Contacts of the helix formed by residues 59 - 73 (chain B) in PDB entry 3CWR
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 59 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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39B MSE 3.5 16.0 - - - +
57B ALA* 3.4 1.7 - - - +
58B SER* 1.3 82.3 - - - +
60B ARG* 1.3 66.3 + - - -
61B ALA 3.2 3.6 - - - -
62B ASP* 3.1 15.5 + - - +
63B LEU* 3.2 13.2 + - - +
209B EDO 3.3 17.5 - - - -
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Residues in contact with ARG 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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34B ALA* 3.1 34.1 + - - +
35B ALA* 4.4 4.2 - - - +
37B MSE 3.0 39.2 - - + +
38B THR* 4.3 13.1 - - - +
39B MSE 4.0 4.7 - - + -
59B GLY* 1.3 68.8 - - - -
61B ALA* 1.3 66.7 + - - +
63B LEU* 3.0 19.9 + - + +
64B ILE* 3.0 16.3 + - - +
119B LEU* 4.8 4.4 - - - +
122B ARG* 3.8 27.3 - - - +
123B PHE* 3.6 22.1 - - + -
209B EDO 3.1 37.6 + - - +
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Residues in contact with ALA 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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59B GLY 3.2 1.0 - - - -
60B ARG* 1.3 76.4 - - - +
62B ASP* 1.3 66.8 + - - +
64B ILE* 3.2 4.0 + - - +
65B GLY 3.0 17.5 + - - -
122B ARG 3.5 24.5 - - - +
123B PHE* 3.8 14.5 - - + -
126B ALA* 3.1 23.2 - - + +
209B EDO 5.2 2.2 + - - -
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Residues in contact with ASP 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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56B PHE 4.7 3.1 - - - +
57B ALA* 3.6 19.2 - - + -
58B SER* 2.8 31.7 + - - -
59B GLY 3.1 11.6 + - - +
61B ALA* 1.3 82.9 - - - +
63B LEU* 1.3 62.2 + - - +
65B GLY* 3.2 2.8 + - - +
66B LEU* 3.0 26.0 + - + +
126B ALA* 5.0 2.9 - - - +
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Residues in contact with LEU 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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21B ILE* 3.8 26.5 - - + -
22B VAL* 5.7 0.2 - - - +
25B ALA* 4.7 8.4 - - + +
37B MSE 4.0 29.4 - - + +
38B THR 4.5 1.8 - - - +
39B MSE 3.7 19.7 - - - -
42B VAL* 3.6 34.3 - - + -
53B LEU* 4.3 4.5 - - + -
57B ALA* 3.7 19.3 - - + -
59B GLY 3.2 10.6 + - - +
60B ARG* 3.0 12.6 + - + +
62B ASP* 1.3 76.8 - - - +
64B ILE* 1.3 62.0 + - - +
66B LEU* 3.2 6.3 + - + +
67B LEU* 2.9 24.5 + - - +
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Residues in contact with ILE 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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29B LEU* 4.2 10.1 - - + -
37B MSE 3.8 26.0 - - + -
60B ARG 3.0 16.2 + - - +
61B ALA* 3.2 8.3 + - - +
63B LEU* 1.3 76.6 - - - +
65B GLY* 1.3 61.7 + - - +
67B LEU* 3.2 6.5 + - + +
68B VAL* 2.9 31.5 + - + +
109B LEU* 4.1 28.7 - - + -
113B LEU* 5.7 0.2 - - + -
123B PHE* 3.7 33.0 - - + -
127B TYR* 4.0 31.2 - - + +
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Residues in contact with GLY 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 ALA 3.0 13.8 + - - -
62B ASP* 3.2 4.4 + - - -
64B ILE* 1.3 75.8 - - - +
66B LEU* 1.3 57.9 + - - +
69B GLU* 2.9 31.8 + - - +
126B ALA* 3.9 10.3 - - - +
130B ASN* 3.5 29.3 - - - +
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Residues in contact with LEU 66 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18B ARG* 4.1 31.6 - - + +
21B ILE* 4.0 26.5 - - + -
22B VAL* 3.7 14.1 - - + +
56B PHE* 3.7 32.5 - - + +
57B ALA* 4.2 9.0 - - + -
62B ASP 3.0 17.8 + - - +
63B LEU* 3.6 9.4 - - + +
65B GLY* 1.3 75.6 - - - +
67B LEU* 1.3 62.2 + - - +
69B GLU* 3.7 22.0 - - - +
70B SER* 3.0 23.2 + - - -
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Residues in contact with LEU 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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22B VAL* 3.7 33.4 - - + +
25B ALA* 5.0 6.5 - - + -
26B GLN* 3.6 33.4 - - + +
29B LEU* 3.6 31.9 - - + -
37B MSE 5.4 0.2 - - - -
63B LEU 2.9 16.5 + - - +
64B ILE* 3.5 7.6 - - + +
66B LEU* 1.3 78.3 - - - +
68B VAL* 1.3 63.1 + - - +
70B SER* 2.6 23.2 + - - -
71B TRP* 3.4 31.5 + - + +
109B LEU* 4.6 6.5 - - + -
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Residues in contact with VAL 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 ILE* 2.9 22.1 + - + +
65B GLY* 4.2 2.2 - - - +
67B LEU* 1.3 74.8 - - - +
69B GLU* 1.3 63.4 + - - +
71B TRP* 3.1 35.1 + - + +
72B ILE* 3.5 8.5 + - + +
109B LEU* 3.7 29.4 - - + -
127B TYR* 3.9 22.4 - - + +
130B ASN* 3.5 6.5 - - + +
131B GLY* 3.3 35.0 - - - +
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Residues in contact with GLU 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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137A ARG* 4.7 12.0 + - - -
18B ARG* 4.7 10.2 + - - -
65B GLY 2.9 19.3 + - - +
66B LEU* 3.7 25.4 - - - +
68B VAL* 1.3 76.0 - - - +
70B SER* 1.3 56.5 + - - +
72B ILE* 3.1 7.3 + - + -
73B ALA* 2.7 48.8 + - + +
130B ASN* 3.6 27.6 + - - +
134B ARG* 4.7 12.3 + - - +
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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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22B VAL* 3.2 29.9 - - - +
66B LEU 3.0 14.5 + - - -
67B LEU 2.6 19.8 + - - -
69B GLU* 1.3 77.7 - - - +
71B TRP* 1.3 70.0 + - - +
73B ALA* 4.7 4.0 - - - -
74B PRO* 3.2 19.8 - - - +
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Residues in contact with TRP 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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22B VAL* 5.7 0.2 - - - +
26B GLN* 3.5 22.9 + - - -
67B LEU* 3.6 29.6 + - + +
68B VAL* 3.4 32.5 - - + +
69B GLU 3.1 0.8 - - - -
70B SER* 1.3 89.4 - - - +
72B ILE* 1.3 66.0 + - + +
74B PRO* 4.0 6.6 - - - +
75B ILE* 3.9 5.9 - - - +
100B ALA* 3.5 40.3 - - + +
101B VAL* 5.5 4.3 - - + -
103B SER* 5.5 1.3 - - - -
105B GLU* 3.9 14.4 - - + +
106B ALA* 3.6 29.6 - - + -
109B LEU* 3.8 22.4 - - + -
127B TYR* 5.5 2.7 - + - -
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Residues in contact with ILE 72 (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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68B VAL* 3.7 9.2 - - + +
69B GLU* 3.1 10.5 + - + +
71B TRP* 1.3 83.6 - - + +
73B ALA* 1.3 73.7 + - + +
74B PRO* 3.2 2.9 - - - -
75B ILE* 3.1 30.3 + - + +
76B PHE* 4.4 4.9 + - - -
97B ILE* 5.6 0.2 - - + -
100B ALA* 4.5 0.9 - - + -
101B VAL* 4.2 23.6 - - + -
130B ASN 3.4 25.8 - - - +
131B GLY* 4.2 11.0 - - - +
132B ILE 5.1 0.2 - - - +
134B ARG* 3.9 33.4 - - + +
135B SER* 3.4 25.9 + - - +
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Residues in contact with ALA 73 (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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69B GLU* 2.7 34.9 + - + +
70B SER* 4.7 2.2 - - - -
72B ILE* 1.3 79.6 - - + +
74B PRO* 1.3 63.1 - - + +
75B ILE 3.3 0.2 + - - -
76B PHE 4.1 0.3 + - - -
77B PRO* 3.0 26.9 - - - +
134B ARG* 5.1 7.6 - - - +
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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