Contacts of the helix formed by residues 81 - 94 (chain B) in PDB entry 4F5G
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 LEU 81 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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76B LEU* 3.5 24.5 - - + +
79B ASP 4.0 3.0 + - - +
80B GLY* 1.3 70.6 - - - -
82B PRO* 1.3 76.3 - - + +
83B GLU* 3.2 10.1 - - + +
84B PHE* 2.9 19.1 + - + +
85B GLY* 3.2 9.2 + - - -
109B GLN* 2.9 16.9 + - - +
298B ALA* 6.6 0.2 - - - -
301B ALA* 4.2 4.0 - - + +
302B SER* 3.9 28.5 - - - +
305B ALA* 3.8 28.7 - - + -
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Residues in contact with PRO 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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76B LEU* 5.0 2.0 - - + -
79B ASP* 6.4 1.1 - - - -
80B GLY 3.3 10.1 - - - +
81B LEU* 1.3 89.8 - - + +
83B GLU* 1.3 64.3 + - - +
85B GLY* 3.0 4.8 + - - +
86B ARG* 2.9 22.8 + - - +
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Residues in contact with GLU 83 (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 LEU* 3.2 11.8 - - + +
82B PRO* 1.3 79.5 - - - +
84B PHE* 1.3 57.4 + - - +
86B ARG* 3.3 22.0 + - - +
87B CYS* 2.9 28.9 + - - -
305B ALA* 3.5 22.4 - - + +
306B THR* 4.8 0.7 + - - -
309B SER* 2.8 36.7 + - - +
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Residues in contact with PHE 84 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81B LEU* 2.9 23.7 + - + +
83B GLU* 1.3 79.5 - - - +
85B GLY* 1.3 60.6 + - - +
87B CYS* 3.3 3.7 + - + +
88B THR* 2.9 53.3 + - - -
109B GLN* 3.7 27.6 - - + -
254B CYS* 4.1 7.6 - - - -
265B VAL* 3.5 32.3 - - + -
266B GLY* 3.3 31.6 - - - -
267B ALA* 4.0 4.9 - - + -
301B ALA* 3.6 27.4 - - + +
304B VAL* 3.8 23.6 - - + -
305B ALA* 4.2 5.3 - - - +
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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
----------------------------------------------------------
79B ASP 6.1 1.1 - - - -
81B LEU 3.2 8.1 + - - -
82B PRO* 3.0 8.2 + - - -
84B PHE* 1.3 80.1 - - - +
86B ARG* 1.3 61.9 + - - +
88B THR* 3.3 2.6 + - - -
89B GLN* 3.0 31.2 + - - +
107B THR* 4.0 27.5 + - - -
109B GLN* 5.8 1.1 - - - -
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Residues in contact with ARG 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 PRO 2.9 12.4 + - - +
83B GLU* 3.7 20.0 + - - +
85B GLY* 1.3 76.0 - - - +
87B CYS* 1.3 75.7 + - - +
89B GLN* 3.2 10.2 + - + +
90B GLU* 2.9 64.2 + - + +
95B LYS* 5.4 3.4 - - - +
309B SER* 3.7 24.0 + - - +
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Residues in contact with CYS 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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83B GLU* 2.9 23.0 + - - +
84B PHE* 3.7 6.3 - - - +
86B ARG* 1.3 91.0 - - - +
88B THR* 1.3 63.5 + - - +
90B GLU* 3.3 9.5 + - - +
91B LEU* 3.0 28.1 + - - +
304B VAL* 5.3 2.0 - - + -
305B ALA* 4.5 6.5 - - - -
308B LEU* 3.6 37.0 - - + +
309B SER* 3.7 22.0 - - - -
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Residues in contact with THR 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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84B PHE* 2.9 45.2 + - - -
85B GLY* 3.6 6.7 - - - -
87B CYS* 1.3 77.6 - - - +
89B GLN* 1.3 63.4 + - - +
91B LEU* 3.2 11.2 + - + +
92B LEU* 2.9 40.9 + - + +
107B THR* 4.6 3.4 - - + -
252B SER* 3.4 26.5 - - - +
254B CYS* 5.4 2.8 - - - -
267B ALA* 4.1 10.1 - - + -
269B THR* 4.5 4.9 - - - +
304B VAL* 5.8 0.3 - - - +
308B LEU* 5.3 0.2 - - - +
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Residues in contact with GLN 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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85B GLY 3.0 19.3 + - - +
86B ARG* 3.2 7.0 + - - +
88B THR* 1.3 75.0 - - - +
90B GLU* 1.3 58.0 + - - +
92B LEU* 4.5 3.1 - - - -
93B PHE* 2.9 44.7 + - + +
100B ILE* 3.7 24.4 - - + +
105B ALA* 3.5 34.7 + - - +
106B ARG* 3.5 2.4 - - - +
107B THR* 2.6 45.3 + - - +
269B THR* 4.2 6.5 - - + +
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Residues in contact with GLU 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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86B ARG* 2.9 61.1 + - + +
87B CYS* 3.8 6.3 - - - +
88B THR 3.2 0.2 - - - -
89B GLN* 1.3 75.2 - - - +
91B LEU* 1.3 61.0 + - - +
94B GLY* 2.8 32.8 + - - -
95B LYS* 3.1 47.3 + - + +
100B ILE* 4.2 16.6 - - + -
232B GLU* 5.0 1.0 - - - +
239B ARG* 4.0 0.7 + - - -
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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 CYS 3.0 16.3 + - - +
88B THR* 3.5 11.7 - - + +
90B GLU* 1.3 76.6 - - - +
92B LEU* 1.3 59.6 + - + +
225B GLN* 2.8 32.2 + - - +
231B LEU* 4.2 33.0 - - + -
232B GLU* 4.4 3.7 - - - +
239B ARG* 2.9 17.2 + - - +
254B CYS* 5.7 4.9 - - - -
257B ASN* 5.7 4.3 - - - +
258B PHE* 4.8 7.6 - - + -
304B VAL* 5.7 0.2 - - + -
308B LEU* 3.7 29.4 - - + -
317B TRP* 4.6 14.6 - - + -
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Residues in contact with LEU 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 THR* 2.9 38.6 + - + +
89B GLN* 3.8 3.1 - - - +
91B LEU* 1.3 78.5 - - + +
93B PHE* 1.3 76.6 + - + +
222B ILE* 3.6 30.5 - - + -
225B GLN* 3.9 13.9 - - - +
235B ALA* 3.7 5.9 - - - +
238B LEU* 3.6 22.1 - - + +
239B ARG* 2.8 23.2 + - - +
250B VAL* 3.8 20.9 - - + -
252B SER* 4.2 8.7 - - - +
269B THR* 3.9 14.6 - - - +
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Residues in contact with PHE 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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89B GLN* 2.9 34.5 + - + +
92B LEU* 1.3 80.3 - - + +
94B GLY* 1.3 62.7 + - - +
97B SER* 3.5 29.1 + - - +
99B LEU* 4.0 29.2 - - + -
100B ILE* 4.5 4.9 - - + -
105B ALA* 4.3 3.4 - - + -
238B LEU* 3.4 28.7 - - + -
239B ARG* 3.4 23.0 + - + +
242B ALA* 4.0 16.8 - - + -
248B LEU* 4.6 1.3 - - + -
250B VAL* 4.2 13.9 - - + -
269B THR* 3.9 23.8 - - + -
271B VAL* 3.8 22.2 - - + -
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Residues in contact with GLY 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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90B GLU* 2.8 18.0 + - - -
93B PHE* 1.3 77.9 - - - +
95B LYS* 1.3 67.4 + - - -
96B GLY 3.4 0.2 + - - -
97B SER* 3.1 21.8 + - - -
100B ILE* 3.9 6.1 - - - +
232B GLU* 4.9 4.3 - - - -
239B ARG* 3.4 18.7 - - - +
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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