Contacts of the helix formed by residues 75 - 88 (chain C) in PDB entry 1C7G
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 GLU 75 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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41A LYS* 3.4 41.1 - - + +
68C ASP* 3.0 24.6 + - + +
73C GLY 3.4 1.2 + - - +
74C SER* 1.3 73.3 + - - +
76C ASN* 1.3 63.2 + - - +
78C TYR* 3.2 35.2 + - - +
79C HIS* 3.1 50.9 + - + -
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Residues in contact with ASN 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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66C ILE* 3.5 19.4 + - - +
67C GLY* 4.3 0.2 - - - -
68C ASP* 2.6 30.5 + - - +
74C SER* 3.2 9.5 + - - +
75C GLU* 1.3 77.7 - - - +
77C PHE* 1.3 65.2 + - - +
79C HIS* 3.2 5.7 + - - +
80C LEU* 3.0 23.2 + - - +
296C GLY* 3.0 33.9 - - - +
299C MET* 4.0 8.3 - - + +
300C GLU* 2.7 40.7 + - - +
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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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73C GLY 6.1 1.1 - - - -
74C SER* 3.3 17.3 + - - +
75C GLU 3.2 0.4 - - - -
76C ASN* 1.3 79.2 - - - +
78C TYR* 1.3 77.7 + + - +
80C LEU* 3.2 5.0 + - + +
81C GLU* 2.8 63.4 + - + +
93C ILE* 4.5 13.9 - - + -
95C PRO* 3.9 14.6 - - + -
289C PRO 3.6 21.1 - - - -
290C SER* 3.6 36.6 - - - +
299C MET* 4.0 20.1 - - + +
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Residues in contact with TYR 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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37A LEU 5.2 1.4 + - - -
38A LEU 4.7 0.9 + - - -
39A ASN* 2.5 33.8 + - - -
73C GLY* 3.4 35.5 - - - -
74C SER 3.5 7.2 - - - -
75C GLU* 3.2 30.4 + - - +
76C ASN 3.3 0.4 - - - -
77C PHE* 1.3 98.2 - + - +
79C HIS* 1.3 59.6 + - + +
81C GLU* 3.8 14.6 - - - +
82C LYS* 2.9 34.2 + - - +
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Residues in contact with HIS 79 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66C ILE* 5.4 6.3 - - + -
75C GLU* 3.1 39.7 + - + -
76C ASN* 3.4 9.0 - - - +
78C TYR* 1.3 79.6 - - + +
80C LEU* 1.3 56.3 + - - +
82C LYS* 3.9 6.3 - - + +
83C THR* 2.9 34.3 + - - +
300C GLU* 2.5 43.8 + - - +
303C ALA* 4.1 7.6 - - + -
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Residues in contact with LEU 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 ASN 3.0 15.6 + - - +
77C PHE* 3.7 5.4 - - + +
79C HIS* 1.3 74.6 - - - +
81C GLU* 1.3 65.1 + - - +
83C THR* 3.4 1.0 + - + -
84C VAL* 3.0 41.2 + - + +
93C ILE* 3.9 17.7 - - + -
95C PRO* 4.4 14.1 - - + -
266C PHE* 4.8 3.6 - - + -
299C MET* 3.8 28.0 - - + +
302C MET* 3.8 34.1 - - + -
303C ALA* 3.7 28.4 - - - +
306C LEU* 5.6 1.3 - - + -
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Residues in contact with GLU 81 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77C PHE* 2.8 44.3 + - + +
78C TYR* 3.8 17.1 - - - +
80C LEU* 1.3 75.9 - - - +
82C LYS* 1.3 63.8 + - - +
84C VAL* 4.2 0.9 - - - +
85C LYS* 3.1 65.2 + - - +
93C ILE* 3.8 24.7 + - + +
275C PHE* 6.1 0.5 - - - -
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Residues in contact with LYS 82 (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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78C TYR 2.9 18.6 + - - +
79C HIS* 3.9 6.7 - - + +
81C GLU* 1.3 79.1 - - - +
83C THR* 1.3 63.5 + - - +
85C LYS* 3.7 7.3 - - - +
86C GLU* 3.0 48.6 + - - +
307C ARG* 4.7 4.9 - - - +
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Residues in contact with THR 83 (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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79C HIS* 2.9 22.3 + - - +
80C LEU 3.7 4.0 - - - +
81C GLU 3.3 0.2 - - - -
82C LYS* 1.3 77.7 - - - +
84C VAL* 1.3 59.4 + - + +
86C GLU* 3.2 2.9 + - - +
87C LEU* 2.9 46.5 + - + +
303C ALA* 3.6 32.0 + - - +
306C LEU* 4.3 9.9 - - + -
307C ARG* 3.1 32.6 + - - +
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Residues in contact with VAL 84 (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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80C LEU* 3.0 38.6 + - + +
81C GLU 4.2 0.9 - - - +
83C THR* 1.3 73.7 - - + +
85C LYS* 1.3 62.6 + - + +
88C PHE* 2.8 40.4 + - + +
89C GLY 3.4 0.2 + - - -
90C PHE* 4.5 2.2 + - + +
93C ILE* 3.9 17.3 - - + -
266C PHE* 3.9 16.8 - - + -
268C CYS* 3.6 30.5 - - - -
306C LEU* 3.9 22.4 - - + -
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Residues in contact with LYS 85 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81C GLU* 3.1 59.8 + - - +
82C LYS* 3.7 7.6 - - - +
84C VAL* 1.3 77.8 - - + +
86C GLU* 1.3 58.1 + - - +
89C GLY* 3.0 26.9 + - - -
90C PHE 3.5 20.0 - - - +
91C LYS* 3.0 26.7 + - - +
92C HIS* 4.4 7.2 + - - +
93C ILE* 4.5 5.4 - - + +
242C HIS* 5.0 0.5 - - - -
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Residues in contact with GLU 86 (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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82C LYS* 3.0 35.6 + - + +
83C THR 3.5 3.1 - - - +
85C LYS* 1.3 80.0 - - - +
87C LEU* 1.3 67.8 + - + +
238C LYS* 4.5 13.0 + - - +
242C HIS* 3.7 17.0 + - - -
307C ARG* 3.1 38.5 + - - -
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Residues in contact with LEU 87 (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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83C THR* 2.9 30.4 + - + +
86C GLU* 1.3 86.1 - - + +
88C PHE* 1.3 76.0 + - + +
238C LYS* 3.8 36.5 - - + +
241C VAL* 4.0 6.2 - - + +
242C HIS* 3.5 24.9 + - - +
306C LEU* 3.8 36.3 - - + +
307C ARG* 4.2 21.1 - - + +
310C MET* 4.2 18.6 - - + -
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Residues in contact with PHE 88 (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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84C VAL* 2.8 25.0 + - + +
87C LEU* 1.3 84.0 - - + +
89C GLY* 1.3 61.8 + - - +
90C PHE* 3.6 15.2 + + + -
218C CYS* 4.0 14.6 - - - -
241C VAL* 4.1 10.8 - - + -
242C HIS* 4.4 6.9 + - - +
245C PHE* 3.4 63.8 - + + +
246C SER* 5.8 0.2 - - - -
251C CYS* 4.2 14.6 - - - -
253C MET* 4.1 16.6 - - + -
266C PHE* 3.6 35.2 - + - -
306C LEU* 4.0 26.5 - - + -
310C MET* 5.1 1.6 - - + -
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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