Contacts of the helix formed by residues 60 - 80 (chain C) in PDB entry 3DC5
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 LEU 60 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41C ILE* 4.1 13.8 - - + +
44C LYS* 3.6 33.4 - - + +
45C LEU* 3.6 43.5 - - + +
48C ALA* 4.4 3.1 - - + -
56C GLU* 3.2 21.2 + - + +
57C ALA 3.7 7.0 - - - +
58C ILE 3.2 0.8 - - - -
59C ALA* 1.3 78.4 - - + +
61C GLN* 1.3 64.4 + - - +
62C PRO* 3.4 0.7 - - - -
63C ALA* 3.2 13.4 + - + +
64C LEU* 3.0 22.0 + - - +
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Residues in contact with GLN 61 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45A LEU* 5.8 1.4 - - - +
61A GLN* 3.1 73.2 + - + +
64A LEU* 3.3 33.1 - - + +
65A LYS* 3.6 19.9 - - - +
45C LEU* 5.5 4.3 - - + -
57C ALA 3.4 9.9 - - - +
58C ILE* 3.1 20.3 + - - +
60C LEU* 1.3 78.4 - - - +
62C PRO* 1.3 69.7 - - + +
64C LEU* 3.1 2.1 + - - -
65C LYS* 2.9 20.1 + - - +
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Residues in contact with PRO 62 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
146A GLU* 6.0 1.6 - - - +
58C ILE 3.9 4.5 - - - +
59C ALA* 3.3 16.8 - - - +
61C GLN* 1.3 93.3 - - + +
63C ALA* 1.3 56.6 + - - +
65C LYS* 3.4 7.1 + - + +
66C PHE* 2.9 31.0 + - - +
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Residues in contact with ALA 63 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41C ILE* 3.4 28.2 - - + +
59C ALA 5.1 0.9 + - - +
60C LEU* 3.2 15.4 + - + +
61C GLN 3.2 0.4 - - - -
62C PRO* 1.3 76.9 - - - +
64C LEU* 1.3 60.9 + - - +
66C PHE* 4.4 3.8 - - - -
67C ASN* 2.9 39.2 + - - +
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Residues in contact with LEU 64 (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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54A LEU* 4.3 10.3 - - + -
57A ALA* 4.8 13.5 - - + +
58A ILE* 4.0 14.1 - - + +
61A GLN* 3.4 24.5 - - + +
38C LEU* 3.6 27.1 - - + -
41C ILE* 3.6 17.1 - - + +
42C GLU* 3.7 19.7 - - + +
45C LEU* 3.7 25.1 - - + -
60C LEU 3.0 13.0 + - - +
61C GLN 3.7 1.1 - - - +
63C ALA* 1.3 76.8 - - - +
65C LYS* 1.3 55.0 + - - +
68C GLY* 2.7 34.5 + - - +
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Residues in contact with LYS 65 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58A ILE* 3.8 25.7 - - + +
61A GLN* 3.6 13.8 - - - +
62A PRO* 6.1 3.0 - - - +
61C GLN 2.9 16.3 + - - +
62C PRO* 3.8 6.7 - - + +
64C LEU* 1.3 75.1 - - - +
66C PHE* 1.3 56.7 + - - +
69C GLY* 2.8 30.7 + - - -
142C GLN 3.8 2.8 - - - +
143C ASP* 3.3 44.4 + - - +
144C PRO* 4.1 12.3 - - + -
146C GLU* 4.7 8.7 + - - -
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Residues in contact with PHE 66 (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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34C TYR* 3.8 20.2 - + - -
62C PRO 2.9 19.0 + - - +
63C ALA* 3.8 4.7 - - - +
65C LYS* 1.3 77.0 - - - +
67C ASN* 1.3 74.1 + - - +
70C GLY* 2.9 23.0 + - - -
141C ASN* 4.4 11.9 - - + -
142C GLN* 3.2 30.8 - - + +
143C ASP* 6.0 0.4 - - - -
157C TRP* 3.7 33.2 - + - -
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Residues in contact with ASN 67 (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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33C THR* 5.5 0.2 - - - +
34C TYR* 3.5 40.7 - - - +
37C ASN* 3.3 31.3 + - - +
38C LEU* 3.8 16.6 - - + +
41C ILE* 2.9 23.3 - - + +
63C ALA* 2.9 17.3 + - - +
64C LEU* 4.6 0.4 - - - +
66C PHE* 1.3 88.1 - - - +
68C GLY* 1.3 60.5 + - - +
70C GLY* 3.2 1.2 + - - -
71C HIS* 2.9 29.5 + - - +
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Residues in contact with GLY 68 (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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54A LEU* 3.7 12.6 - - - -
58A ILE* 3.9 9.6 - - - -
38C LEU* 3.6 20.8 - - - +
64C LEU 2.7 22.4 + - - -
67C ASN* 1.3 72.3 - - - +
69C GLY* 1.3 60.8 + - - +
71C HIS* 3.1 4.0 + - - +
72C ILE* 2.9 27.0 + - - +
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Residues in contact with GLY 69 (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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58A ILE* 3.8 3.2 - - - +
65C LYS 2.8 19.2 + - - -
68C GLY* 1.3 72.3 - - - +
70C GLY* 1.3 56.9 + - - +
72C ILE* 3.2 2.4 + - - -
73C ASN* 2.8 35.8 + - - -
142C GLN 3.1 24.7 - - - -
144C PRO* 4.1 15.9 - - - -
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Residues in contact with GLY 70 (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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34C TYR* 3.8 16.6 - - - -
66C PHE 2.9 21.4 + - - -
67C ASN 3.2 2.8 + - - -
69C GLY* 1.3 71.3 - - - +
71C HIS* 1.3 61.1 + - - +
74C HIS* 2.7 32.4 + - - +
142C GLN* 3.4 23.9 - - - +
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Residues in contact with HIS 71 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54A LEU* 4.5 6.7 - - + -
2C HIS* 3.8 30.3 + + + +
3C THR 3.5 24.4 + - - -
5C PRO* 4.0 3.6 - - + -
31C HIS* 2.9 32.7 - + + -
34C TYR* 4.0 3.0 - - + +
35C VAL* 3.4 13.6 - - + +
38C LEU* 3.8 15.5 - - + -
67C ASN 2.9 13.0 + - - +
68C GLY 3.5 7.9 - - - +
70C GLY* 1.3 75.1 - - - +
72C ILE* 1.3 65.8 + - + +
75C SER* 2.7 49.0 + - - -
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Residues in contact with ILE 72 (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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54A LEU* 3.9 22.4 - - + -
55A LYS* 3.9 44.2 - - + +
58A ILE* 4.1 9.9 - - + -
68C GLY 2.9 21.3 + - - +
69C GLY* 3.7 5.2 - - - +
71C HIS* 1.3 79.0 - - + +
73C ASN* 1.3 74.4 + - - +
75C SER* 3.3 4.8 + - - -
76C ILE* 3.1 44.3 + - + +
144C PRO* 4.5 10.8 - - + -
150C PRO* 6.0 0.2 - - + -
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Residues in contact with ASN 73 (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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69C GLY 2.8 23.0 + - - +
70C GLY 4.1 0.2 - - - +
72C ILE* 1.3 78.7 - - - +
74C HIS* 1.3 57.8 + - - +
76C ILE* 3.3 3.6 + - - +
77C PHE* 2.9 27.7 + - - +
122C TRP* 3.4 34.3 - - + +
124C TRP* 3.9 21.6 - - + -
142C GLN* 3.0 46.4 + - - +
143C ASP 3.9 5.4 + - - +
144C PRO* 3.7 18.1 - - - +
145C LEU 4.5 0.5 + - - -
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Residues in contact with HIS 74 (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 HIS* 3.3 18.0 + + - -
30C HIS* 5.3 0.4 - - - +
31C HIS* 3.5 28.5 - + + -
34C TYR* 3.4 16.7 - + - -
70C GLY* 2.7 27.7 + - - +
73C ASN* 1.3 76.8 - - - +
75C SER* 1.3 63.6 + - - +
77C PHE* 3.1 5.2 + + - +
78C TRP* 3.0 42.8 + + + -
122C TRP* 3.7 12.7 - + - -
142C GLN* 3.4 26.0 - - - -
155C ASP* 3.5 3.5 + - - -
159C HIS* 3.9 0.2 + - - -
195C MN 2.2 35.7 + - - -
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Residues in contact with SER 75 (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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5C PRO* 3.8 12.0 - - - +
31C HIS* 3.3 14.8 + - - -
71C HIS* 2.7 39.4 + - - -
72C ILE* 3.6 5.8 - - - -
74C HIS* 1.3 76.6 - - - +
76C ILE* 1.3 65.1 + - - +
78C TRP* 3.7 8.5 + - - +
79C THR* 3.4 23.2 + - - +
188C ARG* 5.1 0.4 - - - -
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Residues in contact with ILE 76 (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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72C ILE* 3.1 32.5 + - + +
73C ASN* 3.7 5.6 - - - +
75C SER* 1.3 76.5 - - - +
77C PHE* 1.3 65.0 + - - +
79C THR* 2.7 19.8 + - - -
80C ASN* 3.0 26.3 + - - +
124C TRP* 3.8 22.0 - - + -
150C PRO* 3.5 33.4 - - + -
151C LEU 4.9 1.1 - - - +
188C ARG* 3.8 37.0 - - - +
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Residues in contact with PHE 77 (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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18C ILE* 4.9 5.4 - - + -
23C MET* 6.2 0.2 - - - -
26C HIS* 4.0 24.2 - + - -
73C ASN 2.9 17.3 + - - +
74C HIS* 3.4 5.8 - + - +
76C ILE* 1.3 77.4 - - - +
78C TRP* 1.3 85.9 + + - +
80C ASN* 3.0 16.2 + - + +
81C LEU* 3.3 39.6 - - + +
122C TRP* 3.7 22.2 - + + -
124C TRP* 5.2 1.1 - - - -
153C GLY 3.2 27.8 - - - -
155C ASP* 3.8 15.5 - - + -
160C ALA* 5.4 0.2 - - + -
172C TYR* 3.6 21.1 - - - -
176C ILE* 3.7 19.1 - - + -
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Residues in contact with TRP 78 (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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5C PRO* 4.2 13.5 - - + -
6C ASP 5.4 1.3 - - - +
7C LEU* 3.4 30.3 - - + -
8C PRO* 3.5 15.2 - - + +
9C PHE* 3.4 22.8 - + - -
23C MET* 3.7 23.6 - - + -
26C HIS* 3.6 42.2 - + + -
27C HIS* 3.7 26.1 + - + -
31C HIS* 2.8 33.0 - + - -
74C HIS* 3.0 27.3 + + + +
75C SER* 4.1 8.7 - - - +
76C ILE 3.3 0.4 - - - -
77C PHE* 1.3 95.6 - + - +
79C THR* 1.3 63.6 + - + +
80C ASN 3.4 0.7 + - - -
81C LEU* 3.4 12.1 + - + +
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Residues in contact with THR 79 (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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8C PRO* 4.3 11.9 - - + -
75C SER 3.4 14.4 - - - +
76C ILE 2.7 17.6 + - - -
78C TRP* 1.3 77.7 - - + +
80C ASN* 1.3 56.0 + - - +
81C LEU 3.3 1.3 - - - -
181C ASN* 3.0 26.1 + - - -
184C ASN* 3.1 29.2 + - - +
188C ARG* 2.9 24.2 + - - +
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Residues in contact with ASN 80 (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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76C ILE* 3.0 26.7 + - - +
77C PHE* 3.0 13.2 + - - +
79C THR* 1.3 75.8 + - - +
81C LEU* 1.3 54.2 + - + +
151C LEU 3.2 18.9 + - - -
152C PHE* 3.4 24.3 - - + -
153C GLY* 2.9 28.9 + - - +
180C ALA* 3.6 6.6 - - - -
181C ASN* 2.7 33.3 + - - +
184C ASN* 2.9 21.7 + - - -
185C ILE* 4.2 3.2 - - - +
188C ARG* 3.8 5.7 - - - +
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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
------------------------------------------------------------
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