Contacts of the strand formed by residues 40 - 45 (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 ILE 40 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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6C ARG* 3.0 24.7 + - - -
7C PRO* 3.3 10.1 - - + +
9C VAL* 3.8 29.8 - - + -
35C LEU* 2.9 30.2 + - + +
36C ILE* 3.3 31.6 - - + +
39C VAL* 1.3 83.7 - - + +
41C SER* 1.3 64.9 - - - +
42C MET* 4.1 19.1 - - + +
159C VAL* 4.0 15.7 - - + -
163C LEU* 3.9 20.9 - - + -
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Residues in contact with SER 41 (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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6C ARG* 3.8 14.4 + - - +
7C PRO 2.5 15.4 + - - -
8C SER* 4.3 0.2 - - - -
9C VAL* 2.9 28.1 + - - -
40C ILE* 1.3 76.4 - - - +
42C MET* 1.3 57.7 + - - +
43C ASP* 2.7 28.8 + - - +
166D GLN* 3.4 43.2 + - - +
168D GLY* 4.5 3.5 - - - -
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Residues in contact with MET 42 (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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6C ARG* 5.1 0.2 - - - +
9C VAL* 3.9 15.0 - - + +
11C TYR* 4.1 17.7 - - + -
24C VAL* 6.0 5.6 - - + -
35C LEU* 5.9 0.9 - - + -
36C ILE* 4.1 34.3 + - + +
40C ILE* 3.9 22.0 + - + +
41C SER* 1.3 68.4 + - - +
43C ASP* 1.3 62.2 + - - +
44C TYR 4.0 15.5 - - - +
45C HIS* 3.8 38.4 - - + -
48C LEU* 5.8 3.1 - - + -
155C PHE* 6.4 1.6 - - + -
168D GLY* 3.1 26.1 - - - -
169D ILE* 3.4 14.7 + - + +
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Residues in contact with ASP 43 (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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8C SER* 2.6 31.3 + - - +
9C VAL 2.9 11.8 + - - +
10C VAL* 4.4 0.9 - - + -
41C SER* 2.7 31.4 + - - -
42C MET* 1.3 75.2 - - - +
44C TYR* 1.3 59.3 + - - +
49C MET* 3.0 20.0 - - - +
59C ALA* 4.5 9.5 - - - +
63C ALA* 4.0 23.3 - - + +
166D GLN* 5.0 4.4 + - - +
168D GLY* 3.8 13.3 + - - +
171D THR* 4.7 3.1 + - - +
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Residues in contact with TYR 44 (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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9C VAL 3.7 3.0 + - - -
10C VAL* 4.3 10.1 - - + -
11C TYR* 2.9 48.5 + - - +
12C LEU* 4.2 10.1 - - + -
42C MET* 3.5 3.3 - - - +
43C ASP* 1.3 79.6 - - - +
45C HIS* 1.3 64.0 + - - +
46C GLU* 3.4 38.9 + - + +
49C MET* 4.0 12.3 - - + -
56C VAL* 3.5 32.8 - - + -
57C GLU* 2.8 26.4 + - - -
60C LEU* 3.6 52.9 - - + +
63C ALA* 5.6 0.2 - - + -
87C VAL* 4.7 2.3 - - - +
13D PRO* 4.1 1.9 - - - +
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Residues in contact with HIS 45 (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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11C TYR* 3.6 40.4 - + + -
13C HIS* 3.1 32.9 + + - -
21C SER* 3.8 13.3 + - - -
24C VAL* 6.3 0.6 - - - +
25C LEU* 6.1 1.6 - - + +
42C MET* 3.8 28.7 - - + -
44C TYR* 1.3 76.9 - - - +
46C GLU* 1.3 62.1 + - - +
47C THR* 3.1 22.1 + - - -
48C LEU* 3.1 28.4 + - + +
49C MET* 3.2 22.3 + - - +
169D ILE* 4.4 6.7 - - + +
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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