Contacts of the helix formed by residues 86 - 94 (chain A) in PDB entry 1OGS
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 THR 86 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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84A ALA* 3.2 9.1 + - + +
85A MET* 1.3 76.8 - - - +
87A ASP* 1.3 65.4 + - - +
88A ALA 3.6 3.2 + - - -
89A ALA* 3.1 18.8 + - - +
90A ALA* 3.0 21.7 + - - +
122A PRO* 4.0 15.9 - - + -
126A CYS* 4.5 2.0 - - - -
128A PHE* 4.0 8.7 - - + -
157A LYS* 4.6 1.8 - - - -
381A TRP* 3.4 38.8 - - + -
382A ASN* 2.6 30.2 + - - +
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Residues in contact with ASP 87 (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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86A THR* 1.3 74.1 - - - +
88A ALA* 1.3 58.1 + - - +
90A ALA* 3.3 6.0 + - - +
91A LEU* 2.9 43.3 + - + +
122A PRO* 5.5 0.6 - - - +
124A ALA 5.0 3.0 - - - +
125A SER* 4.5 0.3 - - - -
126A CYS* 5.8 0.6 - - - -
128A PHE 3.4 9.5 + - - +
129A SER* 2.7 32.4 + - - -
130A ILE* 4.9 2.1 + - + +
133A TYR* 2.7 28.5 + - - -
152A GLU* 3.5 20.5 - - + +
156A LEU* 4.8 2.2 - - + +
157A LYS* 3.3 23.5 + - - +
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Residues in contact with ALA 88 (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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86A THR* 3.1 1.5 - - - +
87A ASP* 1.3 73.8 - - - +
89A ALA* 1.3 66.7 + - - +
91A LEU* 3.4 1.8 + - - +
92A ASN* 2.8 31.1 + - - -
128A PHE* 3.0 31.3 + - + +
385A LEU* 4.1 6.3 - - + -
391A PRO* 3.3 46.0 - - + +
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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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84A ALA 3.9 7.6 - - - +
85A MET* 4.5 5.4 - - - -
86A THR* 3.1 20.8 + - - +
88A ALA* 1.3 78.5 - - - +
90A ALA* 1.3 64.3 + - - +
92A ASN* 3.2 2.8 + - - +
93A ILE* 2.9 30.1 + - + +
382A ASN 4.6 0.2 - - - -
383A LEU* 3.8 16.2 - - + +
384A ALA* 3.3 34.3 + - + +
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Residues in contact with ALA 90 (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 MET* 4.3 7.1 - - - -
86A THR 3.0 15.8 + - - +
87A ASP* 3.6 4.5 - - - +
89A ALA* 1.3 77.5 - - - +
91A LEU* 1.3 58.0 + - - +
93A ILE* 3.3 0.9 + - - +
94A LEU* 2.9 37.8 + - - +
156A LEU* 3.8 26.9 - - + -
157A LYS* 4.2 6.1 - - + +
160A LEU* 3.5 25.1 - - + -
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Residues in contact with LEU 91 (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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87A ASP* 2.9 28.4 + - + +
88A ALA 3.7 3.8 - - - +
90A ALA* 1.3 77.0 - - - +
92A ASN* 1.3 61.5 + - - +
94A LEU* 3.9 5.1 - - - +
95A ALA* 3.3 22.2 + - - +
130A ILE* 3.5 45.5 - - + -
151A GLU* 5.9 0.7 - - - +
152A GLU* 6.4 0.7 - - + -
156A LEU* 3.5 29.4 - - + -
391A PRO* 4.1 13.7 - - + -
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Residues in contact with ASN 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 ALA 2.8 28.2 + - - +
89A ALA 3.6 3.6 - - - +
91A LEU* 1.3 74.4 - - - +
93A ILE* 1.3 65.5 + - - +
95A ALA* 3.2 19.4 + - - +
96A LEU 3.9 0.3 + - - -
384A ALA* 3.8 6.3 + - + -
385A LEU* 3.5 11.2 - - - +
386A ASN* 3.5 28.8 + - - +
390A GLY 3.1 24.1 + - - +
391A PRO* 3.4 8.9 - - - +
404A VAL* 3.5 35.2 - - + +
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Residues in contact with ILE 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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85A MET* 4.4 15.7 - - + -
89A ALA* 2.9 24.3 + - + +
90A ALA 3.8 3.1 - - - +
92A ASN* 1.3 75.8 - - - +
94A LEU* 1.3 59.1 + - - +
95A ALA 3.1 4.3 + - - -
96A LEU* 3.2 15.6 + - - +
101A GLN* 3.2 35.7 - - + +
104A LEU* 4.1 37.7 - - + -
105A LEU* 4.5 10.3 - - + -
108A TYR* 6.2 0.2 - - + -
160A LEU* 4.0 32.8 - - + -
383A LEU* 4.9 7.2 - - + -
384A ALA* 4.3 9.4 - - + -
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Residues in contact with LEU 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 ALA 2.9 20.0 + - - +
91A LEU* 3.9 5.2 - - - +
93A ILE* 1.3 74.1 - - - +
95A ALA* 1.3 59.5 + - - +
96A LEU 3.2 1.7 - - - +
101A GLN* 3.6 33.4 + - - +
155A LYS 4.1 4.9 - - - +
156A LEU* 3.6 52.0 - - + +
159A PRO* 6.2 2.2 - - + -
160A LEU* 3.8 22.2 - - + -
163A ARG* 4.1 5.4 - - - +
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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