Contacts of the strand formed by residues 80 - 86 (chain A) in PDB entry 2FG5
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 80 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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7A LYS 3.1 4.0 + - - -
8A VAL* 3.3 14.9 - - + -
9A CYS 3.1 20.4 + - - -
78A SER* 3.2 9.9 - - - -
79A ALA* 1.3 82.5 - - + +
81A ALA* 1.3 61.9 + - - +
111A ILE* 3.8 5.4 - - - -
112A VAL* 3.3 24.5 - - + +
162A ILE* 3.7 32.8 - - + -
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Residues in contact with ALA 81 (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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9A CYS* 3.3 24.7 - - - +
11A LEU* 4.2 5.2 - - + -
80A ALA* 1.3 75.3 - - - +
82A VAL* 1.3 62.6 + - - +
83A ILE* 3.7 2.8 + - + +
103A LEU* 3.5 31.2 - - + -
111A ILE* 4.1 8.1 - - + -
112A VAL 2.8 10.9 + - - +
113A MET* 3.9 1.6 - - - -
114A ALA* 3.1 25.9 + - - +
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Residues in contact with VAL 82 (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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8A VAL* 3.9 12.5 - - + +
9A CYS 2.8 8.1 + - - -
10A LEU* 3.3 18.9 - - + +
11A LEU* 2.8 28.2 + - - +
21A ILE* 5.4 0.7 - - + -
81A ALA* 1.3 72.5 - - - +
83A ILE* 1.3 62.4 + - - +
84A VAL* 3.8 19.8 + - + +
114A ALA* 3.4 13.0 - - + +
116A ALA* 4.3 3.8 - - + -
158A LEU* 3.9 31.4 - - + -
159A PHE* 4.7 6.5 - - + -
162A ILE* 3.7 30.1 - - + -
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Residues in contact with ILE 83 (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 LEU* 3.2 19.3 - - + +
12A GLY* 5.0 0.4 - - - -
81A ALA 4.1 6.7 - - - +
82A VAL* 1.3 77.3 - - - +
84A VAL* 1.3 60.6 + - - +
96A LEU* 3.4 29.5 - - + +
99A TRP* 3.9 25.8 - - + -
100A VAL* 3.8 26.0 - - + +
103A LEU* 3.9 26.5 - - + -
113A MET* 4.0 13.9 - - + -
114A ALA 2.8 13.9 + - - +
115A ILE* 3.2 13.1 - - + -
116A ALA 2.9 21.9 + - - -
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Residues in contact with VAL 84 (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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10A LEU* 4.7 2.9 - - + -
11A LEU 2.9 7.8 + - - +
12A GLY* 3.7 10.9 - - - -
13A ASP 4.3 0.9 + - - -
16A VAL* 3.6 33.7 - - + +
18A LYS* 4.0 19.5 - - + +
21A ILE* 3.8 21.3 - - + -
82A VAL* 3.8 23.1 - - + +
83A ILE* 1.3 77.4 - - - +
85A TYR* 1.3 74.8 + - - +
92A SER 4.7 2.3 - - - +
96A LEU* 4.1 5.8 - - - +
116A ALA* 3.4 9.9 - - + +
118A ASN* 3.7 17.0 - - + -
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Residues in contact with TYR 85 (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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16A VAL* 3.8 9.4 - - - +
84A VAL* 1.3 75.3 - - - +
86A ASP* 1.3 70.9 + - - +
87A ILE* 4.0 9.6 - - + -
92A SER* 3.3 26.0 - - - +
93A PHE* 3.9 25.1 - + + +
96A LEU* 4.0 7.9 - - + -
115A ILE* 3.5 28.0 - - + -
116A ALA 3.0 11.9 + - - -
117A GLY* 3.2 26.9 - - - -
118A ASN* 2.9 30.0 + - - +
128A VAL* 3.7 25.8 + - + +
129A PRO 5.3 0.2 + - - -
133A ALA* 3.2 27.5 - - + +
144A VAL* 4.8 3.4 - - + +
146A GLU* 4.4 13.7 + - - +
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Residues in contact with ASP 86 (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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15A GLY 5.3 0.3 - - - -
16A VAL* 3.7 20.6 - - + +
85A TYR* 1.3 75.9 - - - +
87A ILE* 1.3 56.5 + - - +
88A THR* 2.6 47.3 + - - +
89A LYS* 3.0 31.7 + - + +
92A SER* 2.9 23.4 + - - +
118A ASN 3.7 4.7 - - - -
119A LYS* 2.8 36.7 + - - +
128A VAL* 4.6 0.3 - - - +
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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