Contacts of the helix formed by residues 59 - 73 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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39A MSE 3.6 18.2 - - - +
57A ALA* 3.5 2.1 - - - +
58A SER* 1.3 78.7 - - - +
60A ARG* 1.3 66.6 + - - -
61A ALA 3.2 2.9 - - - -
62A ASP* 3.1 16.9 + - - +
63A LEU* 3.2 13.7 + - - +
122A ARG* 5.2 4.5 - - - -
210A SO4 5.2 3.1 - - - -
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Residues in contact with ARG 60 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34A ALA* 2.8 45.5 + - - +
35A ALA* 4.1 4.8 - - - +
37A MSE 3.0 35.5 - - + +
38A THR* 4.3 4.0 - - - +
39A MSE 4.0 1.3 - - + +
59A GLY* 1.3 71.0 - - - -
61A ALA* 1.3 63.3 + - - +
63A LEU* 3.0 15.8 + - + +
64A ILE* 3.0 23.7 + - - +
118A ASP* 5.4 2.8 + - - -
119A LEU* 4.6 7.3 - - - +
122A ARG* 2.8 52.2 - - - +
123A PHE* 3.6 22.9 - - + -
210A SO4 3.9 22.7 + - - +
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Residues in contact with ALA 61 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59A GLY 3.2 1.2 - - - -
60A ARG* 1.3 79.2 - - - +
62A ASP* 1.3 59.1 + - - +
64A ILE* 3.1 3.6 + - - +
65A GLY 3.0 22.9 + - - -
122A ARG* 3.5 28.9 - - + +
123A PHE* 3.8 13.7 - - + -
126A ALA* 3.2 23.5 - - + +
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Residues in contact with ASP 62 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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56A PHE 4.9 2.0 - - - +
57A ALA* 3.6 18.5 - - + -
58A SER* 2.8 31.9 + - - -
59A GLY 3.1 11.9 + - - +
61A ALA* 1.3 80.2 - - - +
63A LEU* 1.3 56.9 + - - +
65A GLY* 3.2 2.4 + - - +
66A LEU* 2.8 33.3 + - - +
126A ALA* 5.1 2.7 - - - +
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Residues in contact with LEU 63 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21A ILE* 3.9 25.8 - - + -
25A ALA* 4.7 9.0 - - + +
37A MSE 4.0 29.8 - - + +
38A THR 4.6 0.9 - - - +
39A MSE 3.6 20.9 - - - -
42A VAL* 3.8 34.1 - - + -
53A LEU* 4.2 5.2 - - + -
57A ALA* 3.8 17.9 - - + -
59A GLY 3.2 10.6 + - - +
60A ARG* 3.0 12.0 + - - +
62A ASP* 1.3 73.4 - - - +
64A ILE* 1.3 62.1 + - - +
66A LEU* 3.2 6.3 + - + +
67A LEU* 2.9 29.7 + - - +
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Residues in contact with ILE 64 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29A LEU* 4.1 11.4 - - + -
37A MSE 3.9 25.8 - - + -
60A ARG 3.0 16.9 + - - +
61A ALA* 3.1 8.5 + - - +
63A LEU* 1.3 75.2 - - - +
65A GLY* 1.3 63.8 + - - +
67A LEU* 3.2 5.6 + - + +
68A VAL* 2.9 29.4 + - + +
109A LEU* 4.1 39.3 - - + -
123A PHE* 3.8 33.9 - - + +
126A ALA* 4.9 0.2 - - + -
127A TYR* 4.2 22.0 - - + +
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Residues in contact with GLY 65 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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61A ALA 3.0 14.0 + - - -
62A ASP* 3.2 4.9 + - - -
64A ILE* 1.3 78.0 - - - +
66A LEU* 1.3 56.6 + - - +
69A GLU* 2.9 30.9 + - - +
126A ALA* 3.9 9.6 - - - +
130A ASN* 3.5 31.7 - - - +
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Residues in contact with LEU 66 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18A ARG* 4.4 22.6 - - + +
21A ILE* 4.0 27.1 - - + -
22A VAL* 3.6 14.0 - - + +
56A PHE* 3.7 34.5 - - + +
57A ALA* 4.3 7.0 - - + -
62A ASP 2.8 19.4 + - - +
63A LEU* 3.6 6.7 - - - +
65A GLY* 1.3 77.1 - - - +
67A LEU* 1.3 58.6 + - - +
69A GLU* 3.5 22.2 + - - +
70A SER* 3.0 28.9 + - - -
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Residues in contact with LEU 67 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22A VAL* 3.8 27.8 - - + +
25A ALA* 4.9 6.7 - - + -
26A GLN* 3.8 32.1 - - + +
29A LEU* 3.7 31.0 - - + -
63A LEU 2.9 16.8 + - - +
64A ILE* 3.5 8.1 - - + +
66A LEU* 1.3 74.0 - - - +
68A VAL* 1.3 66.9 + - + +
70A SER* 2.6 28.1 + - - +
71A TRP* 3.4 32.5 + - + +
109A LEU* 4.7 6.3 - - + -
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Residues in contact with VAL 68 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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64A ILE* 2.9 20.7 + - + +
65A GLY* 4.1 2.7 - - - +
67A LEU* 1.3 75.4 - - - +
69A GLU* 1.3 62.4 + - - +
71A TRP* 3.1 35.1 + - + +
72A ILE* 3.4 9.1 + - + +
101A VAL* 6.5 0.4 - - + -
109A LEU* 3.7 29.2 - - + -
127A TYR* 3.8 24.7 - - + +
130A ASN* 3.5 4.0 - - + +
131A GLY* 3.3 38.4 - - - +
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Residues in contact with GLU 69 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18A ARG* 4.8 8.5 + - - -
65A GLY 2.9 19.6 + - - +
66A LEU* 3.6 25.9 - - - +
68A VAL* 1.3 76.9 - - - +
70A SER* 1.3 55.4 + - - +
72A ILE* 3.1 2.7 + - - +
73A ALA* 2.8 45.9 + - + +
130A ASN* 3.8 19.8 + - - +
134A ARG* 2.8 36.8 + - - +
137B ARG* 4.4 5.2 + - - -
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Residues in contact with SER 70 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22A VAL* 4.2 21.9 - - - +
66A LEU 3.0 13.8 + - - -
67A LEU* 2.6 27.0 + - - +
69A GLU* 1.3 77.0 - - - +
71A TRP* 1.3 70.3 + - - +
73A ALA* 4.7 4.3 - - - -
74A PRO* 3.3 20.0 - - - +
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Residues in contact with TRP 71 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26A GLN* 3.4 23.1 + - - -
67A LEU* 3.6 29.3 + - + +
68A VAL* 3.1 32.1 + - + +
69A GLU 3.1 0.6 - - - -
70A SER* 1.3 88.6 + - - +
72A ILE* 1.3 63.2 + - + +
74A PRO* 4.0 6.9 - - - +
75A ILE* 4.2 4.0 - - - +
100A ALA* 3.4 37.7 - - + +
101A VAL* 5.4 5.2 - - + -
103A SER* 5.3 2.0 + - - -
105A GLU* 4.0 13.9 - - + +
106A ALA* 3.6 37.5 - - + -
109A LEU* 3.9 21.3 - - + -
127A TYR* 5.4 2.7 - + - -
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Residues in contact with ILE 72 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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68A VAL* 3.7 9.4 - - + +
69A GLU 3.1 6.4 + - - +
71A TRP* 1.3 81.4 - - + +
73A ALA* 1.3 73.4 + - - +
74A PRO* 3.3 3.1 - - - -
75A ILE* 3.2 30.8 + - + +
76A PHE* 4.5 3.8 + - - -
100A ALA* 4.6 0.7 - - + -
101A VAL* 4.1 25.6 - - + -
130A ASN 3.3 26.2 - - - +
131A GLY* 4.3 10.3 - - - +
134A ARG* 3.8 34.3 - - + +
135A SER* 3.4 25.5 + - - +
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Residues in contact with ALA 73 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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69A GLU* 2.8 35.4 + - + +
70A SER* 4.7 2.5 - - - -
72A ILE* 1.3 78.0 - - - +
74A PRO* 1.3 64.5 - - + +
75A ILE 3.3 0.2 + - - -
76A PHE 4.1 0.3 + - - -
77A PRO* 3.2 25.1 - - - +
134A ARG* 5.1 6.3 - - - +
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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