Contacts of the helix formed by residues 56 - 71 (chain B) in PDB entry 3C2B
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 56 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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51B TYR* 5.0 11.0 - - - -
55B GLY* 1.3 76.4 - - - +
57B ARG* 1.3 64.5 + - - +
58B ASP* 3.2 15.5 + - - +
59B GLY* 3.0 19.9 + - - -
60B LEU* 3.3 18.9 + - - +
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Residues in contact with ARG 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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31B GLU* 4.1 26.7 + - - +
34B LEU* 2.2 57.2 + - - +
35B THR* 3.7 10.5 - - - +
36B THR 4.9 0.8 - - - +
51B TYR* 6.0 0.2 - - - -
56B ASP* 1.3 76.8 - - + +
58B ASP* 1.3 66.6 + - - +
60B LEU* 3.3 17.4 + - - +
61B LEU* 3.1 47.4 + - + +
113B LEU* 5.4 2.6 - - - +
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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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56B ASP* 3.2 14.5 + - - +
57B ARG* 1.3 86.2 - - - +
59B GLY* 1.3 56.5 + - - +
61B LEU* 3.9 8.8 - - - +
62B ALA* 2.9 29.8 + - - +
124B LYS* 3.6 48.8 + - - +
128B LEU* 4.0 6.0 - - + +
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Residues in contact with GLY 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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54B PHE* 3.0 26.8 - - - +
56B ASP* 3.0 13.1 + - - -
58B ASP* 1.3 73.9 - - - +
60B LEU* 1.3 59.9 + - - +
62B ALA* 3.6 7.0 - - - +
63B ALA* 2.9 29.3 + - - +
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Residues in contact with LEU 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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19B LEU* 3.9 15.3 - - + -
22B ALA* 4.5 0.4 - - + -
34B LEU* 4.7 11.2 - - + -
35B THR 5.8 1.3 - - - +
36B THR* 5.7 7.4 - - - +
39B LEU* 3.9 30.5 - - + -
50B LEU* 6.5 0.9 - - + -
54B PHE* 3.7 34.5 + - + -
56B ASP 3.3 11.4 + - - +
57B ARG* 3.3 23.5 + - - +
58B ASP 3.2 0.2 - - - -
59B GLY* 1.3 74.3 - - - +
61B LEU* 1.3 57.8 + - + +
63B ALA* 3.2 1.2 + - - +
64B MSE 2.7 55.3 + - + +
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Residues in contact with LEU 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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34B LEU* 3.6 31.4 - - + -
57B ARG* 3.1 38.4 + - + +
58B ASP* 3.9 9.9 - - - +
60B LEU* 1.3 75.9 - - + +
62B ALA* 1.3 65.4 + - - +
64B MSE 3.2 17.7 + - + +
65B ILE* 3.0 25.6 + - - +
110B LEU* 5.8 3.4 - - + -
113B LEU* 5.7 2.2 - - + -
117B GLN* 5.9 0.7 - - - +
124B LYS* 5.8 1.8 - - + -
125B LEU* 4.2 38.4 - - + +
128B LEU* 3.9 14.6 - - + -
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Residues in contact with ALA 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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58B ASP 2.9 18.9 + - - +
59B GLY* 3.6 9.2 - - - +
61B LEU* 1.3 74.6 - - - +
63B ALA* 1.3 57.1 + - - +
65B ILE* 3.0 6.6 + - - +
66B THR 3.0 16.1 + - - -
128B LEU* 3.7 19.5 - - + +
132B ARG* 2.4 40.4 + - - +
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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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11B PHE* 3.6 28.7 - - + -
19B LEU* 3.8 16.9 - - + +
54B PHE* 3.9 13.0 - - + -
59B GLY 2.9 20.9 + - - +
60B LEU 3.2 4.0 + - - +
62B ALA* 1.3 71.2 - - - +
64B MSE 1.3 53.7 + - - +
66B THR* 3.2 7.2 + - - -
67B PHE* 2.6 37.8 + - - +
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Residues in contact with MSE 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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19B LEU* 3.9 17.4 - - + +
22B ALA* 3.7 44.0 - - + +
23B LEU* 3.5 35.2 - - + +
26B LEU* 4.5 11.0 - - + -
34B LEU* 4.0 18.4 - - + -
60B LEU* 2.7 24.1 + - + +
61B LEU* 3.3 31.4 - - + +
63B ALA* 1.3 73.0 - - - +
65B ILE* 1.3 58.9 + - + +
67B PHE* 3.4 4.2 + - - +
68B GLN* 2.9 29.6 + - - +
110B LEU* 4.7 6.3 - - + -
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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 LEU 3.0 15.6 + - - +
62B ALA* 3.0 6.9 + - - +
64B MSE 1.3 73.1 - - + +
66B THR* 1.3 64.8 + - - +
68B GLN* 3.3 6.8 + - - +
69B GLN* 3.0 25.5 + - - +
110B LEU* 4.7 16.2 - - + -
125B LEU* 3.9 13.0 - - + -
128B LEU* 3.7 31.9 - - + -
129B LEU* 3.9 24.5 - - + -
132B ARG* 3.8 34.8 - - + +
133B GLY* 4.0 13.9 - - - -
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Residues in contact with THR 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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11B PHE* 3.5 21.6 - - + -
62B ALA 3.0 7.2 + - - +
63B ALA* 4.2 3.1 - - - +
65B ILE* 1.3 71.8 - - - +
67B PHE* 1.3 68.1 + - - +
69B GLN* 3.0 28.0 + - - +
70B SER* 3.1 9.2 + - - -
132B ARG* 2.8 46.0 - - + +
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Residues in contact with PHE 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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11B PHE* 4.9 3.8 - + + -
16B ASN* 3.3 53.8 - - + -
19B LEU* 3.8 24.5 - - + -
20B ASP* 3.7 29.6 - - + -
23B LEU* 3.5 24.7 - - + -
63B ALA 2.6 21.0 + - - +
64B MSE 3.6 2.7 - - - +
66B THR* 1.3 74.2 + - - +
68B GLN* 1.3 63.1 + - - +
70B SER* 2.9 34.1 + - - -
71B LYS* 3.9 25.3 + - + +
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Residues in contact with GLN 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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23B LEU* 3.3 15.9 - - + +
64B MSE 2.9 17.8 + - - +
65B ILE* 3.3 6.9 + - - +
67B PHE* 1.3 76.2 - - - +
69B GLN* 1.4 65.3 + - - +
71B LYS* 2.7 55.7 + - - +
72B VAL* 4.3 5.7 + - - +
106B VAL* 3.5 35.4 - - + +
107B SER* 5.3 1.7 - - - +
110B LEU* 4.7 7.0 - - + -
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Residues in contact with GLN 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* 3.0 25.6 + - - +
66B THR* 3.0 18.2 + - - +
68B GLN* 1.4 75.3 - - - +
70B SER* 1.3 66.1 + - - +
71B LYS 3.0 2.5 - - - -
72B VAL* 2.9 32.1 + - - +
132B ARG* 3.5 19.7 + - + +
133B GLY 3.3 20.1 + - - +
134B ARG* 3.8 2.6 - - - -
135B ARG* 3.2 25.8 + - + -
136B GLN* 3.3 36.0 + - + +
137B ILE 4.8 0.3 + - - -
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Residues in contact with SER 70 (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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11B PHE* 5.9 1.7 - - - -
16B ASN* 5.3 3.5 + - - -
66B THR 3.1 8.2 + - - -
67B PHE* 2.9 31.2 + - - -
69B GLN* 1.3 78.1 - - - +
71B LYS* 1.3 60.0 + - - -
72B VAL 3.5 4.2 + - - -
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Residues in contact with LYS 71 (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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20B ASP* 4.5 9.9 + - - -
23B LEU* 4.4 6.5 - - - +
67B PHE* 4.1 27.8 - - + +
68B GLN* 2.7 48.5 + - - +
69B GLN 2.9 2.0 + - - -
70B SER* 1.3 76.5 - - - +
72B VAL* 1.3 65.8 + - + +
106B VAL* 4.5 7.9 - - - +
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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