Contacts of the helix formed by residues 82 - 100 (chain B) in PDB entry 1OFD
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 GLU 82 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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80B PRO* 3.5 2.5 - - + +
81B GLN* 1.3 74.9 - - - +
83B PRO* 1.3 74.1 - - + +
84B SER* 2.7 40.9 + - - -
85B ALA* 2.8 27.0 + - + +
86B ARG* 2.8 26.2 + - - +
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Residues in contact with PRO 83 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81B GLN 3.1 9.6 - - - +
82B GLU* 1.3 93.6 - - + +
84B SER* 1.3 60.6 + - - +
86B ARG* 3.2 18.4 + - + +
87B GLU* 3.1 28.9 + - - +
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Residues in contact with SER 84 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82B GLU* 2.7 28.2 + - - -
83B PRO* 1.3 73.2 - - - +
85B ALA* 1.3 64.7 + - - +
87B GLU* 3.2 9.5 + - - +
88B VAL* 3.2 27.0 + - - +
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Residues in contact with ALA 85 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80B PRO* 3.7 20.8 - - + +
82B GLU* 2.8 27.4 + - + +
84B SER* 1.3 74.3 + - - +
86B ARG* 1.3 63.6 + - - +
88B VAL* 3.3 8.0 + - - +
89B ALA* 3.1 23.6 + - - +
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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
----------------------------------------------------------
79B LEU* 4.2 13.4 - - + +
80B PRO* 3.2 29.7 + - - +
81B GLN* 2.8 35.6 + - - -
82B GLU 2.8 9.4 + - - +
83B PRO* 3.3 19.5 - - - +
84B SER 3.2 0.2 - - - -
85B ALA* 1.3 75.9 - - - +
87B GLU* 1.3 61.2 + - - +
89B ALA* 3.4 3.6 + - - +
90B ARG* 3.0 50.1 + - - +
109B GLU* 5.2 1.0 + - - -
127B HIS* 3.3 47.0 + - - -
129B GLU* 4.5 1.0 + - - -
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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
----------------------------------------------------------
83B PRO 3.1 16.5 + - - +
84B SER* 3.2 9.1 + - - +
86B ARG* 1.3 79.6 - - - +
88B VAL* 1.3 61.6 + - + +
90B ARG* 2.8 50.4 + - - +
91B ALA* 2.9 30.7 + - - +
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Residues in contact with VAL 88 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84B SER 3.2 15.1 + - - +
85B ALA* 3.3 10.7 + - - +
87B GLU* 1.3 78.0 - - + +
89B ALA* 1.3 62.3 + - - +
91B ALA* 3.5 5.8 + - - +
92B TYR* 3.1 21.8 + - + +
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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
----------------------------------------------------------
79B LEU* 3.9 4.3 - - + -
80B PRO* 3.7 23.1 - - + -
85B ALA 3.1 12.4 + - - +
86B ARG 3.6 8.3 - - - +
87B GLU 3.3 0.2 - - - -
88B VAL* 1.3 76.4 - - - +
90B ARG* 1.3 64.3 + - - +
92B TYR* 3.2 6.3 + - - +
93B VAL* 3.1 26.0 + - - +
163B PHE* 3.7 29.8 - - + -
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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
----------------------------------------------------------
79B LEU* 4.2 9.5 - - + +
86B ARG* 3.0 30.3 + - - +
87B GLU* 2.8 42.8 + - - +
89B ALA* 1.3 76.0 - - - +
91B ALA* 1.3 64.7 + - - +
93B VAL* 3.2 4.3 + - - +
94B GLU* 3.1 31.2 + - - +
107B TRP* 3.3 51.1 - - + +
129B GLU* 2.7 43.2 + - - -
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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
----------------------------------------------------------
87B GLU 2.9 18.7 + - - +
88B VAL* 3.8 7.0 - - - +
90B ARG* 1.3 77.2 - - - +
92B TYR* 1.3 57.1 + - - +
94B GLU* 3.4 8.5 + - - +
95B GLU* 2.9 29.4 + - - +
98B ARG* 4.4 3.9 + - - +
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Residues in contact with TYR 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 VAL* 3.1 15.9 + - + +
89B ALA* 3.2 9.8 + - - +
91B ALA* 1.3 75.2 - - - +
93B VAL* 1.3 65.0 + - - +
95B GLU* 3.2 25.7 + - + +
96B VAL* 3.0 47.2 + - + +
154B ILE* 3.8 21.9 + - - +
155B ILE* 4.1 15.0 - - + -
157B LYS* 5.5 1.6 - - - +
158B LYS* 3.6 40.3 - - + +
163B PHE* 3.9 23.1 - + + -
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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
----------------------------------------------------------
77B VAL* 4.6 11.9 - - + -
79B LEU* 4.9 0.4 - - + -
89B ALA 3.1 15.2 + - - +
90B ARG* 3.2 6.9 + - - +
92B TYR* 1.3 73.6 - - - +
94B GLU* 1.3 57.5 + - - +
96B VAL* 3.2 3.8 + - - +
97B VAL* 3.0 32.0 + - + +
107B TRP* 3.9 19.3 - - + -
131B ILE* 3.9 28.3 - - + -
155B ILE* 4.1 27.3 - - + +
163B PHE* 3.6 24.0 - - + -
165B VAL* 5.2 1.3 - - + -
168B PHE* 4.9 2.7 - - + -
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Residues in contact with GLU 94 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90B ARG* 3.1 25.4 + - - +
91B ALA* 3.8 4.9 - - - +
93B VAL* 1.3 74.1 - - - +
95B GLU* 1.3 58.7 + - - +
97B VAL* 3.2 3.1 + - - +
98B ARG* 2.9 55.5 + - - +
104B VAL* 3.8 33.1 - - + +
107B TRP* 2.7 34.8 + - - +
131B ILE* 4.3 3.6 - - + -
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Residues in contact with GLU 95 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91B ALA 2.9 19.5 + - - +
92B TYR* 3.4 29.4 - - + +
94B GLU* 1.3 74.9 - - - +
96B VAL* 1.3 64.0 + - + +
98B ARG* 3.5 23.2 + - - +
99B LEU* 3.2 36.6 + - + +
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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
----------------------------------------------------------
92B TYR* 3.0 41.2 + - + +
93B VAL 4.1 0.7 - - - +
95B GLU* 1.3 75.3 - - + +
97B VAL* 1.3 65.9 + - - +
99B LEU* 3.2 18.9 + - + +
100B GLU* 3.3 14.8 + - - +
151B ALA* 3.6 36.8 - - + +
154B ILE* 4.2 22.8 - - + +
155B ILE* 3.7 24.2 - - + -
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Residues in contact with VAL 97 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93B VAL* 3.0 26.6 + - + +
94B GLU 3.2 4.0 + - - +
96B VAL* 1.3 75.7 - - - +
98B ARG* 1.3 61.5 + - - +
100B GLU* 3.2 17.6 + - - +
102B LEU* 3.3 43.4 + - + +
104B VAL* 3.6 24.2 - - + -
131B ILE* 4.4 2.0 - - + -
133B VAL* 3.7 13.7 - - + -
151B ALA* 4.9 5.8 - - + -
155B ILE* 5.2 1.1 - - + -
168B PHE* 3.6 35.7 - - + -
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Residues in contact with ARG 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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91B ALA* 4.4 4.6 + - - +
94B GLU* 2.9 51.9 + - - +
95B GLU* 3.6 28.4 - - - +
97B VAL* 1.3 77.7 - - - +
99B LEU* 1.3 58.2 + - + +
101B LYS* 2.9 22.0 + - - +
102B LEU 3.6 15.0 - - - +
103B THR* 5.9 0.2 - - - -
104B VAL* 5.5 7.0 - - + +
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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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95B GLU* 3.2 33.0 + - + +
96B VAL* 3.2 14.5 + - + +
98B ARG* 1.3 78.9 - - + +
100B GLU* 1.3 58.8 + - + +
101B LYS* 3.2 8.7 + - - +
154B ILE* 6.3 2.9 - - + -
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Residues in contact with GLU 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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96B VAL* 3.3 9.4 + - - +
97B VAL* 3.2 9.0 + - - +
98B ARG 3.1 0.8 - - - -
99B LEU* 1.3 76.1 - - + +
101B LYS* 1.3 70.5 + - - +
102B LEU* 3.3 16.4 + - + +
147B ARG* 2.6 54.5 + - + +
150B ILE* 2.9 22.6 - - + +
151B ALA* 2.4 48.9 + - - +
154B ILE* 4.8 3.3 - - + +
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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
------------------------------------------------------------
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