Contacts of the helix formed by residues 23 - 36 (chain C) in PDB entry 3DCG
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 23 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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21C SER 4.7 4.7 - - - +
22C SER* 1.3 80.7 - - - +
24C VAL* 1.3 64.4 + - - +
25C PHE* 3.6 6.6 + - - +
26C GLU* 3.2 46.4 + - - +
27C LEU* 3.7 3.3 + - - +
53C ASP 3.6 11.7 - - - +
54C GLY* 4.0 17.5 - - - +
55C LYS 3.2 8.1 - - - +
56C THR* 4.1 4.9 - - + +
57C LEU* 4.1 5.9 - - - +
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Residues in contact with VAL 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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23C THR* 1.3 70.0 - - - +
25C PHE* 1.3 65.2 + - - +
27C LEU* 3.1 16.2 + - - +
28C LYS* 3.2 9.9 + - - +
44C LEU* 3.8 21.2 - - + +
51C LEU* 3.9 24.0 - - + +
52C ASP 3.2 25.8 - - - +
53C ASP* 3.5 19.9 + - - +
55C LYS 2.9 11.7 + - - +
57C LEU* 4.1 16.4 - - + +
60C CYS* 3.8 25.6 - - - -
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Residues in contact with PHE 25 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23C THR* 3.2 6.9 - - - +
24C VAL* 1.3 77.2 - - - +
26C GLU* 1.3 63.3 + - + +
28C LYS* 3.1 9.8 + - + +
29C ARG* 3.1 59.0 + - + +
39C PRO* 3.6 25.4 - - + -
53C ASP* 3.2 43.0 + - + +
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Residues in contact with GLU 26 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21C SER 4.8 1.2 - - - +
22C SER* 3.3 25.3 + - - -
23C THR* 3.2 38.5 + - - +
24C VAL 3.2 0.4 - - - -
25C PHE* 1.3 80.2 - - + +
27C LEU* 1.3 60.9 + - + +
29C ARG* 3.1 11.5 + - - +
30C ILE* 3.1 29.6 + - + +
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Residues in contact with LEU 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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5C LEU* 3.6 32.1 - - + -
7C ILE* 4.4 13.8 - - + +
16C THR* 4.7 2.2 - - + -
18C ALA* 4.1 13.5 - - + -
23C THR 3.7 1.5 + - - +
24C VAL* 3.1 10.1 + - - +
26C GLU* 1.3 78.9 - - + +
28C LYS* 1.3 56.3 + - - +
30C ILE* 3.3 17.3 + - + +
31C VAL* 3.0 30.8 + - - +
44C LEU* 3.7 18.6 - - + -
51C LEU* 5.7 1.8 - - + -
57C LEU* 3.7 37.9 - - + -
62C PHE* 5.7 0.7 - - + -
75C VAL* 4.1 19.1 - - + -
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Residues in contact with LYS 28 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24C VAL* 3.2 6.2 + - - +
25C PHE* 3.1 11.9 + - + +
27C LEU* 1.3 76.4 - - - +
29C ARG* 1.3 58.7 + - - +
31C VAL 3.4 0.5 + - - -
32C GLU* 3.0 24.3 + - - +
39C PRO* 3.4 36.2 + - + +
40C ASP* 5.6 0.8 - - - +
42C GLN* 3.2 59.2 + - + +
43C ARG* 4.8 1.4 - - - +
44C LEU* 3.7 26.5 - - + +
51C LEU 5.3 2.9 + - - -
53C ASP* 2.7 40.7 + - - +
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Residues in contact with ARG 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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25C PHE* 3.1 47.4 + - + +
26C GLU* 3.1 11.4 + - - +
28C LYS* 1.3 75.2 - - - +
30C ILE* 1.3 64.2 + - + +
32C GLU* 2.6 44.2 + - - +
33C GLY* 3.1 18.5 + - - -
39C PRO* 4.0 13.3 - - + +
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Residues in contact with ILE 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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7C ILE* 4.8 3.8 - - + -
14C ILE* 5.0 0.9 - - + -
16C THR* 3.7 34.3 - - + +
17C ASP 4.1 13.9 - - - +
18C ALA* 5.0 3.1 - - + -
26C GLU* 3.1 20.1 + - + +
27C LEU* 3.5 26.0 - - + +
28C LYS 3.3 0.2 - - - -
29C ARG* 1.3 72.8 - - + +
31C VAL* 1.3 65.5 + - - +
33C GLY* 3.2 10.1 + - - -
34C ILE* 3.4 30.9 - - + +
18D TYR* 4.4 4.5 - - + +
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Residues in contact with VAL 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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7C ILE* 3.9 34.3 - - + -
14C ILE* 4.3 11.4 - - + -
27C LEU 3.0 18.6 + - - +
28C LYS 3.6 1.3 - - - +
29C ARG 3.4 0.2 - - - -
30C ILE* 1.3 75.2 - - - +
32C GLU* 1.3 54.7 + - - +
34C ILE* 3.1 2.5 + - - +
35C LEU* 2.6 59.1 + - + +
37C ARG 4.9 0.4 - - - +
42C GLN* 3.3 33.9 - - - +
44C LEU* 5.0 3.1 - - + -
77C LEU* 4.0 12.1 - - + -
79C PHE* 4.4 3.1 - - + -
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Residues in contact with GLU 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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28C LYS 3.0 16.1 + - - +
29C ARG* 2.6 42.7 + - - +
30C ILE 3.3 0.4 - - - -
31C VAL* 1.3 76.8 - - - +
33C GLY* 1.3 58.5 + - - +
36C LYS* 2.9 35.1 + - + +
37C ARG 3.2 29.2 - - - +
38C PRO* 3.8 12.4 - - + +
39C PRO* 3.3 14.8 - - + +
42C GLN* 4.2 0.2 - - - +
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Residues in contact with GLY 33 (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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29C ARG 3.1 14.0 + - - -
30C ILE 3.2 5.0 + - - -
32C GLU* 1.3 76.1 - - - +
34C ILE* 1.3 61.0 + - - +
36C LYS* 2.9 22.7 + - - -
17D MET* 6.5 1.3 - - - -
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Residues in contact with ILE 34 (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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14C ILE* 3.7 31.9 - - + -
30C ILE* 3.4 23.1 - - + +
31C VAL 3.1 4.1 + - - +
33C GLY* 1.3 82.7 - - - +
35C LEU* 1.3 70.6 + - + +
36C LYS* 3.5 8.6 + - - +
17D MET* 5.9 1.6 - - + -
18D TYR* 3.8 40.2 - - + -
30D ILE* 3.8 35.4 - - + -
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Residues in contact with LEU 35 (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 ARG* 5.7 1.1 - - + +
12C THR* 4.7 12.3 - - + -
14C ILE* 3.9 16.8 - - + -
31C VAL* 2.6 27.6 + - + +
34C ILE* 1.3 86.7 - - + +
36C LYS* 1.3 67.7 + - - +
37C ARG* 3.2 9.2 + - - +
77C LEU* 3.8 17.5 - - + -
79C PHE* 3.7 33.0 - - + -
30D ILE* 4.5 14.8 - - + -
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Residues in contact with LYS 36 (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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32C GLU* 2.9 23.2 + - + +
33C GLY* 2.9 25.9 + - - -
34C ILE* 4.2 7.3 + - - +
35C LEU* 1.3 80.8 - - - +
37C ARG* 1.3 64.7 + - - +
38C PRO* 4.1 4.7 - - - +
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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