Contacts of the strand formed by residues 15 - 22 (chain C) in PDB entry 5AQO
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 TYR 15 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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10C ASP* 4.3 11.9 + - - +
12C GLY* 3.0 23.2 + - - -
14C THR* 1.3 91.3 + - - +
16C SER* 1.3 63.0 + - - +
17C CYS* 4.3 7.6 - - + -
37C THR* 3.5 36.8 - - + +
38C THR 3.2 13.5 - - - +
39C PRO* 4.5 1.1 - - + -
40C SER* 3.4 6.9 + - - -
201C GLY* 5.5 1.5 - - - -
202C GLY* 4.6 16.4 - - - -
338C GLY* 5.1 5.2 - - - -
365C PRO 4.4 1.7 + - - -
366C ASP* 2.7 53.7 + - + -
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Residues in contact with SER 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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10C ASP 3.1 10.5 - - - -
11C LEU* 3.6 6.9 - - - +
12C GLY 3.3 11.8 + - - -
15C TYR* 1.3 72.3 - - - +
17C CYS* 1.3 61.6 + - - +
37C THR* 3.4 4.5 - - - -
38C THR 2.7 32.8 + - - -
40C SER* 2.9 17.8 + - - -
123C VAL* 3.6 13.2 - - - +
127C MET* 3.7 33.4 - - - +
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Residues in contact with CYS 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 ILE* 3.4 2.4 - - - +
10C ASP* 2.7 42.1 + - + +
15C TYR* 4.3 14.8 - - + -
16C SER* 1.3 75.8 - - - +
18C VAL* 1.3 57.1 + - - +
28C ILE* 3.5 22.9 - - - -
36C ARG 3.5 22.0 - - - +
37C THR* 4.5 1.6 - - + -
127C MET* 3.8 4.3 - - - -
366C ASP 4.4 3.1 - - - +
367C GLU* 4.2 17.9 - - - -
370C ALA* 3.4 23.2 - - + +
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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
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7C VAL* 3.9 20.4 - - + -
8C GLY 3.3 10.8 - - - +
9C ILE* 3.7 19.5 - - + -
17C CYS* 1.3 75.1 - - - +
19C GLY* 1.3 62.6 + - - +
28C ILE* 3.8 5.2 - - - +
29C ILE* 2.9 36.0 + - + +
36C ARG 4.8 1.4 + - - -
127C MET* 3.6 42.9 - - + +
130C ILE* 3.7 19.1 - - + -
131C ALA* 4.2 7.9 - - + +
370C ALA* 4.5 2.7 - - - -
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Residues in contact with GLY 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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7C VAL* 3.5 8.8 - - - +
8C GLY 2.9 33.6 + - - -
18C VAL* 1.3 74.4 - - - +
20C VAL* 1.3 59.8 + - - -
26C VAL* 4.7 0.2 - - - -
27C GLU 3.3 11.2 - - - -
28C ILE* 3.9 13.7 - - - -
29C ILE* 4.5 2.7 - - - -
370C ALA* 4.3 3.2 - - - +
374C ALA* 3.6 12.5 - - - +
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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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5C PRO* 3.7 29.6 - - + -
6C ALA 3.8 14.8 - - - +
7C VAL* 4.1 8.5 - - + -
19C GLY* 1.3 73.9 - - - +
21C PHE* 1.3 67.3 + - - +
22C GLN* 3.6 18.3 + - + +
26C VAL* 4.3 0.4 - - - -
27C GLU* 2.7 48.8 + - + +
29C ILE* 3.8 23.1 - - + -
134C TYR* 4.2 1.8 - - + -
135C LEU* 4.1 15.3 - - + -
374C ALA* 3.8 5.7 - - - +
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Residues in contact with PHE 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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5C PRO* 5.0 6.8 - - - +
6C ALA 4.9 2.7 + - - +
20C VAL* 1.3 78.4 - - - +
22C GLN* 1.3 62.4 + - - +
23C HIS 5.4 0.2 - - - -
24C GLY* 3.5 35.2 - - - -
25C LYS* 3.4 15.7 - - - -
26C VAL* 3.7 22.2 - - + +
374C ALA* 3.8 15.7 + - - +
375C VAL* 4.4 15.9 - - + -
378C ALA* 3.6 33.5 - - + +
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Residues in contact with GLN 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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5C PRO* 5.7 3.7 - - + +
20C VAL* 4.0 15.9 - - + +
21C PHE* 1.3 78.9 - - - +
23C HIS* 1.3 94.8 + - + +
24C GLY 3.3 2.9 - - - +
25C LYS* 2.8 25.1 + - - +
27C GLU* 3.2 23.7 - - + +
134C TYR* 3.0 30.7 + - - -
135C LEU* 3.7 18.2 - - - +
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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