Contacts of the helix formed by residues 55 - 72 (chain C) in PDB entry 3G33
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 PRO 55 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44C VAL* 3.4 11.2 - - + -
45C PRO* 3.1 52.2 - - + +
54C LEU* 1.3 85.9 - - + +
56C ILE* 1.3 66.1 + - - +
57C SER* 3.1 6.1 - - - +
58C THR* 2.8 33.2 + - - +
59C VAL* 3.2 11.9 + - + +
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Residues in contact with ILE 56 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
112B LYS* 2.6 51.8 - - + +
116B THR 5.2 1.1 - - - +
118B PRO* 2.8 43.5 - - + -
54C LEU 2.9 6.3 + - - +
55C PRO* 1.3 71.0 - - - +
57C SER* 1.3 63.2 + - - +
58C THR 3.1 0.3 + - - -
59C VAL* 3.3 5.0 + - - +
60C ARG* 3.0 51.3 + - - +
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Residues in contact with SER 57 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55C PRO* 3.0 5.8 + - - +
56C ILE* 1.3 79.8 - - - +
58C THR* 1.3 63.1 + - - +
60C ARG* 4.0 7.5 - - - +
61C GLU* 3.3 34.7 + - - +
168C ARG* 3.4 53.4 + - - +
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Residues in contact with THR 58 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
150B TRP* 4.4 10.1 - - + -
44C VAL* 4.2 22.3 - - + +
45C PRO* 5.0 0.3 - - - +
55C PRO* 2.8 31.4 + - - +
57C SER* 1.3 80.1 + - - +
59C VAL* 1.3 62.1 + - + +
60C ARG 3.2 1.8 - - - -
61C GLU* 3.5 2.5 + - - +
62C VAL* 3.0 39.8 + - + +
94C VAL* 5.7 1.1 - - + -
168C ARG 4.2 11.4 + - - -
169C ILE* 4.1 26.6 - - + -
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Residues in contact with VAL 59 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
109B LEU* 4.5 7.6 - - + +
112B LYS* 5.3 10.1 - - + -
113B LEU* 4.0 8.9 - - + +
141B GLU* 4.9 2.0 - - - +
145B LEU* 4.1 18.6 - - + -
150B TRP* 4.0 22.4 - - + +
152B LEU* 3.8 28.3 - - + -
54C LEU* 4.2 20.0 - - + -
55C PRO* 3.2 12.4 + - + +
56C ILE* 3.9 7.9 - - - +
58C THR* 1.3 78.7 - - + +
60C ARG* 1.3 62.9 + - + +
62C VAL* 4.2 0.9 - - - +
63C ALA* 3.2 22.3 + - - +
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Residues in contact with ARG 60 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
112B LYS 3.0 22.8 + - - +
113B LEU* 3.3 35.3 + - + +
114B ARG 4.4 0.8 - - - -
115B GLU 2.7 40.0 + - - +
116B THR* 4.8 2.6 + - - +
153B ALA* 5.8 0.2 - - - +
56C ILE* 3.0 30.4 + - - +
57C SER* 4.0 7.6 - - - +
59C VAL* 1.3 76.5 - - + +
61C GLU* 1.3 56.0 + - + +
63C ALA* 3.1 3.6 + - - +
64C LEU* 2.7 35.1 + - - +
168C ARG* 5.8 5.0 - - - +
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Residues in contact with GLU 61 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57C SER 3.3 13.8 + - - +
58C THR 4.3 0.9 - - - +
60C ARG* 1.3 81.0 - - + +
62C VAL* 1.3 61.4 + - - +
64C LEU* 3.4 14.9 + - + +
65C LEU* 3.2 28.9 + - - +
165C GLY 3.2 21.9 - - - +
167C ALA* 3.5 8.4 + - - +
168C ARG* 3.1 52.7 + - - +
169C ILE* 3.7 16.2 - - + +
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Residues in contact with VAL 62 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
150B TRP* 3.3 48.2 - - + -
58C THR* 3.0 31.6 + - + +
59C VAL 4.2 0.2 - - - +
61C GLU* 1.3 75.9 - - - +
63C ALA* 1.3 61.9 + - - +
65C LEU* 3.5 9.7 + - - +
66C ARG* 3.2 22.7 + - - +
79C LEU* 4.1 5.8 - - + +
82C VAL* 4.1 15.9 - - + -
94C VAL* 5.4 4.9 - - + -
96C LEU* 4.5 11.9 - - + -
169C ILE* 4.3 16.6 - - + -
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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
----------------------------------------------------------
113B LEU* 4.1 11.7 - - + -
150B TRP 3.2 21.1 + - - +
151B ASP* 4.4 1.9 - - - +
152B LEU* 3.7 16.6 - - + +
153B ALA* 3.8 15.7 - - + +
59C VAL 3.2 19.9 + - - +
60C ARG 3.1 4.4 + - - +
62C VAL* 1.3 74.9 - - - +
64C LEU* 1.3 65.1 + - - +
66C ARG* 3.6 2.9 + - - +
67C ARG* 3.2 22.2 + - - +
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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
----------------------------------------------------------
153B ALA* 4.7 5.3 - - + +
60C ARG 2.7 16.2 + - - +
61C GLU* 3.6 17.7 - - + +
62C VAL 3.3 0.2 - - - -
63C ALA* 1.3 79.3 - - - +
65C LEU* 1.3 62.6 + - + +
67C ARG* 3.4 27.3 - - - +
68C LEU* 3.2 27.2 - - + +
139C ASN* 4.8 11.2 - - + +
140C CYS* 4.8 5.6 - - + +
141C ILE* 4.0 28.7 - - + -
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Residues in contact with LEU 65 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61C GLU 3.2 19.5 + - - +
62C VAL* 3.7 4.0 - - - +
63C ALA 3.3 0.2 - - - -
64C LEU* 1.3 76.6 - - + +
66C ARG* 1.3 66.8 + - - +
67C ARG 3.0 1.6 - - - -
68C LEU* 2.9 22.1 + - - +
69C GLU* 3.4 5.0 + - - +
79C LEU* 3.7 32.4 + - + +
96C LEU* 5.0 2.2 - - + -
98C PHE* 4.5 9.4 - - + -
141C ILE* 4.1 15.9 - - + -
164C PHE* 4.1 27.1 - - + -
165C GLY* 4.1 18.8 - - - +
166C LEU* 3.8 29.2 - - + -
169C ILE* 4.9 2.7 - - + -
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Residues in contact with ARG 66 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37B ARG* 3.6 25.9 + - - +
149B LYS* 2.7 54.1 + - - +
150B TRP 3.8 5.8 - - - +
151B ASP* 3.8 22.5 + - + +
62C VAL 3.2 17.4 + - - +
63C ALA 3.8 5.2 - - - +
65C LEU* 1.3 76.7 - - - +
67C ARG* 1.3 62.8 + - - +
69C GLU* 2.4 49.3 + - - +
70C ALA 3.8 0.2 + - - -
79C LEU* 2.7 35.8 + - + -
80C MET 3.4 11.5 + - - -
81C ASP 5.0 0.2 - - - -
82C VAL* 3.8 18.7 - - + +
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Residues in contact with ARG 67 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31B LEU* 4.0 13.3 - - - +
34B LEU* 3.4 33.4 - - + +
38B TYR* 3.5 23.6 - - + +
151B ASP* 4.2 0.2 + - - -
153B ALA* 3.5 29.5 + - + +
154B ALA 5.5 0.8 + - - -
155B VAL* 3.7 16.4 - - - +
159B ASP* 5.7 1.6 + - - -
63C ALA 3.2 14.1 + - - +
64C LEU* 3.4 26.4 - - - +
65C LEU 3.0 0.4 - - - -
66C ARG* 1.3 78.0 - - - +
68C LEU* 1.3 64.5 + - + +
70C ALA* 3.0 22.3 + - - +
71C PHE* 3.7 11.8 - - + -
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Residues in contact with LEU 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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64C LEU* 3.2 25.4 - - + +
65C LEU* 2.9 11.2 + - + +
67C ARG* 1.3 79.8 - - + +
69C GLU* 1.3 67.3 + - - +
71C PHE* 2.9 28.8 + - + +
72C GLU* 3.5 3.1 + - - -
73C HIS 5.0 0.9 + - - -
76C VAL* 5.6 5.6 - - + +
135C PHE* 3.9 31.1 - - + -
136C LEU* 4.2 9.0 - - + -
139C ASN* 4.1 20.4 - - + -
141C ILE* 3.4 31.6 - - + -
164C PHE* 3.9 23.1 - - + -
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Residues in contact with GLU 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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37B ARG* 2.7 23.7 + - - -
65C LEU 3.4 4.3 + - - +
66C ARG* 2.4 45.3 + - - +
67C ARG 3.2 0.2 - - - -
68C LEU* 1.3 77.6 - - - +
70C ALA* 1.3 62.1 + - - +
72C GLU* 2.9 24.0 + - - +
78C ARG* 3.2 52.0 + - + +
79C LEU 4.2 15.2 - - - +
80C MET* 4.4 4.0 - - - +
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Residues in contact with ALA 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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34B LEU* 3.8 19.1 - - + -
37B ARG* 3.4 43.1 - - + +
66C ARG 3.8 0.4 + - - -
67C ARG 3.0 16.7 + - - +
68C LEU 2.9 0.6 + - - -
69C GLU* 1.3 80.1 - - - +
71C PHE* 1.3 61.1 + - - +
72C GLU* 3.1 12.0 + - - +
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Residues in contact with PHE 71 (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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30B SER* 4.0 27.8 - - - -
33B ARG* 4.9 27.1 + - - +
34B LEU* 3.7 39.9 - - + -
67C ARG* 3.7 17.0 - - + -
68C LEU* 2.9 22.4 + - + +
70C ALA* 1.3 76.0 - - - +
72C GLU* 1.3 69.1 + - - +
73C HIS* 3.3 1.4 + - + -
135C PHE* 3.7 31.6 - + + -
139C ASN* 4.0 21.3 - - - -
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Residues in contact with GLU 72 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68C LEU 3.5 2.2 + - - -
69C GLU* 2.9 23.7 + - + +
70C ALA* 3.8 8.0 - - - +
71C PHE* 1.3 81.8 - - - +
73C HIS* 1.3 65.1 + - - +
74C PRO* 3.6 6.4 - - - +
78C ARG* 4.2 32.8 + - - +
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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
------------------------------------------------------------
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