Contacts of the helix formed by residues 75 - 86 (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 ARG 75 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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71B ASN* 2.9 43.5 + - - +
72B ARG* 3.6 45.1 + - - +
74B ASP* 1.3 73.1 - - - +
76B VAL* 1.3 67.5 + - - +
77B ILE 3.2 0.6 + - - -
78B PRO* 3.6 11.9 - - + +
79B PHE* 3.4 20.6 + - - +
103B SER* 3.5 24.9 + - - +
104B LEU* 2.9 39.7 + - + +
105B GLY* 4.9 1.2 - - - -
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Residues in contact with VAL 76 (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 3.6 13.9 - - - +
73B PHE* 3.3 18.4 - - - +
75B ARG* 1.3 79.9 - - - +
77B ILE* 1.3 58.0 + - + +
79B PHE* 3.3 5.7 + - + +
80B LEU* 2.9 33.8 + - + +
104B LEU* 4.1 13.2 - - + -
127B PHE* 4.0 28.3 - - + +
130B ALA* 3.9 42.2 - - + +
131B THR* 4.2 9.4 - - - +
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Residues in contact with ILE 77 (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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73B PHE 4.6 3.8 - - - +
74B ASP* 3.6 14.4 - - - +
76B VAL* 1.3 74.8 - - + +
78B PRO* 1.4 74.5 - - + +
80B LEU* 3.0 17.3 + - + +
81B GLN* 3.1 32.3 + - - +
127B PHE* 3.8 23.1 - - + -
446B ARG* 4.6 18.4 - - - +
448B LEU* 3.4 38.1 - - + -
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Residues in contact with PRO 78 (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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74B ASP 3.1 19.3 - - - +
75B ARG* 3.6 12.8 - - + +
77B ILE* 1.4 88.7 - - + +
79B PHE* 1.3 59.3 + - - +
81B GLN* 3.3 14.9 + - + +
82B VAL* 3.2 26.5 + - + +
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Residues in contact with PHE 79 (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 3.4 13.4 + - - +
76B VAL* 3.3 15.7 + - + +
77B ILE 3.1 1.0 - - - -
78B PRO* 1.3 80.7 - - - +
80B LEU* 1.3 69.3 + - + +
82B VAL* 3.2 8.5 + - - +
83B VAL* 3.0 36.3 + - + +
96B VAL* 4.4 2.9 - - + -
99B LEU* 3.6 29.2 - - + -
100B ALA* 3.5 41.5 - - + -
103B SER* 4.1 18.4 - - - -
104B LEU* 3.7 23.8 - - + -
108B LEU* 4.0 9.4 - - + -
126B ILE* 3.8 25.4 - - + -
130B ALA* 5.5 0.2 - - + -
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Residues in contact with LEU 80 (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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76B VAL* 2.9 21.0 + - + +
77B ILE* 3.0 10.1 + - + +
79B PHE* 1.3 80.2 - - + +
81B GLN* 1.3 52.8 + - - +
83B VAL* 3.3 5.3 + - + +
84B ALA* 2.8 35.1 + - - +
123B LEU* 3.7 37.0 - - + +
126B ILE* 3.6 31.0 - - + -
127B PHE* 3.6 39.3 - - + +
448B LEU* 4.1 15.7 - - + -
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Residues in contact with GLN 81 (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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77B ILE* 3.1 32.4 + - - +
78B PRO* 3.4 14.1 - - + +
79B PHE 3.3 0.2 - - - -
80B LEU* 1.3 75.1 - - - +
82B VAL* 1.3 64.4 + - + +
84B ALA* 3.4 8.3 + - - +
85B GLY* 3.3 17.2 + - - -
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Residues in contact with VAL 82 (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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78B PRO 3.2 15.1 + - - +
79B PHE* 3.2 7.6 + - - +
81B GLN* 1.3 75.8 - - + +
83B VAL* 1.3 66.9 + - - +
85B GLY* 3.0 13.4 + - - -
86B ILE* 3.4 16.0 + - + +
95B ARG* 5.9 2.7 - - - +
99B LEU* 3.6 31.2 - - + -
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Residues in contact with VAL 83 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79B PHE* 3.0 45.7 + - + +
80B LEU* 3.6 8.1 - - + +
82B VAL* 1.3 75.1 - - - +
84B ALA* 1.3 62.9 + - - +
86B ILE* 3.1 27.9 + - + +
96B VAL* 4.3 17.3 - - + -
99B LEU* 4.4 5.6 - - + -
121B HIS* 3.2 27.7 + - + +
123B LEU* 3.7 19.5 - - + -
126B ILE* 4.4 13.2 - - + -
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Residues in contact with ALA 84 (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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80B LEU 2.8 19.7 + - - +
81B GLN* 3.6 10.3 - - - +
82B VAL 3.2 0.4 - - - -
83B VAL* 1.3 72.6 - - - +
85B GLY* 1.3 58.0 + - - +
86B ILE 3.6 5.5 + - - +
121B HIS* 4.1 12.7 - - - -
123B LEU* 3.8 22.9 - - + +
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Residues in contact with GLY 85 (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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81B GLN 3.3 8.6 + - - -
82B VAL* 3.0 9.7 + - - -
84B ALA* 1.3 75.9 - - - +
86B ILE* 1.3 61.3 + - - +
87B PRO* 3.5 7.1 - - - +
95B ARG* 5.5 1.4 + - - -
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Residues in contact with ILE 86 (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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82B VAL* 3.4 15.2 + - + +
83B VAL* 3.1 28.7 + - + +
84B ALA 4.0 1.9 - - - +
85B GLY* 1.3 77.9 - - - +
87B PRO* 1.3 76.7 - - + +
88B LEU* 3.6 1.7 + - - +
92B HIS* 3.6 34.8 - - + +
95B ARG* 3.8 36.1 - - + +
96B VAL* 3.7 28.3 - - + -
99B LEU* 5.2 3.8 - - + -
121B HIS* 2.8 26.4 + - + -
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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