Contacts of the helix formed by residues 21 - 32 (chain C) in PDB entry 2P5L
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 21 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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10B T 3.8 37.9 - - - +
11B T 3.6 12.3 - - - -
19C ILE* 3.2 7.4 - - - +
20C GLU* 1.3 93.6 - - + +
22C GLN* 1.3 64.6 + - - +
23C ASP* 3.6 9.6 + - - +
24C GLU* 2.9 38.1 + - - +
25C LEU 3.1 8.8 + - - -
52C LYS* 5.0 0.9 - - - +
62C TYR* 3.9 5.8 - - - -
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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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11B T 2.7 28.6 + - - +
12B A 3.0 24.5 + - - -
21C THR* 1.3 70.6 - - - +
23C ASP* 1.3 66.1 + - - +
25C LEU* 2.9 9.9 + - - +
26C VAL* 2.7 28.2 + - - +
38C GLN* 2.7 37.3 + - + +
41C VAL* 3.7 9.9 - - + -
42C SER* 3.6 10.2 - - - +
45C ILE* 3.3 29.2 - - + +
62C TYR* 3.1 26.4 + - + +
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Residues in contact with ASP 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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10B T 4.6 13.4 + - - +
11B T 4.2 12.5 + - - +
21C THR* 3.2 9.7 + - - +
22C GLN* 1.3 76.4 - - - +
24C GLU* 1.3 62.7 + - + +
26C VAL* 2.9 18.6 + - - +
27C ASP* 3.0 20.6 + - - +
38C GLN* 4.0 21.2 - - - +
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Residues in contact with GLU 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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18C GLU 3.6 6.2 - - - +
19C ILE* 3.5 15.4 - - + +
20C GLU* 2.8 45.2 + - - +
21C THR* 2.9 27.4 + - - +
23C ASP* 1.3 76.7 - - + +
25C LEU* 1.3 62.5 + - - +
27C ASP* 3.2 10.4 + - - +
28C MET* 2.9 28.8 + - + +
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Residues in contact with LEU 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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10C ILE* 3.6 26.7 - - + -
13C ILE* 3.7 38.1 - - + -
14C ILE* 4.2 15.3 - - + -
19C ILE* 3.8 11.2 - - + +
21C THR 3.1 10.2 + - - +
22C GLN* 2.9 12.2 + - - +
24C GLU* 1.3 77.7 - - - +
26C VAL* 1.3 57.9 + - - +
28C MET* 3.3 1.5 + - - -
29C LEU* 2.9 46.1 + - + +
41C VAL* 4.0 18.6 - - + -
45C ILE* 4.5 11.7 - - + -
50C LEU* 5.4 0.4 - - + -
62C TYR* 5.4 3.4 - - + -
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Residues in contact with VAL 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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22C GLN 2.7 22.0 + - - +
23C ASP* 2.9 11.9 + - - +
25C LEU* 1.3 78.4 - - - +
27C ASP* 1.3 63.7 + - - +
29C LEU* 3.3 11.0 + - - +
30C LYS* 3.0 37.3 + - + +
34C TYR 4.5 0.9 - - - +
36C VAL* 3.2 25.1 - - + +
37C THR* 4.3 2.2 - - - -
38C GLN* 3.9 22.7 - - + +
41C VAL* 3.8 19.1 - - + -
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Residues in contact with ASP 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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23C ASP* 3.0 19.5 + - - +
24C GLU* 3.6 10.2 - - - +
26C VAL* 1.3 75.4 - - - +
28C MET* 1.3 66.4 + - + +
30C LYS* 2.7 46.8 + - - +
31C GLN* 2.9 29.6 + - - +
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Residues in contact with MET 28 (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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13C ILE* 3.8 23.6 - - + -
17C ASN* 3.6 33.2 - - - +
19C ILE* 4.0 21.5 - - + -
24C GLU* 2.9 21.5 + - + +
25C LEU 3.6 4.9 - - - +
27C ASP* 1.3 77.9 - - + +
29C LEU* 1.3 62.8 + - - +
31C GLN* 3.2 28.4 + - + +
32C ASP* 3.0 35.4 + - - +
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Residues in contact with LEU 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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6C ARG* 4.3 7.0 - - + -
9C LYS* 4.0 16.2 - - + -
10C ILE* 4.0 28.9 - - + -
13C ILE* 3.6 21.8 - - + -
25C LEU* 2.9 24.6 + - + +
26C VAL* 3.6 3.8 - - - +
28C MET* 1.3 77.6 - - - +
30C LYS* 1.3 57.1 + - - +
32C ASP* 3.0 4.6 + - - -
33C GLY 2.9 5.2 + - - -
34C TYR* 2.7 54.1 + - + +
36C VAL* 3.9 12.8 - - + -
41C VAL* 3.8 26.9 - - + -
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Residues in contact with LYS 30 (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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26C VAL* 3.0 23.6 + - + +
27C ASP* 2.7 45.1 + - - +
29C LEU* 1.3 72.4 - - - +
31C GLN* 1.3 60.3 + - + +
33C GLY* 2.6 25.7 + - - +
34C TYR 3.3 8.9 + - - +
35C LYS* 4.0 29.4 - - + +
36C VAL 5.4 1.3 - - - +
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Residues in contact with GLN 31 (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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27C ASP* 2.9 31.7 + - - +
28C MET* 3.5 30.1 - - + +
30C LYS* 1.3 77.0 - - + +
32C ASP* 1.3 61.5 + - - +
33C GLY 3.4 2.3 + - - -
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Residues in contact with ASP 32 (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 LYS* 3.4 41.6 + - + -
13C ILE* 3.8 14.6 - - - +
28C MET* 3.0 23.3 + - - +
29C LEU* 3.2 10.8 - - - +
30C LYS 3.0 1.2 - - - -
31C GLN* 1.3 79.5 - - - +
33C GLY* 1.3 55.6 + - - +
34C TYR* 3.4 13.0 - - + -
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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