Contacts of the helix formed by residues 85 - 98 (chain B) in PDB entry 2FQ6
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 CYS 85 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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83B PHE* 3.2 2.5 - - - +
84B PRO* 1.3 81.1 - - - +
86B GLY* 1.3 65.4 + - - +
87B ALA* 3.7 5.6 - - - -
88B ALA* 3.3 24.8 + - - +
89B ALA 3.0 17.8 + - - -
219B MET* 3.9 17.7 - - + -
220B ILE 3.6 10.5 - - - +
221B GLY* 3.3 12.1 - - - -
700B P3F 3.4 23.3 - - - +
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Residues in contact with GLY 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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85B CYS* 1.3 71.6 - - - +
87B ALA* 1.3 56.1 + - - +
89B ALA* 3.0 3.6 + - - +
90B VAL* 2.9 33.8 + - - +
205B ILE* 4.8 0.3 - - - +
206B GLN 4.1 2.2 - - - -
207B ALA* 3.6 22.9 - - - -
220B ILE 3.7 3.8 + - - -
221B GLY* 4.0 4.7 - - - -
700B P3F 2.9 28.3 + - - -
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Residues in contact with ALA 87 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85B CYS* 4.0 6.1 - - - -
86B GLY* 1.3 71.8 - - - +
88B ALA* 1.3 56.6 + - - +
90B VAL* 3.4 7.7 + - - +
91B ALA* 3.0 31.8 + - - +
111B TYR* 5.1 2.7 - - + +
113B PRO* 5.1 15.9 - - + -
700B P3F 2.8 29.5 + - - +
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Residues in contact with ALA 88 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83B PHE* 3.9 2.5 - - + -
84B PRO* 3.4 35.0 - - + -
85B CYS* 3.3 16.5 + - - +
87B ALA* 1.3 74.2 - - - +
89B ALA* 1.3 59.9 + - - +
91B ALA* 4.9 1.8 - - - -
92B ASN* 3.0 41.4 + - - +
242B GLN* 3.7 12.6 - - - +
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Residues in contact with ALA 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 PHE* 3.2 34.5 - - + +
85B CYS 3.0 7.3 + - - -
86B GLY 3.0 7.2 + - - +
88B ALA* 1.3 74.8 - - - +
90B VAL* 1.3 57.2 + - - +
93B SER* 2.8 37.0 + - - +
205B ILE* 3.8 18.6 - - + -
206B GLN 4.4 0.4 - - - +
221B GLY* 3.8 17.7 - - - -
222B THR 3.9 4.5 - - - +
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Residues in contact with VAL 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 GLY 2.9 18.6 + - - +
87B ALA* 3.7 9.6 - - - +
88B ALA 3.3 0.2 - - - -
89B ALA* 1.3 74.9 - - - +
91B ALA* 1.3 67.7 + - - +
93B SER* 3.9 1.2 - - - -
94B ILE* 3.1 37.0 + - + +
111B TYR* 6.0 0.4 - - + -
114B SER* 3.6 35.0 - - - +
117B PHE* 5.4 0.9 - - + -
152B PHE* 3.8 22.2 - - + -
185B ASP* 4.1 15.3 - - - +
205B ILE* 4.1 20.0 - - + -
700B P3F 5.0 3.8 - - + -
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Residues in contact with ALA 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 ALA 3.0 20.5 + - - +
88B ALA* 4.3 2.5 - - - +
90B VAL* 1.3 74.5 - - - +
92B ASN* 1.3 64.6 + - - +
94B ILE 3.4 0.2 + - - -
95B LEU* 2.9 25.4 + - - +
117B PHE* 3.3 51.0 - - + -
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Residues in contact with ASN 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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83B PHE* 3.5 18.2 - - + -
88B ALA* 3.0 29.6 + - - +
91B ALA* 1.3 83.0 - - - +
93B SER* 1.3 64.8 + - - +
95B LEU* 3.8 10.4 - - - +
96B ALA* 2.9 24.9 + - - +
233B LEU* 4.4 1.2 - - - +
237B ALA* 5.0 5.7 - - + +
240B MET* 3.4 34.3 - - - +
242B GLN* 3.5 27.9 - - + +
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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
----------------------------------------------------------
83B PHE* 4.0 3.2 - - - -
89B ALA 2.8 24.7 + - - -
90B VAL 3.9 0.7 - - - -
92B ASN* 1.3 78.1 - - - +
94B ILE* 1.3 61.8 + - - +
96B ALA* 3.4 2.8 + - - +
97B PHE* 3.4 24.1 - - - -
183B MET* 3.4 8.4 - - - +
203B VAL* 4.8 0.2 - - - -
205B ILE* 3.7 21.5 - - - +
223B ALA* 3.6 25.6 - - - +
233B LEU* 3.7 22.9 - - - +
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Residues in contact with ILE 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 VAL* 3.1 28.6 + - + +
93B SER* 1.3 76.0 - - - +
95B LEU* 1.3 64.0 + - - +
97B PHE 3.1 10.7 + - - -
98B ILE* 3.4 12.7 + - + +
104B VAL* 4.4 6.7 - - + -
106B MET* 3.9 15.5 - - + -
117B PHE* 3.6 31.2 - - + -
118B CYS* 4.4 1.6 - - - -
122B LEU* 3.7 16.4 - - + -
150B ILE* 3.5 27.5 - - + +
152B PHE* 3.8 31.4 - - + -
183B MET* 4.1 9.2 - - - -
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Residues in contact with LEU 95 (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 ALA 2.9 19.1 + - - +
92B ASN* 3.8 10.5 - - - +
93B SER 3.4 0.2 - - - -
94B ILE* 1.3 75.7 - - - +
96B ALA* 1.3 62.8 + - - +
97B PHE 3.1 1.6 + - - -
98B ILE* 3.3 41.2 + - + +
117B PHE* 4.2 11.9 - - + -
121B ILE* 5.8 0.9 - - + -
122B LEU* 4.6 5.4 - - + -
125B LEU* 4.4 20.6 - - + -
240B MET* 4.0 41.7 - - + -
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Residues in contact with ALA 96 (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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92B ASN 2.9 17.9 + - - +
93B SER 3.5 7.6 - - - +
94B ILE 3.2 0.6 - - - -
95B LEU* 1.3 78.0 - - - +
97B PHE* 1.3 60.6 + - + +
98B ILE 5.1 1.1 - - - +
232B GLN* 2.8 18.2 + - - +
233B LEU* 3.9 27.8 - - + +
236B ASN* 2.9 39.0 + - + +
237B ALA 4.7 2.7 - - - +
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Residues in contact with PHE 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 SER 3.4 14.6 - - - -
94B ILE 3.1 6.4 + - - +
95B LEU 3.1 0.8 - - - -
96B ALA* 1.3 79.0 - - + +
98B ILE* 1.3 62.9 - - - +
149B LYS* 3.1 30.7 + - - +
150B ILE* 4.3 11.4 - - + -
181B ILE* 3.7 36.8 - - + -
183B MET* 3.6 13.0 - - + -
203B VAL* 4.5 3.6 - - + -
229B CYS* 3.3 39.5 - - + -
232B GLN* 3.4 37.1 + - + +
233B LEU* 3.7 36.3 - - + -
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Residues in contact with ILE 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 ILE* 3.4 12.3 - - + +
95B LEU* 3.3 34.2 + - + +
96B ALA 5.1 0.7 - - - +
97B PHE* 1.3 82.0 - - - +
99B GLU* 1.3 71.8 + - - +
102B ASP* 3.4 16.4 - - + +
104B VAL* 3.9 19.3 - - + -
122B LEU* 3.8 23.8 - - + -
125B LEU* 5.6 3.6 - - + -
127B VAL* 4.3 14.8 - - + -
149B LYS* 4.5 2.2 - - + -
150B ILE* 3.6 27.6 - - + -
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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