Contacts of the helix formed by residues 92 - 105 (chain B) in PDB entry 2FGY
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 HIS 92 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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86B ILE* 3.6 24.5 - - + -
87B PRO 3.6 10.1 + - - -
88B LEU* 4.8 1.6 - - - -
89B GLY 5.1 1.1 - - - -
90B LEU 2.7 23.8 + - - +
91B ASP* 1.3 75.7 + - - +
93B VAL* 1.3 69.4 + - + +
94B THR 3.5 2.0 - - - -
95B ARG* 3.4 20.5 + - - +
96B VAL* 2.9 40.0 + - + +
113B LEU* 4.8 6.8 + - + -
115B ASP* 3.2 16.8 + - - -
121B HIS* 3.5 8.7 - + - -
721B ZN 2.1 36.5 - - - -
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Residues in contact with VAL 93 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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91B ASP* 3.6 25.5 + - - +
92B HIS* 1.3 79.6 - - + +
94B THR* 1.3 68.2 + - - +
96B VAL* 3.0 5.5 + - - +
97B GLN* 2.9 39.2 + - - +
110B GLU* 3.9 22.4 - - - +
113B LEU* 4.1 38.1 - - + +
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Residues in contact with THR 94 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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91B ASP* 4.7 4.4 + - - -
92B HIS 3.5 0.4 - - - -
93B VAL* 1.3 80.2 - - - +
95B ARG* 1.3 56.9 + - - +
97B GLN* 4.5 6.1 - - + +
98B GLU* 2.9 55.4 + - + +
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Residues in contact with ARG 95 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82B VAL* 5.9 3.2 - - - +
85B GLY 5.5 0.8 + - - -
86B ILE* 3.8 43.6 - - + +
87B PRO* 4.1 12.7 - - - +
92B HIS* 3.5 26.2 - - - +
93B VAL 3.2 0.2 - - - -
94B THR* 1.3 79.8 - - - +
96B VAL* 1.3 59.5 + - - +
98B GLU* 4.1 7.3 - - - +
99B LEU* 3.2 24.4 + - + +
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Residues in contact with VAL 96 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79B PHE* 4.4 1.3 - - + -
83B VAL* 4.3 25.1 - - + -
86B ILE* 3.7 23.1 - - + -
92B HIS* 2.9 40.2 + - + +
93B VAL* 3.7 2.9 - - - +
95B ARG* 1.3 73.7 - - - +
97B GLN* 1.3 61.5 + - - +
99B LEU* 3.3 6.1 + - - +
100B ALA* 2.8 27.5 + - - +
108B LEU* 3.8 13.7 - - + -
113B LEU* 3.6 31.0 - - + -
126B ILE* 5.0 0.7 - - + -
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Residues in contact with GLN 97 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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93B VAL* 2.9 21.5 + - - +
94B THR* 4.1 6.9 - - + +
96B VAL* 1.3 77.1 - - - +
98B GLU* 1.3 57.2 + - + +
100B ALA* 3.7 4.7 - - - +
101B GLN* 3.0 28.8 + - - +
107B THR* 3.3 27.8 + - - +
108B LEU* 2.4 40.6 + - + +
110B GLU* 3.3 30.6 + - - +
113B LEU* 3.8 18.6 - - + +
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Residues in contact with GLU 98 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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94B THR* 2.9 41.3 + - + +
95B ARG* 4.1 5.8 - - - +
97B GLN* 1.3 75.4 - - + +
99B LEU* 1.3 60.6 + - - +
101B GLN* 3.4 6.7 + - - +
102B SER* 3.0 30.5 + - - -
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Residues in contact with LEU 99 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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79B PHE* 3.6 27.1 - - + -
82B VAL* 3.6 38.4 - - + -
83B VAL* 4.4 9.0 - - + -
86B ILE* 5.2 5.6 - - + -
95B ARG* 3.2 18.6 + - + +
96B VAL* 3.7 4.0 - - - +
98B GLU* 1.3 78.0 - - - +
100B ALA* 1.3 56.7 + - - +
102B SER* 3.6 7.4 + - - +
103B SER* 2.8 48.5 + - - +
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Residues in contact with ALA 100 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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79B PHE* 3.5 15.8 - - + -
96B VAL 2.8 19.5 + - - +
97B GLN* 3.7 5.2 - - - +
99B LEU* 1.3 76.1 - - - +
101B GLN* 1.3 56.9 + - - +
104B LEU* 2.8 36.9 + - + +
105B GLY 3.3 0.9 + - - -
106B HIS 3.1 19.1 - - - +
107B THR* 4.7 0.4 - - - -
108B LEU* 3.7 29.6 - - + -
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Residues in contact with GLN 101 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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97B GLN 3.0 18.0 + - - +
98B GLU* 3.7 7.6 - - - +
99B LEU 3.4 0.2 - - - -
100B ALA* 1.3 74.9 - - - +
102B SER* 1.3 59.7 + - - +
105B GLY* 3.0 38.5 + - - +
106B HIS* 3.2 22.4 + - - +
107B THR* 4.0 8.1 + - - +
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Residues in contact with SER 102 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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98B GLU 3.0 16.1 + - - -
99B LEU* 3.6 13.3 + - - +
101B GLN* 1.3 77.7 - - - +
103B SER* 1.3 64.6 + - - +
105B GLY 4.6 0.6 + - - -
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Residues in contact with SER 103 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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75B ARG* 3.5 29.7 + - - +
79B PHE* 4.1 20.8 - - - +
99B LEU* 2.8 39.3 + - - +
102B SER* 1.3 75.7 + - - +
104B LEU* 1.3 64.2 + - - +
105B GLY 3.7 0.4 - - - -
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Residues in contact with LEU 104 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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72B ARG* 5.2 1.7 + - - +
75B ARG* 2.9 52.9 + - + +
76B VAL* 4.1 25.4 - - + -
79B PHE* 3.7 38.1 - - + -
100B ALA* 2.8 19.5 + - + +
103B SER* 1.3 79.5 - - - +
105B GLY* 1.3 62.7 + - - +
106B HIS* 3.4 40.5 - - + +
108B LEU* 5.2 1.3 - - + -
130B ALA* 4.1 11.2 - - + -
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Residues in contact with GLY 105 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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75B ARG* 4.9 1.3 - - - -
100B ALA 3.3 0.2 + - - -
101B GLN* 3.0 34.4 + - - +
102B SER 4.6 0.6 + - - -
103B SER 3.7 0.8 - - - -
104B LEU* 1.3 78.2 - - - +
106B HIS* 1.3 59.9 + - - +
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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