Contacts of the helix formed by residues 92 - 102 (chain C) in PDB entry 2FRV
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 MET 92 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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13C HIS 4.7 0.4 - - - +
14C ASN* 2.9 56.8 - - - +
15C ALA 3.8 2.7 - - - -
76C ILE* 4.3 2.0 - - + -
77C PRO* 4.1 16.6 - - + -
82C GLY 4.6 0.8 + - - -
85C GLY* 3.0 42.4 + - - +
86C LYS* 3.7 7.4 - - - +
87C VAL* 4.4 11.7 - - + -
90C ARG 3.4 0.2 + - - -
91C ASN* 1.3 67.9 - - - +
93C TYR* 1.3 66.2 + - - +
94C ASP 3.3 0.2 + - - -
95C ILE* 3.3 9.1 + - + +
96C CYS* 3.1 27.7 + - - -
20D HIS* 3.6 32.5 - - + +
41D LEU* 4.0 7.9 - - + -
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Residues in contact with TYR 93 (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* 3.5 24.2 - - + +
77C PRO 4.2 12.7 + - - +
78C MET* 3.7 26.9 - - + -
81C GLY 5.8 1.6 - - - +
82C GLY* 5.7 2.0 - - - -
91C ASN* 3.2 6.9 - - + +
92C MET* 1.3 78.4 - - - +
94C ASP* 1.3 71.2 + - - +
96C CYS* 3.8 1.6 - - - +
97C ALA* 2.9 38.8 + - + +
134C ALA 3.7 9.9 - - - -
135C LEU* 3.3 26.9 - - + -
137C LYS* 2.8 34.5 + - - -
138C LEU* 3.9 9.7 - - - +
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Residues in contact with ASP 94 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90C ARG* 3.8 4.0 + - - -
91C ASN* 2.8 30.5 + - - +
93C TYR* 1.3 88.3 - - - +
95C ILE* 1.3 66.0 + - - +
97C ALA* 3.3 5.3 + - - +
98C GLU* 3.1 23.2 + - - +
201I THR* 3.7 24.7 - - - +
216I GLU* 3.4 31.6 - - - +
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Residues in contact with ILE 95 (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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12C LEU* 4.3 19.3 - - + -
57C GLU* 5.7 3.1 - - - +
60C LEU* 4.3 11.9 - - + -
87C VAL* 3.6 36.8 - - + +
90C ARG* 3.4 56.1 - - + +
91C ASN 3.1 9.8 + - - +
92C MET* 3.3 8.7 + - + +
94C ASP* 1.3 76.1 - - - +
96C CYS* 1.3 56.1 + - - +
98C GLU* 3.2 2.4 + - - +
99C VAL* 2.9 41.5 + - + +
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Residues in contact with CYS 96 (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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12C LEU* 4.0 21.5 - - - -
14C ASN* 3.4 31.0 - - - -
72C ILE* 4.4 7.4 - - + -
76C ILE* 3.9 16.8 - - + -
92C MET 3.1 19.4 + - - +
93C TYR 3.8 3.8 - - - +
95C ILE* 1.3 72.8 - - - +
97C ALA* 1.3 64.1 + - - +
99C VAL 4.4 0.2 - - - +
100C ALA* 2.9 36.0 + - - +
101C PRO* 3.4 0.2 - - - +
135C LEU* 3.7 20.3 - - + +
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Residues in contact with ALA 97 (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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93C TYR* 2.9 36.6 + - + +
94C ASP* 3.3 6.0 + - - +
96C CYS* 1.3 77.7 - - - +
98C GLU* 1.3 56.9 + - - +
101C PRO* 2.9 25.1 - - - +
135C LEU* 4.4 1.7 - - - +
138C LEU* 3.4 29.6 - - + +
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Residues in contact with GLU 98 (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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60C LEU* 6.5 0.4 - - - -
61C HIS* 4.8 2.9 + - - -
64C ILE* 3.7 24.7 - - + +
90C ARG* 2.7 35.3 + - - +
94C ASP 3.1 11.1 + - - +
95C ILE* 3.5 7.5 - - - +
96C CYS 3.1 0.2 - - - -
97C ALA* 1.3 79.1 - - - +
99C VAL* 1.3 65.1 + - + +
101C PRO* 3.8 2.3 - - - +
102C LYS* 3.1 33.1 + - - +
215I TYR* 2.8 24.1 + - - -
264I ALA* 4.1 31.8 - - + +
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Residues in contact with VAL 99 (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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10C VAL* 4.2 7.2 - - + -
12C LEU* 4.1 13.0 - - + -
60C LEU* 4.4 10.8 - - + -
64C ILE* 3.9 30.5 - - + -
68C PHE* 3.7 16.8 - - + -
70C CYS* 4.0 20.9 - - - -
95C ILE* 2.9 35.9 + - + +
98C GLU* 1.3 77.4 - - + +
100C ALA* 1.3 67.0 + - - +
102C LYS* 3.0 23.0 + - - +
103C ALA 3.6 4.0 + - - -
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Residues in contact with ALA 100 (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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12C LEU* 5.9 0.2 - - + -
70C CYS* 4.3 8.5 - - - -
72C ILE* 4.1 17.9 - - + -
96C CYS* 2.9 20.6 + - - +
99C VAL* 1.3 76.5 - - - +
101C PRO* 1.3 66.5 - - + +
103C ALA* 3.2 21.1 + - - +
106C VAL* 3.6 13.6 - - + +
135C LEU* 4.0 12.3 - - + -
140C VAL* 3.9 18.1 - - + +
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Residues in contact with PRO 101 (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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96C CYS 3.4 1.1 - - - +
97C ALA 2.9 29.2 - - - +
98C GLU 3.8 2.7 - - - +
99C VAL 3.4 3.6 - - - -
100C ALA* 1.3 95.2 - - + +
102C LYS* 1.3 59.8 + - + +
103C ALA 3.5 4.7 + - - +
138C LEU* 4.0 35.9 - - + +
139C GLY 6.3 0.2 - - - -
140C VAL* 4.1 9.6 - - + -
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Residues in contact with LYS 102 (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 ILE* 3.9 42.0 - - + +
66C GLY 4.4 5.0 - - - +
68C PHE* 3.6 17.0 - - + -
98C GLU* 3.1 25.4 + - - +
99C VAL 3.0 7.5 + - - +
101C PRO* 1.3 76.2 - - + +
103C ALA* 1.3 61.6 + - - +
104C LYS* 4.5 8.0 - - - -
264I ALA 3.7 24.5 + - - -
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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