Contacts of the helix formed by residues 27 - 35 (chain C) in PDB entry 3CMM
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 GLY 27 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23C LEU* 3.8 12.5 - - - +
26C LEU* 1.3 79.3 - - - +
28C LYS* 1.3 66.3 + - - -
29C GLU* 3.2 3.4 - - - -
30C ALA* 4.0 7.1 - - - +
31C MET* 3.5 16.6 + - - +
381C LYS* 3.8 16.7 - - - +
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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
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124A GLN* 6.1 2.8 - - - +
12C GLY 4.9 5.6 - - - -
14C ILE* 4.4 32.7 - - + +
23C LEU* 4.1 14.7 - - + +
27C GLY* 1.3 71.6 - - - -
29C GLU* 1.3 70.0 + - + +
31C MET* 3.2 3.4 + - - +
32C LEU* 3.0 46.4 + - + +
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Residues in contact with GLU 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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33A LYS* 3.0 35.0 + - + +
174A LEU* 5.5 4.0 - - - +
27C GLY* 3.2 1.6 - - - -
28C LYS* 1.3 86.9 - - + +
30C ALA* 1.3 60.2 + - - +
32C LEU* 3.5 11.4 + - + +
33C LYS* 3.2 42.2 + - - +
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Residues in contact with ALA 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 LEU* 4.0 25.4 - - + -
27C GLY* 3.7 8.7 + - - +
28C LYS 3.3 0.4 - - - -
29C GLU* 1.3 78.1 - - - +
31C MET* 1.3 58.3 + - - +
33C LYS* 3.2 5.6 + - - +
34C MET* 2.8 31.9 + - - +
379C SER* 3.7 26.1 - - - +
381C LYS* 4.0 18.2 - - + -
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Residues in contact with MET 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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14C ILE* 4.5 12.6 - - + -
19C TYR* 3.5 37.2 - - + -
22C GLN* 3.3 30.3 - - - +
23C LEU* 3.4 36.3 - - + -
26C LEU* 4.2 9.9 - - + -
27C GLY 3.5 11.1 + - - +
28C LYS 3.2 4.9 + - - +
30C ALA* 1.3 76.6 - - - +
32C LEU* 1.3 66.6 + - - +
34C MET* 3.5 20.2 + - + +
35C GLN* 3.1 36.0 + - - +
58C ALA 3.9 5.6 - - - +
59C GLY 4.9 1.1 - - - +
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Residues in contact with LEU 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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33A LYS* 6.5 1.1 - - + -
36A THR* 4.7 17.0 - - + +
11C ALA 3.8 9.2 - - - +
12C GLY* 3.7 37.9 - - - +
14C ILE* 4.6 8.3 - - + -
28C LYS* 3.0 43.0 + - + +
29C GLU* 3.8 10.8 - - + +
31C MET* 1.3 75.8 - - - +
33C LYS* 1.3 66.3 + - + +
35C GLN* 3.4 17.6 + - - +
36C THR* 3.3 20.4 + - - +
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Residues in contact with LYS 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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29A GLU* 4.0 20.9 - - - +
32A LEU* 5.4 9.2 - - + -
33A LYS* 6.2 2.0 - - - +
29C GLU* 3.2 34.9 + - - +
30C ALA* 3.2 6.9 + - - +
32C LEU* 1.3 75.3 - - - +
34C MET* 1.3 57.7 + - - +
36C THR* 2.8 34.2 + - - +
37C SER* 3.4 8.1 + - - -
174C LEU* 3.9 25.0 - - + +
378C CYS 3.4 18.3 - - - +
379C SER* 3.3 24.0 + - - +
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Residues in contact with MET 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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22C GLN* 4.1 0.2 - - - +
26C LEU* 3.7 28.3 - - + -
30C ALA 2.8 20.8 + - - +
31C MET* 3.7 22.7 - - + +
32C LEU 3.3 0.2 - - - -
33C LYS* 1.3 75.7 - - - +
35C GLN* 1.3 56.0 + - - +
36C THR 3.2 0.4 - - - -
37C SER* 3.3 18.4 + - - -
58C ALA* 3.3 35.4 - - + +
59C GLY 3.6 10.8 - - - +
60C VAL* 3.1 23.4 - - + +
61C LYS 3.2 4.5 + - - -
375C LEU* 4.2 25.8 - - + +
378C CYS* 3.8 21.3 - - + -
379C SER* 4.4 3.4 - - - -
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Residues in contact with GLN 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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11C ALA* 3.9 15.9 - - - +
13C GLU 3.7 24.3 + - - +
14C ILE* 4.8 7.5 - - - +
19C TYR* 4.5 22.4 + - - -
31C MET* 3.1 24.1 + - - +
32C LEU* 3.8 15.1 - - - +
33C LYS 3.1 0.6 + - - -
34C MET* 1.3 75.4 - - - +
36C THR* 1.3 60.4 + - + +
37C SER 3.4 2.5 - - - -
59C GLY 4.0 14.9 + - - +
60C VAL 5.0 2.5 - - - +
61C LYS* 3.0 29.0 - - - +
105C TYR* 6.3 0.4 - - - +
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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