Contacts of the helix formed by residues 119 - 126 (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 LYS 119 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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15A GLY* 2.8 30.8 + - - -
16A VAL 3.7 10.5 - - - +
86A ASP* 2.8 35.4 + - - +
87A ILE* 3.6 6.9 - - - +
88A THR* 4.5 0.7 - - + -
89A LYS* 4.8 5.7 - - - +
118A ASN* 1.3 88.8 + - - +
120A CYS* 1.3 56.6 + - - +
121A ASP* 3.0 9.6 - - - -
122A LEU* 2.8 48.7 + - + +
147A THR 3.0 4.6 + - - -
302A GNP 3.6 51.7 + - + +
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Residues in contact with CYS 120 (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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87A ILE* 3.6 13.2 - - + -
117A GLY 4.2 1.8 - - - +
118A ASN 3.4 0.8 - - - -
119A LYS* 1.3 77.0 - - - +
121A ASP* 1.3 62.3 + - - +
122A LEU 3.2 1.0 + - - -
123A SER* 3.5 19.6 + - - -
126A ARG* 5.1 1.2 + - - +
146A GLU* 4.0 32.1 - - + +
147A THR* 2.8 37.5 + - - +
148A SER* 3.8 8.3 - - - -
153A ILE* 4.2 19.3 - - - -
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Residues in contact with ASP 121 (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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119A LYS 3.6 2.5 - - - -
120A CYS* 1.3 80.7 - - - +
122A LEU* 1.3 63.9 + - - +
123A SER* 3.2 8.6 + - - -
124A ASP* 4.7 2.8 - - - +
148A SER* 2.7 27.6 + - - +
150A LYS* 3.5 13.5 + - - +
151A ASN* 3.5 25.6 - - - +
153A ILE* 5.5 2.7 - - + -
302A GNP 2.9 40.9 + - - +
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Residues in contact with LEU 122 (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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87A ILE* 4.2 1.0 - - - +
88A THR* 3.4 21.0 - - + +
119A LYS* 2.8 38.7 + - + +
121A ASP* 1.3 83.9 - - - +
123A SER* 1.3 62.5 + - - +
124A ASP* 3.3 9.2 - - - +
125A ILE* 3.1 32.3 + - + +
126A ARG 3.4 4.9 + - - -
150A LYS* 6.0 1.3 - - - +
302A GNP 3.5 30.3 - - - +
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Residues in contact with SER 123 (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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87A ILE* 4.1 12.6 - - - -
120A CYS 3.5 15.5 + - - -
121A ASP 3.2 5.2 + - - -
122A LEU* 1.3 73.3 - - - +
124A ASP* 1.3 58.9 + - - +
125A ILE 3.0 5.4 - - - -
126A ARG* 2.9 35.8 + - - +
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Residues in contact with ASP 124 (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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121A ASP 4.7 2.1 - - - +
122A LEU* 3.9 13.5 - - - +
123A SER* 1.3 76.5 + - - +
125A ILE* 1.3 71.6 + - - +
126A ARG 3.6 0.4 - - - -
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Residues in contact with ILE 125 (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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88A THR* 3.6 30.7 - - + +
122A LEU* 3.3 33.7 - - + +
123A SER 3.0 0.4 - - - -
124A ASP* 1.3 89.6 - - - +
126A ARG* 1.3 69.2 + - - +
127A GLU* 3.4 6.1 + - - +
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Residues in contact with ARG 126 (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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87A ILE* 3.5 29.5 - - + +
88A THR* 4.3 0.7 - - - +
120A CYS* 5.1 2.0 + - - +
122A LEU 3.4 5.5 + - - -
123A SER* 2.9 28.3 + - - +
124A ASP 3.6 0.2 - - - -
125A ILE* 1.3 79.8 - - - +
127A GLU* 1.3 66.7 + - - +
128A VAL 2.9 34.8 + - - +
129A PRO* 4.0 9.4 - - + -
130A LEU* 3.6 11.5 - - - +
146A GLU* 2.4 45.6 + - - -
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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