Contacts of the helix formed by residues 82 - 100 (chain A) 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 A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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80A PRO* 3.4 2.0 - - + +
81A GLN* 1.3 77.1 - - - +
83A PRO* 1.3 69.1 - - + +
84A SER* 2.7 42.1 + - - -
85A ALA* 2.8 29.1 + - + +
86A ARG* 2.8 32.3 + - - +
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Residues in contact with PRO 83 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81A GLN 3.3 8.5 - - - +
82A GLU* 1.3 94.5 - - + +
84A SER* 1.3 61.9 + - - +
86A ARG* 3.3 19.6 + - + +
87A GLU* 3.1 28.6 + - - +
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Residues in contact with SER 84 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82A GLU* 2.7 30.4 + - - -
83A PRO* 1.3 73.2 - - - +
85A ALA* 1.3 62.8 + - - +
87A GLU* 3.3 7.9 + - - +
88A VAL* 3.3 24.4 + - - +
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Residues in contact with ALA 85 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80A PRO* 3.8 20.8 - - + +
82A GLU* 2.8 24.7 + - + +
84A SER* 1.3 78.3 + - - +
86A ARG* 1.3 60.8 + - - +
88A VAL* 3.3 9.4 + - - +
89A ALA* 3.1 23.0 + - - +
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Residues in contact with ARG 86 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79A LEU* 4.2 15.0 - - + +
80A PRO* 3.1 29.9 + - - +
81A GLN* 2.7 36.1 + - - -
82A GLU 2.8 14.3 + - - +
83A PRO* 3.4 18.7 - - - +
84A SER 3.3 0.2 - - - -
85A ALA* 1.3 72.9 - - - +
87A GLU* 1.3 61.2 + - - +
89A ALA* 3.5 2.3 + - - +
90A ARG* 2.9 46.9 + - - +
127A HIS* 3.3 48.9 + - - -
129A GLU* 4.6 1.0 + - - -
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Residues in contact with GLU 87 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83A PRO 3.1 17.8 + - - +
84A SER* 3.8 6.7 - - - +
85A ALA 3.2 0.4 - - - -
86A ARG* 1.3 84.0 - - - +
88A VAL* 1.3 58.8 + - + +
90A ARG* 2.9 48.3 + - - +
91A ALA* 3.0 31.2 + - - +
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Residues in contact with VAL 88 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84A SER 3.3 14.4 + - - +
85A ALA* 3.3 10.7 + - - +
87A GLU* 1.3 76.7 - - - +
89A ALA* 1.3 63.2 + - - +
91A ALA* 3.5 6.4 + - - +
92A TYR* 3.1 22.4 + - + +
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Residues in contact with ALA 89 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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79A LEU* 3.8 4.3 - - + -
80A PRO* 3.7 22.4 - - + -
85A ALA 3.1 14.1 + - - +
86A ARG 3.6 7.2 - - - +
87A GLU 3.2 0.2 - - - -
88A VAL* 1.3 76.0 - - - +
90A ARG* 1.3 64.6 + - - +
92A TYR* 3.1 6.0 + - - +
93A VAL* 3.1 25.6 + - - +
163A PHE* 3.7 29.9 - - + -
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Residues in contact with ARG 90 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79A LEU* 4.1 9.2 - - + +
86A ARG* 2.9 29.0 + - - +
87A GLU* 2.9 42.6 + - - +
89A ALA* 1.3 75.1 - - - +
91A ALA* 1.3 63.3 + - - +
93A VAL* 3.3 3.2 + - - +
94A GLU* 3.0 30.9 + - - +
107A TRP* 3.2 58.3 - - + +
129A GLU* 2.7 43.8 + - - -
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Residues in contact with ALA 91 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87A GLU 3.0 18.6 + - - +
88A VAL* 3.7 6.7 - - - +
90A ARG* 1.3 76.4 - - - +
92A TYR* 1.3 57.8 + - - +
94A GLU* 3.9 8.2 - - - +
95A GLU* 2.9 30.0 + - - +
98A ARG* 4.7 3.4 + - - +
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Residues in contact with TYR 92 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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88A VAL* 3.1 14.9 + - + +
89A ALA* 3.1 9.6 + - - +
91A ALA* 1.3 74.9 - - - +
93A VAL* 1.3 66.9 + - - +
95A GLU* 3.2 25.8 + - - +
96A VAL* 3.1 47.7 + - + +
154A ILE* 3.8 20.9 + - - +
155A ILE* 4.1 17.9 - - + -
157A LYS* 5.6 1.6 - - - +
158A LYS* 3.4 50.1 - - + +
163A PHE* 4.2 15.5 - + + -
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Residues in contact with VAL 93 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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77A VAL* 4.6 12.1 - - + -
79A LEU* 4.9 0.4 - - + -
89A ALA 3.1 14.2 + - - +
90A ARG 3.3 6.5 + - - +
92A TYR* 1.3 76.1 - - - +
94A GLU* 1.3 63.4 + - - +
96A VAL* 3.3 2.1 + - - +
97A VAL* 3.0 30.6 + - + +
107A TRP* 3.9 18.8 - - + -
131A ILE* 3.8 30.1 - - + -
155A ILE* 4.1 29.6 - - + +
163A PHE* 3.7 24.0 - - + -
165A VAL* 5.3 0.9 - - + -
168A PHE* 4.9 1.8 - - + -
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Residues in contact with GLU 94 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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90A ARG* 3.0 25.4 + - - +
91A ALA* 3.9 5.6 - - - +
93A VAL* 1.3 75.5 - - - +
95A GLU* 1.3 61.9 + - - +
97A VAL* 3.4 3.4 + - - +
98A ARG* 3.0 50.2 + - - +
104A VAL* 3.9 33.8 - - + +
107A TRP* 2.7 34.7 + - + +
131A ILE* 4.3 3.8 - - + -
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Residues in contact with GLU 95 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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91A ALA 2.9 17.7 + - - +
92A TYR* 3.2 31.5 + - + +
94A GLU* 1.3 77.3 - - - +
96A VAL* 1.3 62.9 + - + +
98A ARG* 3.4 22.0 + - - +
99A LEU* 3.1 40.4 + - + +
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Residues in contact with VAL 96 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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92A TYR* 3.1 48.5 + - + +
95A GLU* 1.3 74.0 - - + +
97A VAL* 1.3 67.2 + - - +
99A LEU* 3.1 22.4 + - + +
100A GLU* 3.1 13.9 + - - +
151A ALA* 3.6 38.8 - - + +
154A ILE* 4.1 23.7 - - + +
155A ILE* 3.8 14.6 - - + -
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Residues in contact with VAL 97 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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93A VAL* 3.0 25.7 + - + +
94A GLU 3.7 4.7 - - - +
96A VAL* 1.3 76.2 - - - +
98A ARG* 1.3 60.9 + - - +
100A GLU* 3.2 11.8 + - - +
102A LEU* 3.1 48.4 + - + +
104A VAL* 4.0 14.1 - - + -
131A ILE* 4.2 9.0 - - + -
133A VAL* 3.8 21.3 - - + -
151A ALA* 5.0 7.0 - - + -
155A ILE* 5.1 1.1 - - + -
168A PHE* 3.7 32.8 - - + -
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Residues in contact with ARG 98 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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91A ALA* 4.7 3.8 + - - +
94A GLU* 3.0 51.9 + - - +
95A GLU* 3.6 29.1 - - - +
97A VAL* 1.3 72.6 - - - +
99A LEU* 1.3 61.3 + - + +
101A LYS* 2.9 21.5 + - - +
102A LEU 3.7 14.8 - - - +
103A THR* 5.9 0.4 - - - -
104A VAL* 5.4 8.2 - - + +
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Residues in contact with LEU 99 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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95A GLU* 3.1 40.2 + - + +
96A VAL* 3.1 16.9 + - + +
98A ARG* 1.3 77.1 - - + +
100A GLU* 1.3 67.8 + - - +
101A LYS* 3.2 7.8 + - - +
154A ILE* 6.0 2.9 - - + -
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Residues in contact with GLU 100 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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96A VAL* 3.1 12.2 + - + +
97A VAL* 3.6 9.0 - - - +
98A ARG 3.1 0.8 - - - -
99A LEU* 1.3 82.5 - - - +
101A LYS* 1.3 70.7 + - - +
102A LEU* 3.2 16.6 + - + +
147A ARG* 3.5 48.8 + - + +
150A ILE* 3.6 37.6 - - - +
151A ALA* 4.2 12.6 - - + +
154A ILE* 4.1 9.7 - - - +
256A GLU* 5.1 4.2 - - - +
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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