Contacts of the helix formed by residues 59 - 76 (chain C) in PDB entry 4GKH
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 C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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58C LYS* 1.3 73.0 - - - +
60C SER* 1.3 66.8 + - - -
62C ALA* 3.0 18.0 + - - +
63C ASN* 3.7 6.0 + - - -
89C ARG* 4.9 1.6 + - - -
92C ASP* 2.8 24.0 + - - -
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Residues in contact with SER 60 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58C LYS 3.4 0.8 + - - -
59C GLY* 1.3 71.0 - - - -
61C VAL* 1.3 61.7 + - - +
63C ASN* 2.9 36.6 + - - +
64C ASP* 3.5 9.1 + - - +
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Residues in contact with VAL 61 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36C SER* 3.4 24.7 - - - +
37C GLY* 3.9 6.3 - - - +
38C ALA* 3.6 40.6 - - + +
57C GLY* 3.7 7.0 - - - -
58C LYS 3.2 14.8 + - - +
59C GLY 3.1 0.6 - - - -
60C SER* 1.3 76.1 - - - +
62C ALA* 1.3 64.7 + - - +
64C ASP* 3.1 18.5 + - - +
65C VAL* 3.1 12.7 + - + +
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Residues in contact with ALA 62 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57C GLY* 3.5 24.1 - - - +
58C LYS 3.6 3.0 + - - -
59C GLY 3.0 15.3 + - - +
61C VAL* 1.3 77.4 - - - +
63C ASN* 1.3 60.3 + - - +
65C VAL 3.3 0.8 + - - +
66C THR* 2.8 29.8 + - - -
89C ARG* 3.7 26.5 - - - +
92C ASP 4.0 5.6 - - - +
93C ASP 3.9 1.1 - - - -
94C ALA* 3.5 15.5 - - - +
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Residues in contact with ASN 63 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59C GLY 4.3 2.4 + - - -
60C SER* 2.9 25.8 + - - +
62C ALA* 1.3 78.5 - - - +
64C ASP* 1.3 60.9 + - - +
66C THR* 3.5 5.9 + - - -
67C ASP* 3.0 36.1 + - - +
89C ARG* 3.0 17.5 + - - +
73D ASN* 2.8 32.0 + - - +
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Residues in contact with ASP 64 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36C SER* 3.0 42.0 - - - +
60C SER* 3.8 6.7 - - - +
61C VAL* 3.1 20.6 + - + +
63C ASN* 1.3 77.8 - - - +
65C VAL* 1.3 60.0 + - + +
67C ASP* 3.3 15.1 + - - +
68C GLU* 3.0 25.6 + - - +
218C GLY* 5.1 2.3 - - - -
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Residues in contact with VAL 65 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38C ALA* 3.7 28.7 - - + -
55C LYS* 4.4 12.1 - - + +
56C HIS 4.5 0.4 - - - -
57C GLY* 3.8 12.1 - - - +
61C VAL* 3.1 14.4 + - + +
62C ALA 3.3 6.3 + - - +
63C ASN 3.3 0.2 - - - -
64C ASP* 1.3 74.9 - - + +
66C THR* 1.3 60.6 + - - +
68C GLU* 3.2 8.8 + - - +
69C MSE 3.0 26.0 + - - +
87C PHE* 4.2 3.1 - - + -
94C ALA* 4.0 22.4 - - + +
96C LEU* 3.6 31.2 - - + +
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Residues in contact with THR 66 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62C ALA 2.8 21.2 + - - -
63C ASN* 3.6 8.1 - - - -
65C VAL* 1.3 75.7 - - - +
67C ASP* 1.3 66.7 + - - +
69C MSE 3.2 2.8 + - - +
70C VAL* 3.2 22.3 + - - +
87C PHE* 3.6 20.5 - - + -
89C ARG* 3.6 16.9 + - - +
69D MSE 3.9 22.2 - - + -
70D VAL* 3.6 25.4 - - + -
73D ASN* 4.6 11.0 - - - +
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Residues in contact with ASP 67 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63C ASN* 3.0 25.3 + - - +
64C ASP* 3.4 20.7 - - - +
66C THR* 1.3 77.8 - - - +
68C GLU* 1.3 62.1 + - - +
70C VAL* 3.3 4.1 - - - +
71C ARG* 3.1 53.4 + - - +
151C GLN* 5.8 2.4 + - - -
218C GLY* 4.0 12.6 - - - +
70D VAL* 5.9 2.6 - - - +
73D ASN* 5.7 1.9 + - - -
140D PRO* 6.0 3.0 - - - +
141D PHE* 6.1 1.2 - - - -
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Residues in contact with GLU 68 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55C LYS* 2.9 40.3 + - - +
64C ASP 3.0 13.2 + - - +
65C VAL* 3.2 8.8 + - - +
67C ASP* 1.3 73.2 - - - +
69C MSE 1.3 61.5 - - - +
71C ARG* 3.3 1.5 + - - +
72C LEU* 2.8 41.8 + - + +
82C PRO* 6.2 0.2 - - - +
96C LEU* 3.8 11.3 - - + +
98C THR* 6.3 0.2 - - - -
216C ASP* 3.4 25.8 + - - +
217C VAL* 3.5 12.6 + - + +
218C GLY* 3.7 26.4 - - - +
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Residues in contact with MSE 69 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65C VAL 3.0 13.6 + - - +
66C THR 3.2 6.9 + - - +
68C GLU* 1.3 78.2 - - - +
70C VAL* 1.3 82.9 + - + +
72C LEU* 3.3 3.7 + - - +
73C ASN* 3.0 21.2 + - - -
84C ILE* 3.5 16.9 - - + +
87C PHE* 3.6 46.4 - - + -
96C LEU* 4.0 17.4 - - + +
66D THR* 3.9 13.2 - - + -
69D MSE 3.4 33.4 - - + -
87D PHE* 4.2 2.5 - - + -
89D ARG* 4.6 12.3 - - - -
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Residues in contact with VAL 70 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66C THR 3.2 7.3 + - - +
67C ASP* 3.3 17.7 - - - +
69C MSE 1.3 93.7 - - + +
71C ARG* 1.3 71.7 + - - +
73C ASN* 3.4 6.3 + - - +
74C TRP* 3.0 27.5 + - - +
141C PHE* 3.8 17.8 - - + -
66D THR* 3.6 16.8 - - + -
67D ASP* 5.9 1.6 - - - +
70D VAL* 3.3 39.3 - - + -
141D PHE* 5.7 1.1 - - + -
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Residues in contact with ARG 71 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67C ASP* 3.1 47.1 + - - +
68C GLU 3.9 2.0 - - - +
70C VAL* 1.3 85.5 - - - +
72C LEU* 1.3 59.0 + - - +
74C TRP* 4.0 0.3 - - - +
75C LEU* 2.9 34.7 + - - +
141C PHE* 3.6 47.8 - - + +
142C ASN 5.0 0.8 + - - -
143C SER* 5.0 4.2 + - - -
147C PHE* 5.9 1.4 - - - -
217C VAL* 3.4 24.2 - - + +
218C GLY 3.3 24.9 + - - -
219C ARG 4.4 0.8 - - - -
220C VAL* 2.9 28.6 + - + +
140D PRO* 4.0 24.7 + - - +
141D PHE* 5.5 4.0 - - - -
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Residues in contact with LEU 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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68C GLU* 2.8 32.8 + - + +
69C MSE 3.5 4.9 - - - +
71C ARG* 1.3 75.8 - - - +
73C ASN* 1.3 63.7 + - - +
76C THR* 3.2 29.8 + - - +
81C LEU* 3.9 9.9 - - + +
82C PRO* 3.9 39.4 - - + +
84C ILE* 3.8 18.4 - - + -
96C LEU* 4.0 15.3 - - + -
98C THR* 3.8 28.9 - - + -
216C ASP 5.9 0.9 - - - +
217C VAL* 3.6 21.9 - - + +
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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 MSE 3.0 18.1 + - - +
70C VAL* 3.6 9.3 + - - +
71C ARG 3.3 0.2 - - - -
72C LEU* 1.3 81.3 - - - +
74C TRP* 1.3 63.9 + - - +
76C THR* 3.4 16.8 - - - +
77C ALA* 4.6 1.4 + - - +
84C ILE* 3.7 15.2 - - + +
63D ASN* 3.0 33.6 + - - +
66D THR* 5.0 6.1 - - - +
89D ARG* 3.8 21.6 + - - +
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Residues in contact with TRP 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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70C VAL 3.0 18.2 + - - +
71C ARG 4.0 0.9 - - - +
73C ASN* 1.3 81.5 - - - +
75C LEU* 1.3 98.4 + - + +
76C THR 3.2 1.2 + - - -
77C ALA* 3.3 18.9 + - + +
78C PHE* 3.6 29.1 - + - -
134C ILE* 4.6 2.9 - - + -
138C ASN* 2.9 34.3 + - + -
139C CYS* 3.5 31.9 - - + -
140C PRO* 3.7 16.4 - - + +
141C PHE* 3.7 25.8 - + + -
194C VAL* 3.9 17.7 - - + -
220C VAL* 3.9 14.4 - - + -
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Residues in contact with LEU 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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71C ARG 2.9 20.7 + - - +
74C TRP* 1.3 94.0 - - + +
76C THR* 1.3 59.2 + - - +
77C ALA 3.0 2.9 - - - -
78C PHE* 2.8 23.6 + - + -
79C MSE 3.0 23.2 + - + +
81C LEU* 3.6 24.9 - - + -
131C LEU* 4.0 17.0 - - + -
134C ILE* 3.9 26.5 - - + -
194C VAL* 4.8 0.4 - - + -
196C HIS* 5.8 1.1 - - + -
214C CYS* 5.2 3.4 - - - -
217C VAL* 4.5 5.2 - - + -
220C VAL* 3.8 29.6 - - + -
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Residues in contact with THR 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 LEU 3.2 20.2 + - - +
73C ASN* 3.4 16.4 - - - +
75C LEU* 1.3 77.4 - - - +
77C ALA* 1.3 65.8 + - + +
78C PHE 3.0 0.9 + - - -
79C MSE 3.4 19.7 + - - +
81C LEU* 3.7 22.2 + - - +
82C PRO 4.8 4.4 + - - -
83C THR* 5.6 3.0 + - - -
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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