Contacts of the helix formed by residues 74 - 89 (chain C) in PDB entry 2R7I
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 LYS 74 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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73C VAL* 1.3 78.0 - - - +
75C LYS* 1.3 69.7 + - - +
76C LYS* 2.9 29.6 + - + +
77C LYS* 3.0 35.7 + - + +
78C ILE* 3.6 4.3 + - - +
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Residues in contact with LYS 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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73C VAL 3.2 6.0 + - - -
74C LYS* 1.3 74.5 - - - +
76C LYS* 1.3 62.2 + - + +
78C ILE* 3.4 13.4 + - + +
79C LYS* 3.4 40.6 + - + +
102C LYS* 6.3 0.9 - - - +
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Residues in contact with LYS 76 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26C TYR* 3.7 24.4 + - + -
27C GLU* 3.2 37.7 + - + +
74C LYS* 3.9 32.4 - - + +
75C LYS* 1.3 74.4 - - + +
77C LYS* 1.3 58.0 + - + +
79C LYS* 3.1 13.4 + - - +
80C ARG* 2.7 34.1 + - - +
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Residues in contact with LYS 77 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26C TYR* 5.3 0.2 - - - -
73C VAL* 3.8 31.9 - - + +
74C LYS* 3.0 26.0 + - + +
76C LYS* 1.3 81.4 - - + +
78C ILE* 1.3 56.7 + - - +
80C ARG* 3.6 40.2 + - - +
81C GLU* 3.1 28.2 + - - +
177C GLY 4.4 9.6 + - - +
178C LEU* 5.0 9.1 - - - +
336C SO4 4.2 17.5 + - - +
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Residues in contact with ILE 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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31C VAL* 6.2 0.4 - - + -
33C TRP* 4.5 15.5 - - + -
70C LEU* 3.6 40.2 - - + -
71C LYS 4.8 1.8 - - - +
73C VAL* 3.4 27.1 - - + +
74C LYS 3.8 9.2 - - - +
75C LYS* 3.5 19.3 - - + +
76C LYS 3.1 0.2 - - - -
77C LYS* 1.3 74.1 - - - +
79C LYS* 1.3 67.6 + - + +
80C ARG 3.1 0.3 + - - -
81C GLU* 3.1 6.7 + - + +
82C ILE* 2.9 41.3 + - + +
109C PRO* 4.7 12.3 - - + -
111C LEU* 5.1 0.4 - - + -
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Residues in contact with LYS 79 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26C TYR* 3.3 25.1 - - - +
27C GLU* 3.5 18.2 - - - +
29C HIS* 3.0 33.8 + - + +
30C VAL* 4.8 1.0 - - - +
31C VAL* 4.2 25.2 - - + +
75C LYS* 3.4 33.2 + - + +
76C LYS* 3.1 10.9 + - - +
78C ILE* 1.3 79.1 - - + +
80C ARG* 1.3 58.1 + - - +
82C ILE* 3.4 6.1 + - - +
83C LYS* 2.8 33.1 + - - +
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Residues in contact with ARG 80 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26C TYR* 3.5 46.7 + - + -
76C LYS 2.7 19.4 + - - +
77C LYS* 3.6 30.1 + - - +
78C ILE 3.1 0.2 - - - -
79C LYS* 1.3 72.4 - - - +
81C GLU* 1.3 59.2 + - - +
83C LYS* 3.1 2.4 + - - +
84C ILE* 2.9 41.6 + - + +
155C ARG* 4.2 0.4 - - - -
177C GLY 3.2 25.1 + - - -
178C LEU* 4.1 4.4 - - - +
179C ALA 3.1 26.2 + - - +
180C GLU* 3.0 31.1 + - - +
181C PHE* 4.6 0.7 - - + -
336C SO4 3.1 35.6 + - - -
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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
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68C LYS* 2.9 27.2 + - - -
70C LEU* 4.2 12.1 - - - +
77C LYS 3.1 15.4 + - - +
78C ILE* 3.7 4.7 - - - +
80C ARG* 1.3 79.8 - - - +
82C ILE* 1.3 57.7 + - - +
84C ILE* 3.5 3.9 + - - +
85C LEU* 2.9 45.3 + - + +
111C LEU* 3.4 22.6 - - + +
113C PHE* 4.8 2.1 - - - -
176C TRP 4.0 25.5 + - - +
177C GLY* 3.6 24.8 + - - -
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Residues in contact with ILE 82 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29C HIS* 3.8 23.3 - - + +
31C VAL* 3.5 32.5 - - + -
33C TRP* 4.5 1.1 - - + -
78C ILE* 2.9 34.0 + - + +
79C LYS* 3.7 3.6 - - - +
81C GLU* 1.3 73.9 - - - +
83C LYS* 1.3 67.5 + - - +
85C LEU* 3.3 7.6 + - - +
86C GLU* 3.0 30.3 + - + +
97C LEU* 4.3 3.8 - - + +
100C ILE* 3.7 35.0 - - + -
111C LEU* 3.7 21.5 - - + -
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Residues in contact with LYS 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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22C GLU* 3.5 28.7 + - - +
23C TYR* 3.7 18.9 - - - +
26C TYR* 4.0 20.9 - - + -
29C HIS* 4.0 31.9 - - + +
79C LYS 2.8 21.8 + - - +
80C ARG 3.6 3.4 - - - +
82C ILE* 1.3 75.6 - - - +
84C ILE* 1.3 53.1 + - - +
86C GLU* 3.0 16.5 + - - +
87C ASN* 2.8 59.1 + - - +
181C PHE* 4.2 3.1 - - + -
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Residues in contact with ILE 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 ARG* 2.9 22.7 + - + +
81C GLU* 3.8 3.8 - - - +
83C LYS* 1.3 77.5 - - - +
85C LEU* 1.3 62.1 + - - +
87C ASN* 3.3 6.9 + - - +
88C LEU* 3.0 45.0 + - + +
152C ILE* 3.9 11.4 - - + -
176C TRP* 4.1 23.3 - - + +
179C ALA* 3.4 42.2 - - + +
180C GLU* 3.8 7.9 - - - +
181C PHE* 3.6 29.4 - - + -
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Residues in contact with LEU 85 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81C GLU* 2.9 42.0 + - + +
82C ILE* 3.6 4.7 - - - +
83C LYS 3.3 0.2 - - - -
84C ILE* 1.3 75.7 - - - +
86C GLU* 1.3 63.0 + - - +
88C LEU* 3.5 3.3 + - + +
89C ARG* 3.1 25.5 + - - +
94C ILE* 5.2 3.3 - - + +
95C ILE* 3.8 35.4 - - + +
97C LEU* 3.9 25.2 + - + +
111C LEU* 4.1 7.6 - - + -
113C PHE* 3.8 28.0 - - + -
176C TRP* 3.8 22.2 - - + +
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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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29C HIS* 3.7 22.0 + - - -
82C ILE* 3.0 34.2 + - - +
83C LYS* 3.0 16.7 + - + +
85C LEU* 1.3 77.2 - - - +
87C ASN* 1.3 66.0 + - - +
88C LEU 3.2 0.7 + - - -
89C ARG* 3.3 43.9 + - - +
97C LEU* 4.3 7.5 - - + +
100C ILE* 4.3 10.6 - - - +
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Residues in contact with ASN 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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23C TYR* 2.9 71.0 + - + +
83C LYS* 2.8 37.0 + - - +
84C ILE* 3.6 6.7 - - - +
86C GLU* 1.3 79.0 - - - +
88C LEU* 1.3 62.0 + - - +
89C ARG 3.5 1.3 + - - +
146C TYR* 4.4 7.8 + - - -
150C MET* 4.4 4.9 - - - +
152C ILE* 4.5 4.5 - - + -
181C PHE* 3.6 14.6 - - - -
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Residues in contact with LEU 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 ILE* 3.0 24.6 + - + +
85C LEU* 3.8 3.1 - - + +
87C ASN* 1.3 76.8 - - - +
89C ARG* 1.3 67.2 + - - +
90C GLY 3.3 0.2 + - - -
91C GLY* 3.0 19.8 + - - -
94C ILE* 3.8 21.4 - - + +
146C TYR* 3.9 11.2 - - + -
147C CYS* 3.9 14.4 - - + -
150C MET* 3.6 36.6 - - + -
152C ILE* 3.7 13.9 - - + -
176C TRP* 3.5 45.8 - - + -
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Residues in contact with ARG 89 (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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85C LEU 3.1 13.0 + - - +
86C GLU* 3.3 44.6 + - - +
87C ASN 4.9 1.4 - - - +
88C LEU* 1.3 79.6 - - - +
90C GLY* 1.3 61.3 + - - +
91C GLY 3.5 1.6 + - - -
95C ILE 5.1 7.2 - - - -
96C THR* 4.3 18.3 - - + +
97C LEU* 2.5 47.7 + - - +
146C TYR* 4.8 3.6 + - - -
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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