Contacts of the helix formed by residues 3 - 17 (chain C) in PDB entry 2B05
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 ASP 3 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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2C VAL* 1.3 79.4 - - - +
4C ARG* 1.3 65.2 + - - +
5C GLU* 4.1 6.5 - - + +
6C GLN* 3.2 38.7 + - + +
7C LEU* 3.2 12.9 + - - +
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Residues in contact with ARG 4 (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 ASP* 1.3 74.0 - - - +
5C GLU* 1.3 64.0 + - - +
7C LEU* 3.3 13.5 + - - +
8C VAL* 3.1 24.5 + - - +
30C VAL* 3.5 32.0 + - + +
33C LEU* 3.5 23.8 - - + +
35C GLU* 3.9 35.6 + - - +
36C PRO 3.4 15.6 + - - -
37C LEU* 4.0 2.2 - - - +
41C GLU* 2.5 44.7 + - - -
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Residues in contact with GLU 5 (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 ASP* 3.3 3.4 - - + +
4C ARG* 1.3 80.3 - - + +
6C GLN* 1.3 73.6 + - - +
8C VAL* 3.4 7.2 + - - +
9C GLN* 2.9 37.5 + - - +
12C ARG* 5.4 0.3 + - - -
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Residues in contact with GLN 6 (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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77B LYS* 4.6 19.0 - - + +
78B LYS* 4.5 11.6 + - - +
81B MET* 4.6 15.8 - - + +
2C VAL* 4.6 11.7 - - + -
3C ASP* 3.2 41.2 + - + +
5C GLU* 1.3 90.1 - - - +
7C LEU* 1.3 51.4 + - - +
9C GLN* 2.7 31.6 + - - +
10C LYS* 2.8 34.2 + - - +
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Residues in contact with LEU 7 (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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2C VAL* 3.3 33.2 - - + +
3C ASP 3.2 11.6 + - - +
4C ARG* 3.3 12.1 + - - +
6C GLN* 1.3 76.2 - - - +
8C VAL* 1.3 57.4 + - - +
10C LYS* 3.3 9.9 - - + +
11C ALA* 2.9 23.7 + - - +
26C ALA* 3.5 18.2 - - + +
29C ASN* 3.7 39.9 - - + +
30C VAL* 3.5 23.1 - - + +
33C LEU* 4.5 11.9 - - + -
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Residues in contact with VAL 8 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4C ARG* 3.1 20.1 + - - +
5C GLU* 3.8 6.5 - - - +
6C GLN 3.3 0.2 - - - -
7C LEU* 1.3 75.4 - - - +
9C GLN* 1.3 56.6 + - - +
11C ALA* 3.2 9.0 + - - +
12C ARG* 3.0 58.3 + - - +
27C MET* 4.7 2.2 - - - -
30C VAL* 3.9 18.8 - - + -
40C GLU* 5.0 0.2 - - - -
41C GLU* 3.6 35.2 - - + +
44C LEU* 4.0 16.8 - - + -
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Residues in contact with GLN 9 (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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75B ASN* 4.6 7.3 - - - +
78B LYS* 3.6 29.8 - - + +
81B MET* 3.6 15.1 - - + +
5C GLU* 2.9 22.1 + - + +
6C GLN* 2.7 34.1 + - - +
8C VAL* 1.3 73.0 - - - +
10C LYS* 1.3 59.9 + - - +
12C ARG* 3.2 26.1 + - - +
13C LEU* 2.9 28.8 + - - +
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Residues in contact with LYS 10 (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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81B MET* 3.7 27.3 + - + +
84B ALA* 6.2 1.0 - - - +
85B TYR* 3.5 49.4 - - + +
88B LYS* 5.7 1.8 - - - +
6C GLN 2.8 16.4 + - - +
7C LEU* 3.3 15.9 - - + +
9C GLN* 1.3 73.1 - - - +
11C ALA* 1.3 53.9 + - - +
13C LEU* 3.0 2.9 + - + +
14C ALA* 2.8 37.6 + - + +
22C ASP* 5.1 7.0 - - + +
26C ALA* 4.0 15.0 - - + -
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Residues in contact with ALA 11 (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 LEU 2.9 10.8 + - - +
8C VAL 3.3 10.1 - - - +
10C LYS* 1.3 75.9 - - - +
12C ARG* 1.3 56.5 + - - +
14C ALA 3.4 0.3 + - - -
15C GLU* 3.0 25.8 + - - +
23C MET* 3.4 22.8 - - + +
26C ALA* 4.0 8.5 - - + +
27C MET* 3.5 38.6 - - + -
44C LEU* 4.4 9.0 - - + -
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Residues in contact with ARG 12 (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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8C VAL* 3.0 39.8 + - - +
9C GLN* 3.2 32.0 + - - +
11C ALA* 1.3 74.7 - - - +
13C LEU* 1.3 60.9 + - - +
15C GLU* 3.6 9.5 + - - +
16C GLN* 3.1 31.8 + - - +
40C GLU* 2.5 46.6 + - - +
44C LEU* 4.4 13.5 - - + -
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Residues in contact with LEU 13 (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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63B ILE* 3.8 26.0 - - + +
66B ILE* 4.8 18.6 - - + -
81B MET* 4.3 15.7 - - + -
82B VAL* 4.9 11.2 - - + -
85B TYR* 4.5 12.8 - - + -
9C GLN 2.9 16.6 + - - +
10C LYS* 3.0 5.1 + - - +
12C ARG* 1.3 73.4 - - - +
14C ALA* 1.3 66.4 + - - +
16C GLN* 3.2 10.5 + - - +
17C ALA* 3.0 22.9 + - - +
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Residues in contact with ALA 14 (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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85B TYR* 3.7 24.3 - - + +
10C LYS* 2.8 18.2 + - + +
11C ALA 3.7 3.8 - - - +
13C LEU* 1.3 76.5 - - - +
15C GLU* 1.3 60.2 + - - +
17C ALA* 3.2 2.2 + - - +
18C GLU 3.0 4.5 + - - -
19C ARG* 2.8 46.7 + - - +
22C ASP* 4.0 3.1 - - + -
23C MET* 3.6 18.4 - - - +
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Residues in contact with GLU 15 (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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11C ALA 3.0 17.8 + - - +
12C ARG* 3.8 7.5 - - - +
13C LEU 3.2 0.2 - - - -
14C ALA* 1.3 76.1 - - - +
16C GLN* 1.3 58.8 + - + +
18C GLU* 3.0 21.8 + - - +
20C TYR* 4.0 18.0 + - + +
23C MET* 3.7 26.1 - - + +
44C LEU* 3.6 18.5 - - - +
47C VAL* 3.6 21.5 - - + +
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Residues in contact with GLN 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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62B VAL* 3.4 28.7 - - + +
66B ILE* 3.8 26.9 - - + +
12C ARG* 3.1 21.0 + - - +
13C LEU* 3.2 10.5 + - - +
15C GLU* 1.3 82.2 - - + +
17C ALA* 1.3 58.1 + - - +
18C GLU* 3.3 7.5 + - - +
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Residues in contact with ALA 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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59B SER* 2.9 43.5 + - - +
62B VAL* 4.3 9.0 - - + -
63B ILE* 3.8 22.2 - - + -
85B TYR* 4.8 0.2 - - + -
13C LEU 3.0 15.6 + - - +
14C ALA* 3.8 5.6 - - - +
15C GLU 3.2 0.4 - - - -
16C GLN* 1.3 74.6 - - - +
18C GLU* 1.3 71.0 + - - +
19C ARG* 3.8 10.3 - - - +
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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