1 - - - -
6C THR* 2.8 51.0 + - - +
24C CYS* 1.3 72.3 - - - +
26C ALA* 1.3 80.5 + - - +
27C SER* 5.9 0.2 - - - -
70C THR* 2.8 37.6 + - - +
71C GLU* 3.8 20.1 + - - +
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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 LEU* 4.2 1.6 - - + -
5C MET* 3.7 25.4 - - + +
25C GLN* 1.3 92.2 + - - +
27C SER* 1.3 64.2 + - - +
28C GLN 3.3 20.2 + - - +
30C ILE* 3.8 18.2 - - + -
70C THR* 2.9 23.8 + - - +
72C TYR* 4.2 1.6 - - + -
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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