Contacts of the helix formed by residues 55 - 69 (chain B) in PDB entry 3C0H
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 SER 55 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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48B PHE* 3.5 18.4 - - - -
49B THR* 3.8 11.5 - - - +
53B GLY 5.5 0.7 - - - -
54B LEU* 1.3 75.3 - - - +
56B THR* 1.3 74.9 + - - +
57B GLU* 3.0 24.9 + - - +
58B ASP* 3.0 22.5 + - - -
59B LEU* 3.7 0.9 + - - +
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Residues in contact with THR 56 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45B VAL* 5.9 3.8 - - + -
49B THR* 3.8 20.6 - - + +
55B SER* 1.3 76.1 + - - +
57B GLU* 1.3 62.5 + - - +
59B LEU* 3.2 11.2 + - + +
60B LYS* 3.0 39.9 + - + +
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Residues in contact with GLU 57 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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55B SER* 3.0 15.2 + - - +
56B THR* 1.3 82.7 - - - +
58B ASP* 1.3 60.4 + - - +
60B LYS* 3.3 16.5 - - - +
61B ARG* 2.8 28.8 + - - +
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Residues in contact with ASP 58 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48B PHE* 4.1 15.1 - - + -
53B GLY 3.8 6.9 - - - +
54B LEU* 3.5 15.4 - - + +
55B SER* 3.0 32.3 + - - +
56B THR 3.2 0.8 - - - -
57B GLU* 1.3 77.5 - - - +
59B LEU* 1.3 63.9 - - - +
61B ARG* 3.3 36.5 + - - +
62B GLU* 3.2 20.1 + - - +
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Residues in contact with LEU 59 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43B VAL* 4.1 14.6 - - + -
45B VAL* 3.8 40.2 - - + -
48B PHE* 3.6 48.2 - - + -
49B THR* 4.5 4.5 - - + -
55B SER 3.7 2.8 + - - +
56B THR* 3.2 12.6 + - + +
58B ASP* 1.3 75.8 - - - +
60B LYS* 1.3 60.7 + - - +
62B GLU* 3.5 15.9 + - - +
63B ALA* 3.0 29.8 + - - +
87B LEU* 4.6 21.2 - - + +
89B MET* 6.0 0.2 - - - +
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Residues in contact with LYS 60 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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56B THR* 3.0 30.7 + - + +
57B GLU* 3.3 25.5 + - - +
59B LEU* 1.3 75.3 - - - +
61B ARG* 1.3 60.5 - - - +
63B ALA* 3.5 6.5 + - - +
64B SER* 3.1 27.1 + - - -
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Residues in contact with ARG 61 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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57B GLU 2.8 16.2 + - - +
58B ASP* 3.3 44.5 + - - +
60B LYS* 1.3 74.0 - - - +
62B GLU* 1.3 61.8 + - - +
64B SER* 3.4 6.2 + - - +
65B ILE* 2.9 44.7 + - + +
140B ARG* 4.9 7.8 - - - +
163B PHE 5.2 0.2 + - - -
164B GLY 2.9 28.7 + - - -
165B VAL* 3.7 14.2 - - - +
166B ALA 3.1 22.0 + - - -
167B ILE* 4.3 21.0 - - - +
168B GLN* 5.6 1.1 - - + +
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Residues in contact with GLU 62 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41B LYS* 3.0 29.0 + - - +
43B VAL* 5.5 1.7 - - - +
48B PHE* 5.8 1.9 - - - -
58B ASP 3.2 13.2 + - - +
59B LEU* 4.0 16.9 - - - +
60B LYS 3.4 0.2 - - - -
61B ARG* 1.3 78.4 - - - +
63B ALA* 1.3 67.6 + - - +
65B ILE* 4.6 4.7 - - - -
66B CYS* 3.0 46.6 + - - -
87B LEU* 6.0 0.3 - - - +
89B MET* 3.7 24.0 - - + +
91B PHE* 5.2 1.9 - - - -
163B PHE 3.8 13.8 + - - +
164B GLY* 3.7 25.5 + - - +
166B ALA 5.8 0.2 - - - -
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Residues in contact with ALA 63 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59B LEU 3.0 19.1 + - - +
60B LYS* 3.6 7.9 - - - +
62B GLU* 1.3 77.1 - - - +
64B SER* 1.3 56.9 + - - +
67B HIS* 3.0 28.3 + - - +
77B LEU* 3.9 6.6 - - - +
80B THR* 5.5 8.7 - - + +
87B LEU* 5.6 7.6 - - + -
89B MET* 4.5 14.9 - - + +
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Residues in contact with SER 64 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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60B LYS 3.1 13.6 + - - -
61B ARG* 3.5 9.7 + - - +
62B GLU 3.3 0.2 - - - -
63B ALA* 1.3 75.2 - - - +
65B ILE* 1.3 69.6 + - - +
67B HIS* 3.6 9.8 + - - +
68B MET* 3.2 23.4 + - - +
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Residues in contact with ILE 65 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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61B ARG* 2.9 36.5 + - + +
62B GLU* 3.9 4.5 - - - +
64B SER* 1.3 78.0 + - - +
66B CYS* 1.3 63.9 + - - +
68B MET* 3.0 21.1 + - - +
69B LEU* 3.1 31.8 + - + +
137B ILE* 3.9 23.6 - - + -
163B PHE* 4.8 4.3 - - + +
166B ALA* 4.0 31.9 - - + +
167B ILE* 4.2 1.3 - - - -
168B GLN* 3.9 32.3 - - + +
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Residues in contact with CYS 66 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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62B GLU* 3.0 40.6 + - - +
65B ILE* 1.3 78.1 - - - +
67B HIS* 1.3 62.0 + - - +
69B LEU* 3.6 21.2 + - - +
70B LYS* 4.7 0.7 + - - -
77B LEU* 3.6 36.0 + - + +
89B MET* 4.6 4.7 - - + -
91B PHE* 4.6 12.1 - - + -
163B PHE* 3.8 30.7 - - - -
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Residues in contact with HIS 67 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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63B ALA 3.0 20.3 + - - +
64B SER* 3.8 10.1 - - - +
65B ILE 3.2 0.2 - - - -
66B CYS* 1.3 77.1 - - - +
68B MET* 1.3 62.8 + - + +
70B LYS* 3.2 34.1 + - - +
77B LEU* 3.7 14.8 + - + +
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Residues in contact with MET 68 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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64B SER 3.2 10.7 + - - +
65B ILE* 3.0 19.7 + - - +
67B HIS* 1.3 85.8 - - + +
69B LEU* 1.3 63.2 + - + +
70B LYS* 3.0 15.0 + - - +
131B TYR* 3.3 16.8 + - - +
135B ASN* 3.7 34.5 - - + +
137B ILE* 3.5 27.4 - - + -
168B GLN* 5.2 4.9 - - - +
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Residues in contact with LEU 69 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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65B ILE* 3.1 28.3 + - + +
66B CYS* 3.6 13.3 + - - +
67B HIS 3.4 1.8 - - - -
68B MET* 1.3 80.4 - - + +
70B LYS* 1.3 65.7 + - - +
71B HIS 3.9 2.1 + - - -
74B ILE* 4.2 19.6 - - + +
75B VAL 5.0 0.5 - - - +
76B GLU* 4.9 8.5 - - - +
131B TYR* 3.7 21.1 - - + -
132B CYS* 4.2 18.2 - - - -
135B ASN* 5.4 1.6 - - + -
137B ILE* 4.0 22.0 - - + -
163B PHE* 3.5 44.9 - - + -
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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