Contacts of the helix formed by residues 100 - 111 (chain A) in PDB entry 1OFV
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 ASP 100 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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56A THR* 3.3 2.8 + - + -
60A GLY* 3.7 22.0 - - - +
96A ASP 4.5 1.0 - - - +
97A ASN* 3.0 52.1 + - - +
98A PHE 3.2 0.4 - - - -
99A GLN* 1.3 76.0 - - - +
101A ALA* 1.3 52.4 - - - +
103A GLY* 3.0 3.1 + - - -
104A ILE* 2.8 37.2 + - + +
130A SER* 3.6 2.9 - - - -
131A LYS* 3.0 52.2 + - + +
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Residues in contact with ALA 101 (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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54A CYS* 3.8 16.6 - - - +
55A PRO 3.4 22.0 - - - +
56A THR* 2.9 22.4 + - - +
60A GLY 5.3 0.2 + - - -
61A GLU 4.0 6.3 - - - +
62A LEU* 3.8 14.8 - - + +
100A ASP* 1.3 77.8 - - - +
102A MET* 1.3 63.8 + - - +
104A ILE* 3.0 7.6 + - - +
105A LEU* 2.9 29.9 + - - +
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Residues in contact with MET 102 (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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54A CYS* 4.4 9.0 + - - +
56A THR* 4.4 0.4 + - - -
85A TYR* 3.9 12.1 - - + -
86A PHE* 3.7 37.5 - - - +
87A GLY 3.7 0.4 - - - -
99A GLN* 3.2 36.5 + - + +
101A ALA* 1.3 79.8 - - - +
103A GLY* 1.3 62.8 + - - +
105A LEU* 3.6 4.4 + - - +
106A GLU* 3.0 23.6 + - - +
132A ALA* 4.3 7.9 - - + -
138A PHE* 4.7 3.1 - - + -
139A VAL* 3.9 14.8 - - + -
140A GLY* 3.7 34.8 - - - +
141A LEU 3.8 11.9 - - - +
142A ALA* 4.1 5.6 - - + -
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Residues in contact with GLY 103 (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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99A GLN 3.4 3.6 + - - -
100A ASP 3.0 7.6 + - - -
102A MET* 1.3 81.9 - - - +
104A ILE* 1.4 62.2 - - - +
106A GLU* 3.9 6.5 - - - +
107A GLU* 3.0 24.8 + - - +
131A LYS* 3.6 26.6 - - - +
132A ALA* 3.7 11.9 - - - +
139A VAL* 4.6 1.8 - - - -
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Residues in contact with ILE 104 (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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60A GLY 3.6 23.8 - - - +
61A GLU* 5.1 0.4 - - - -
62A LEU* 4.3 20.4 - - + +
70A TYR* 4.0 27.3 + - + +
100A ASP* 2.8 24.7 + - + +
101A ALA* 3.0 10.1 + - - +
103A GLY* 1.4 78.4 - - - +
105A LEU* 1.3 63.1 + - - +
107A GLU* 3.4 10.1 + - - +
108A LYS* 3.1 20.8 + - - +
131A LYS* 4.1 24.0 - - + +
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Residues in contact with LEU 105 (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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52A ILE* 3.7 19.7 - - + -
54A CYS* 3.6 33.7 - - + -
62A LEU* 3.9 11.7 - - + -
66A TRP* 3.7 31.9 - - + -
70A TYR* 4.1 24.5 - - + -
73A LEU* 4.3 10.8 - - + -
85A TYR* 4.1 12.6 - - + -
101A ALA 2.9 14.6 + - - +
102A MET* 4.0 4.9 - - - +
104A ILE* 1.3 76.4 - - - +
106A GLU* 1.3 57.8 - - - +
108A LYS* 3.1 4.8 + - - +
109A ILE* 2.9 35.9 + - + +
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Residues in contact with GLU 106 (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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85A TYR* 3.4 27.3 - - + -
102A MET 3.0 19.0 + - - +
103A GLY* 3.9 3.5 - - - +
104A ILE 3.3 0.2 - - - -
105A LEU* 1.3 77.9 - - - +
107A GLU* 1.3 65.9 + - - +
110A SER* 2.9 41.7 + - - -
116A THR* 2.6 31.2 + - + +
134A ARG* 2.9 43.1 + - - -
139A VAL* 3.8 23.2 - - + +
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Residues in contact with GLU 107 (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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103A GLY 3.0 18.6 + - - +
104A ILE* 3.7 8.1 - - - +
106A GLU* 1.3 85.7 + - - +
108A LYS* 1.3 63.3 + - - +
110A SER* 3.5 4.1 + - - -
111A SER* 3.2 24.2 + - - -
131A LYS* 6.1 0.7 - - - +
134A ARG* 5.5 1.8 - - - +
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Residues in contact with LYS 108 (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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70A TYR* 3.8 61.4 + - + +
71A ASP* 5.2 2.4 + - - -
73A LEU* 4.2 17.0 - - + -
74A ASP* 3.1 32.4 + - - +
104A ILE 3.1 9.8 + - - +
105A LEU* 3.1 8.6 + - - +
107A GLU* 1.3 80.8 - - - +
109A ILE* 1.3 64.9 + - + +
111A SER* 2.6 25.7 + - - +
112A LEU* 3.2 24.5 - - + +
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Residues in contact with ILE 109 (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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44A LEU* 5.3 1.1 - - + -
52A ILE* 4.4 25.8 - - + -
66A TRP* 5.2 3.1 - - + -
73A LEU* 4.3 25.8 - - + -
78A PHE* 3.6 43.0 - - + +
83A VAL* 4.2 8.3 - - + -
85A TYR* 3.4 23.3 - - + +
105A LEU* 2.9 23.8 + - + +
108A LYS* 1.3 71.6 - - + +
110A SER* 1.3 66.0 + - - +
112A LEU* 3.1 20.5 + - - +
114A SER* 3.0 24.8 + - - +
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Residues in contact with SER 110 (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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85A TYR* 4.2 0.8 + - - -
106A GLU* 2.9 41.6 + - - -
107A GLU* 3.5 7.1 + - - +
109A ILE* 1.3 77.4 - - - +
111A SER* 1.3 62.6 + - - +
113A GLY* 3.0 14.0 + - - -
114A SER* 3.6 22.5 + - - +
116A THR* 3.8 10.5 - - - -
134A ARG* 4.9 3.1 + - - -
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Residues in contact with SER 111 (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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107A GLU* 3.2 14.1 + - - -
108A LYS* 2.6 25.1 + - - +
110A SER* 1.3 79.9 + - - +
112A LEU* 1.3 65.2 + - - +
113A GLY 3.2 2.0 + - - -
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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