Contacts of the strand formed by residues 109 - 118 (chain A) in PDB entry 1OGA
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 PHE 109 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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101A CYS* 4.7 0.7 - - + -
102A ASP 3.9 5.2 - - - -
103A VAL* 4.2 1.4 - - - +
107A TRP 4.1 0.6 + - - -
108A ARG* 1.3 76.9 - - - +
110A LEU* 1.3 72.4 + - - +
111A ARG* 3.3 36.8 - - - -
112A GLY* 3.5 7.4 - - - -
128A GLU 5.9 0.4 - - - -
130A LEU* 3.9 10.5 - - + -
160A LEU 3.5 26.7 - - - -
161A GLU* 3.8 41.7 - - + +
165A VAL* 3.8 22.4 - - + +
169A ARG* 4.6 1.6 - - - +
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Residues in contact with LEU 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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2A SER* 4.5 9.0 - - - +
102A ASP* 2.8 29.8 + - + +
103A VAL* 4.1 8.5 - - - +
104A GLY* 4.1 20.4 - - - +
108A ARG 3.3 0.4 + - - +
109A PHE* 1.3 87.3 - - - +
111A ARG* 1.3 64.9 + - + +
128A GLU* 4.9 3.6 - - - +
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Residues in contact with ARG 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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101A CYS* 3.3 3.1 - - - -
102A ASP* 2.8 34.1 + - + +
109A PHE* 3.3 14.6 - - - -
110A LEU* 1.3 84.5 - - + +
112A GLY* 1.3 69.0 + - - +
113A TYR* 3.3 44.2 + - + +
128A GLU* 3.5 48.9 + - + +
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Residues in contact with GLY 112 (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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100A GLY 3.5 8.5 - - - -
109A PHE* 3.5 16.3 - - - -
111A ARG* 1.3 83.7 + - - +
113A TYR* 1.3 67.7 + - - -
126A LEU 5.3 2.1 - - - +
127A LYS 5.2 0.2 - - - +
128A GLU* 5.0 6.4 + - - -
130A LEU* 3.8 24.6 - - - +
160A LEU* 4.4 8.3 - - - -
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Residues in contact with TYR 113 (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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6A ARG* 3.0 35.3 + - - -
98A MET* 4.0 29.8 - - + -
99A TYR* 3.1 4.1 - - - +
100A GLY 2.9 37.1 + - - +
102A ASP* 2.6 29.8 + - - -
111A ARG* 3.3 49.8 + - + -
112A GLY* 1.3 76.6 - - - -
114A HIS* 1.3 66.0 + - - +
115A GLN* 4.5 12.3 - - - +
126A LEU 5.4 3.1 - - - -
130A LEU* 5.4 0.7 - - - -
160A LEU* 3.6 8.2 - - - +
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Residues in contact with HIS 114 (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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97A ARG* 3.0 32.2 + - - -
98A MET 3.3 7.2 - - - -
99A TYR* 3.8 20.9 - + + -
113A TYR* 1.3 78.1 - - - +
115A GLN* 1.3 63.0 + - - +
116A TYR* 3.5 26.4 - + - -
125A ALA* 3.7 0.5 - - - -
126A LEU* 2.9 45.7 + - + +
133A TRP* 3.9 14.2 - + - -
147A TRP* 4.4 0.4 - + - -
156A LEU* 3.6 33.0 - - + +
160A LEU* 4.4 6.5 - - + -
3C LEU* 4.5 0.2 - - + -
7C PHE* 3.6 13.1 - + - -
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Residues in contact with GLN 115 (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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97A ARG* 3.3 4.9 - - - +
98A MET* 2.9 60.4 + - + +
113A TYR* 4.5 17.3 - - - +
114A HIS* 1.3 78.1 + - - +
116A TYR* 1.3 67.6 + - - +
122A ASP* 5.6 2.6 - - - +
124A ILE 3.4 4.9 - - - -
125A ALA* 3.6 24.8 - - + +
126A LEU 5.1 3.8 + - - -
58B LYS* 5.1 5.4 - - - +
60B TRP* 3.5 24.2 - - + -
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Residues in contact with TYR 116 (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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74A HIS* 3.6 25.1 + + - -
77A ASP* 4.6 0.3 + - - -
95A VAL* 4.2 8.3 - - + -
96A GLN 3.2 13.7 - - - -
97A ARG* 3.3 35.4 + - + -
114A HIS* 3.5 26.2 - + - -
115A GLN* 1.3 83.0 - - - +
117A ALA* 1.3 60.6 + - - +
122A ASP* 3.8 1.9 - - - +
123A TYR* 2.9 28.5 + - + -
124A ILE* 2.8 30.2 + - + +
147A TRP* 3.5 15.3 - + - -
60B TRP* 3.6 10.3 - - - -
7C PHE* 4.0 11.8 + - - -
9C LEU* 3.6 33.4 - - + +
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Residues in contact with ALA 117 (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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81A LEU* 5.8 0.2 - - - +
94A THR 3.9 0.7 - - - +
95A VAL* 3.5 6.9 - - - +
96A GLN* 2.9 35.9 + - + +
116A TYR* 1.3 73.1 - - - +
118A TYR* 1.3 60.0 + - - +
119A ASP 4.2 0.2 - - - -
120A GLY 4.4 1.6 - - - -
121A LYS 3.1 19.3 - - - +
123A TYR* 3.9 4.0 - - - +
60B TRP* 3.3 46.0 - - + +
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Residues in contact with TYR 118 (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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78A LEU* 4.5 5.6 + - + -
81A LEU* 3.6 36.8 - - + -
82A ARG* 3.9 9.9 + - - +
85A TYR* 3.5 38.1 - + - +
87A GLN* 2.6 28.5 + - - -
93A HIS* 3.3 30.4 + - + +
94A THR 3.3 13.0 - - - -
95A VAL* 4.1 6.1 - - + -
117A ALA* 1.3 73.2 - - - +
119A ASP* 1.3 85.9 + - + +
120A GLY 3.1 1.0 + - - -
121A LYS* 2.9 24.3 + - - +
123A TYR* 4.1 17.6 - - + +
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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