Contacts of the strand formed by residues 105 - 109 (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 ALA 105 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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68C PHE 4.1 0.2 + - - -
69C VAL* 3.4 14.3 - - + +
70C CYS 2.8 30.1 + - - -
103C ALA* 3.3 4.3 - - - +
104C LYS* 1.3 77.6 - - + +
106C VAL* 1.3 62.0 + - - +
143C ILE* 5.1 4.0 - - + -
162C LEU* 4.1 32.8 - - + -
167C MET* 6.0 2.2 - - - -
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Residues in contact with VAL 106 (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 CYS* 3.2 11.7 - - + +
72C ILE* 3.9 29.2 - - + -
100C ALA 3.6 26.9 - - - +
103C ALA* 4.2 4.9 - - + +
105C ALA* 1.3 78.0 - - - +
107C ILE* 1.3 67.9 + - - +
131C VAL* 4.4 1.1 - - + -
140C VAL* 3.7 24.2 - - + -
141C LYS 4.6 4.1 + - - +
142C ALA* 3.4 20.1 - - + +
143C ILE* 3.0 26.9 + - - +
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Residues in contact with ILE 107 (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 VAL* 4.4 10.8 - - + -
70C CYS 2.7 12.7 + - - +
71C VAL* 3.4 6.5 - - + +
72C ILE* 3.0 25.6 + - - +
106C VAL* 1.3 82.2 - - - +
108C ALA* 1.3 61.9 + - - +
109C ILE 3.8 0.7 + - - +
143C ILE* 3.7 13.9 - - + +
145C ILE* 3.9 22.7 - - + -
155C PHE* 3.8 23.8 - - + -
158C THR* 4.0 12.1 - - + -
159C VAL* 3.7 30.1 - - + -
162C LEU* 3.7 28.0 - - + -
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Residues in contact with ALA 108 (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 ILE* 3.7 7.9 - - - +
106C VAL 4.2 0.8 - - - -
107C ILE* 1.3 70.3 - - - +
109C ILE* 1.3 56.9 + - - +
113C ALA* 3.9 18.6 - - + +
114C THR* 3.2 11.1 - - + +
131C VAL* 4.2 7.9 - - + -
142C ALA* 3.9 12.4 - - + +
143C ILE 2.8 9.8 + - - +
144C ASN* 3.4 24.9 - - - +
145C ILE* 2.9 31.5 + - - +
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Residues in contact with ILE 109 (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* 3.5 19.5 - - - +
20C CYS* 3.7 34.4 - - + +
23C SER* 4.6 5.2 - - - +
24C VAL* 4.0 17.5 - - + -
71C VAL* 4.0 11.9 - - + -
72C ILE 3.1 10.5 + - - +
73C GLU* 3.7 21.9 - - + -
74C GLY 4.2 1.4 + - - -
107C ILE* 3.8 1.6 + - + -
108C ALA* 1.3 68.5 - - - +
110C GLY* 1.3 67.5 + - - +
112C CYS* 5.7 0.2 - - - +
113C ALA* 3.5 11.1 + - - +
145C ILE* 4.0 3.6 - - + -
150C PRO* 4.0 13.5 - - + -
155C PHE* 4.0 33.7 - - + -
267C SF4 5.2 0.2 - - - -
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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