Contacts of the helix formed by residues 86 - 93 (chain B) in PDB entry 3F7G
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 SER 86 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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83B GLY 4.3 1.2 + - - -
84B MET* 3.2 1.0 - - - +
85B GLY* 1.3 77.9 - - - +
87B GLU* 1.3 59.5 + - - +
88B GLU* 3.6 13.0 + - - +
89B LEU* 3.2 30.2 + - - +
90B ARG* 3.0 28.9 + - - +
95D TYR* 4.7 11.6 + - - -
115D HIS 5.5 0.5 + - - -
116D THR 4.4 15.0 - - - -
117D GLY* 5.4 3.7 - - - -
118D HIS* 6.3 0.6 - - - -
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Residues in contact with GLU 87 (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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85B GLY 3.9 1.0 + - - -
86B SER* 1.3 69.5 + - - +
88B GLU* 1.3 60.8 + - - +
90B ARG* 3.2 22.7 + - - +
91B LEU* 2.8 30.6 + - + +
106B GLU 4.4 3.5 - - - +
109B ALA* 4.0 16.0 - - + +
110B ALA* 3.7 33.0 + - - +
95D TYR* 5.6 3.1 + - - +
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Residues in contact with GLU 88 (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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86B SER* 3.4 8.0 + - - +
87B GLU* 1.3 78.7 - - - +
89B LEU* 1.3 58.6 + - + +
91B LEU* 3.3 21.7 + - + +
92B ALA* 2.9 26.7 + - - +
84D MET* 3.5 10.0 - - - +
89D LEU* 2.9 44.4 - - - +
92D ALA* 4.1 22.6 - - + +
93D SER* 3.2 13.7 + - - -
95D TYR* 4.7 17.5 + - + -
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Residues in contact with LEU 89 (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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83B GLY 3.4 22.4 - - - +
84B MET* 3.9 14.2 - - - +
86B SER* 3.2 27.5 + - - +
88B GLU* 1.3 76.6 - - + +
90B ARG* 1.3 67.2 + - - +
92B ALA 3.2 8.5 + - - -
93B SER 3.4 2.1 + - - -
81D PHE* 3.3 24.5 - - + -
84D MET* 3.5 25.6 - - + -
93D SER* 4.3 6.5 - - - -
114D PHE* 3.8 20.4 - - + -
115D HIS 3.9 13.2 - - - +
116D THR* 4.6 5.4 - - - +
300D P33 3.6 24.5 - - - +
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Residues in contact with ARG 90 (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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84B MET* 3.0 40.8 + - + +
85B GLY 3.2 22.2 + - - -
86B SER 3.0 5.9 + - - +
87B GLU* 3.6 27.6 + - - +
89B LEU* 1.3 75.2 - - - +
91B LEU* 1.3 64.2 + - - +
93B SER* 2.6 23.9 + - - -
94B PHE* 3.2 9.1 - - - -
109B ALA* 2.8 32.9 + - + -
110B ALA 4.1 2.6 + - - -
112B GLY* 3.2 32.8 - - - -
113B PHE 3.6 15.3 - - - +
114B PHE* 4.1 14.1 - - + +
125B PHE* 3.7 13.4 - - - -
153B PHE* 3.8 20.6 - - - -
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Residues in contact with LEU 91 (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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87B GLU* 2.8 22.8 + - + +
88B GLU* 3.4 22.4 - - + +
89B LEU 3.1 0.2 - - - -
90B ARG* 1.3 74.3 - - - +
92B ALA* 1.3 62.5 + - - +
94B PHE* 3.0 18.9 + - + +
95B TYR 4.3 0.2 + - - -
105B PRO* 4.1 27.8 - - + -
106B GLU* 4.6 21.3 - - + +
109B ALA* 3.9 14.1 - - + +
89D LEU* 6.0 4.3 - - + -
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Residues in contact with ALA 92 (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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88B GLU* 2.9 11.4 + - - +
89B LEU 3.2 9.4 + - - +
91B LEU* 1.3 76.1 - - - +
93B SER* 1.3 60.9 + - - +
94B PHE 3.1 1.3 + - - -
95B TYR* 3.3 11.1 + - - +
81D PHE* 4.1 3.4 - - + -
83D GLY* 3.2 25.9 - - - +
84D MET* 3.6 42.4 - - + -
89D LEU* 4.3 15.3 - - + -
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Residues in contact with SER 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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84B MET* 3.7 24.7 - - - -
89B LEU 3.4 2.4 + - - -
90B ARG 2.6 21.4 + - - -
92B ALA* 1.3 76.9 - - - +
94B PHE* 1.3 55.7 + - - +
95B TYR* 3.3 10.4 + - - -
96B ASP* 3.4 11.1 - - - +
114B PHE* 3.4 2.6 - - - +
115B HIS* 2.8 48.2 + - - +
81D PHE* 4.2 8.5 - - - -
83D GLY* 4.9 0.7 - - - +
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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