Contacts of the helix formed by residues 22 - 35 (chain L) in PDB entry 2C7N
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 22 (chain L).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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20L SER 3.2 3.1 + - - +
21L ASP* 1.3 75.7 - - - +
23L ILE* 1.3 64.2 + - - +
24L GLU* 3.3 9.9 + - - +
25L ASN* 2.8 52.2 + - - +
26L VAL* 3.2 13.5 + - - +
52L ASP 3.7 8.3 - - - -
53L GLY* 4.9 9.2 - - - +
54L ARG 3.2 13.9 - - - +
55L THR* 4.1 11.0 - - + +
56L LEU 5.1 0.4 - - - -
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Residues in contact with ILE 23 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22L THR* 1.3 71.2 - - - +
24L GLU* 1.3 55.5 + - - +
26L VAL* 3.2 8.5 + - - +
27L LYS* 2.9 43.3 + - + +
43L LEU* 4.5 5.8 - - + +
50L LEU* 3.4 30.5 - - + +
51L GLU 3.4 13.2 - - - +
52L ASP* 3.2 31.6 + - - +
54L ARG 2.8 26.1 + - - +
55L THR 4.1 5.8 - - - +
56L LEU* 4.6 6.5 - - + +
59L TYR* 3.1 39.5 - - + -
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Residues in contact with GLU 24 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22L THR* 3.2 8.5 + - - +
23L ILE* 1.3 74.2 - - - +
25L ASN* 1.3 61.6 + - - +
27L LYS* 3.9 6.9 - - + +
28L ALA* 3.0 29.3 + - + +
38L PRO* 5.5 6.3 - - + +
52L ASP* 3.1 37.1 + - + +
53L GLY* 5.9 0.9 - - - -
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Residues in contact with ASN 25 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20L SER 4.9 0.6 + - - -
21L ASP* 3.8 20.0 + - + +
22L THR* 2.8 52.4 + - - +
24L GLU* 1.3 75.4 - - - +
26L VAL* 1.3 58.7 + - - +
28L ALA* 3.5 7.0 - - - +
29L LYS* 3.1 34.1 + - - +
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Residues in contact with VAL 26 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3L ILE* 5.4 1.6 - - + -
5L VAL* 5.2 0.7 - - + -
15L LEU* 3.8 22.4 - - + -
17L VAL* 4.4 8.7 - - + -
21L ASP* 4.2 8.5 - - + +
22L THR 3.4 13.7 - - - +
23L ILE* 3.2 9.5 + - - +
25L ASN* 1.3 73.8 - - - +
27L LYS* 1.3 59.1 + - - +
28L ALA 3.1 1.3 - - - -
29L LYS* 3.0 11.1 + - - +
30L ILE* 2.9 30.0 + - + +
43L LEU* 3.9 20.0 - - + -
56L LEU* 4.0 34.5 - - + -
67L LEU* 5.0 10.1 - - + -
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Residues in contact with LYS 27 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23L ILE* 2.9 32.0 + - - +
24L GLU* 3.9 6.3 - - - +
26L VAL* 1.3 71.8 - - - +
28L ALA* 1.3 60.8 + - - +
30L ILE* 3.6 2.1 + - - -
31L GLN 3.3 7.6 + - - -
38L PRO* 3.6 35.5 + - + +
41L GLN* 3.1 66.9 + - + +
42L ARG* 4.7 2.0 - - - +
43L LEU* 3.7 26.7 - - + +
50L LEU 4.5 6.7 + - - -
52L ASP* 2.9 30.6 + - - +
72L ARG* 4.9 6.1 - - - +
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Residues in contact with ALA 28 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24L GLU* 3.0 19.1 + - + +
25L ASN* 3.5 8.5 - - - +
26L VAL 3.1 0.2 - - - -
27L LYS* 1.3 75.4 - - - +
29L LYS* 1.3 60.2 + - + +
31L GLN* 3.0 22.2 + - - +
32L ASP* 2.9 20.4 + - - +
38L PRO* 4.4 13.2 - - + +
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Residues in contact with LYS 29 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15L LEU* 3.8 15.8 - - + +
16L GLU 3.4 25.9 + - - +
17L VAL* 3.9 13.8 - - + +
21L ASP* 3.1 32.5 + - - -
25L ASN* 3.1 21.5 + - - +
26L VAL* 3.0 11.3 + - - +
28L ALA* 1.3 75.6 - - - +
30L ILE* 1.3 59.9 + - - +
32L ASP* 3.3 15.4 + - - +
33L LYS* 3.3 27.4 + - - +
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Residues in contact with ILE 30 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5L VAL* 4.2 19.5 - - + -
13L ILE* 4.5 10.5 - - + -
15L LEU* 4.0 18.8 - - + -
26L VAL* 2.9 18.7 + - + +
27L LYS* 3.6 4.3 - - - +
29L LYS* 1.3 74.3 - - - +
31L GLN* 1.3 54.8 + - - +
33L LYS* 3.4 2.2 + - - -
34L GLU* 2.7 37.5 + - + +
36L ILE* 4.2 20.6 + - + -
41L GLN* 3.2 33.4 - - - +
43L LEU* 3.8 27.4 - - + -
69L LEU* 4.4 8.3 - - + -
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Residues in contact with GLN 31 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27L LYS 3.3 8.9 + - - +
28L ALA* 3.0 13.6 + - - +
30L ILE* 1.3 78.6 - - - +
32L ASP* 1.3 59.1 + - - +
35L GLY* 2.8 32.0 + - - +
36L ILE 3.2 21.7 + - - +
37L PRO* 4.1 10.5 - - - +
38L PRO* 3.4 29.2 - - + +
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Residues in contact with ASP 32 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28L ALA* 2.9 20.9 + - - +
29L LYS* 3.3 20.2 + - - +
30L ILE 3.2 0.4 - - - -
31L GLN* 1.3 78.9 - - - +
33L LYS* 1.3 61.8 + - + +
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Residues in contact with LYS 33 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13L ILE* 4.3 17.2 - - + +
14L THR* 3.2 39.0 + - - +
15L LEU* 4.1 11.0 - - + -
29L LYS 3.3 15.6 + - - +
30L ILE 4.2 1.8 - - - +
32L ASP* 1.3 82.7 - - + +
34L GLU* 1.3 68.0 + - + +
35L GLY 3.8 0.2 - - - -
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Residues in contact with GLU 34 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7L THR* 6.0 0.4 - - - -
11L LYS* 3.6 30.9 + - - +
13L ILE* 3.6 48.9 - - + +
30L ILE 2.7 20.0 + - - +
33L LYS* 1.3 82.7 - - - +
35L GLY* 1.3 59.4 + - - +
36L ILE* 3.2 25.5 + - + +
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Residues in contact with GLY 35 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31L GLN* 2.8 26.6 + - - +
32L ASP 4.9 0.2 - - - -
33L LYS 3.8 0.6 - - - -
34L GLU* 1.3 77.6 - - - +
36L ILE* 1.3 61.9 + - - +
37L PRO* 3.5 9.0 - - - +
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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