Contacts of the strand formed by residues 105 - 109 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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68A PHE 4.1 0.4 + - - -
69A VAL* 3.4 14.8 - - + +
70A CYS 2.8 30.1 + - - -
103A ALA* 3.3 5.1 - - - +
104A LYS* 1.3 78.2 - - + +
106A VAL* 1.3 62.0 + - - +
107A ILE 4.3 0.2 - - - -
143A ILE* 5.1 3.8 - - + -
162A LEU* 4.1 33.0 - - + -
167A MET* 6.0 1.8 - - - -
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Residues in contact with VAL 106 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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70A CYS* 3.2 10.8 - - + +
72A ILE* 3.9 29.4 - - + -
100A ALA* 3.6 26.2 - - - +
103A ALA* 4.2 6.1 - - + +
105A ALA* 1.3 78.5 - - - +
107A ILE* 1.3 68.3 - - - +
131A VAL* 4.4 1.3 - - + -
140A VAL* 3.7 25.4 - - + -
141A LYS 4.6 3.8 + - - +
142A ALA* 3.4 20.6 - - + +
143A ILE* 3.0 26.6 + - - +
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Residues in contact with ILE 107 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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69A VAL* 4.4 10.8 - - + -
70A CYS 2.7 12.9 + - - +
71A VAL* 3.4 6.3 - - + +
72A ILE* 3.0 26.0 + - - +
106A VAL* 1.3 81.7 - - - +
108A ALA* 1.3 61.6 - - - +
109A ILE 3.8 1.0 + - - +
143A ILE* 3.7 14.4 - - + +
145A ILE* 3.9 22.7 - - + -
155A PHE* 3.8 23.6 - - + -
158A THR* 4.0 11.4 - - + -
159A VAL* 3.7 30.7 - - + -
162A LEU* 3.7 27.8 - - + -
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Residues in contact with ALA 108 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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72A ILE* 3.7 7.2 - - - -
106A VAL 4.2 0.8 - - - -
107A ILE* 1.3 69.4 - - - +
109A ILE* 1.3 58.0 + - - +
113A ALA* 3.9 18.4 - - + +
114A THR* 3.2 11.1 - - + +
131A VAL* 4.2 7.6 - - + -
142A ALA* 3.9 12.3 - - + +
143A ILE 2.8 10.0 + - - +
144A ASN* 3.4 25.6 - - - +
145A ILE* 2.9 31.2 + - - +
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Residues in contact with ILE 109 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11A TYR* 3.5 18.8 - - - +
20A CYS* 3.7 34.4 - - + +
23A SER* 4.6 4.5 - - - +
24A VAL* 4.0 17.7 - - + -
71A VAL* 4.0 12.8 - - + -
72A ILE 3.1 10.7 + - - +
73A GLU* 3.7 22.5 - - + -
74A GLY 4.2 1.4 + - - -
107A ILE* 3.8 1.0 + - + -
108A ALA* 1.3 69.1 - - - +
110A GLY* 1.3 67.0 + - - +
113A ALA* 3.5 11.3 + - - +
145A ILE* 4.0 3.6 - - + -
150A PRO* 4.0 14.4 - - + -
155A PHE* 4.0 33.9 - - + -
267A 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