Contacts of the helix formed by residues 103 - 109 (chain A) in PDB entry 1OPT
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 LEU 103 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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100A MET* 3.3 32.3 + - + +
101A CYS 6.0 0.9 - - - +
102A GLN* 1.3 77.0 - - - +
104A LEU* 1.3 66.6 + - + +
105A THR 3.8 1.3 + - - -
106A GLY* 4.1 5.0 + - - -
107A LEU 4.3 0.9 + - - -
164A ILE* 3.4 43.7 - - + +
165A ILE* 3.8 43.7 - - + +
168A ARG* 3.9 17.7 - - - +
169A SER* 4.2 11.4 - - - +
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Residues in contact with LEU 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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83A VAL* 5.6 3.4 - - + -
100A MET 5.1 0.2 + - - -
103A LEU* 1.3 81.0 - - + +
105A THR* 1.3 68.7 + - - +
106A GLY 3.5 0.5 + - - -
107A LEU* 3.6 9.0 + - - +
108A TYR* 3.4 44.9 - - + -
165A ILE* 4.6 10.1 - - + -
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Residues in contact with THR 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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87A ALA* 6.1 4.9 - - + +
102A GLN* 5.8 6.8 - - - +
103A LEU 3.8 0.6 - - - +
104A LEU* 1.3 80.7 - - - +
106A GLY* 1.4 57.1 + - - +
108A TYR* 3.3 5.5 + - - +
109A PHE* 3.0 57.3 + - + +
193A PHE* 5.2 19.0 - - + -
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Residues in contact with GLY 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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102A GLN* 5.7 4.0 + - - +
103A LEU 4.1 7.1 + - - -
104A LEU 3.5 1.2 + - - -
105A THR* 1.4 75.5 - - - +
107A LEU* 1.3 61.3 + - - +
109A PHE* 5.1 2.0 - - - -
110A ILE* 3.4 39.5 + - - +
161A LEU* 5.9 0.2 - - - +
164A ILE* 5.1 11.1 - - - +
194A GLN* 6.1 4.0 - - - -
196A LEU 5.0 10.1 - - - -
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Residues in contact with LEU 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 LEU 4.3 4.2 + - - +
104A LEU 3.6 10.6 + - - +
105A THR 3.5 0.4 - - - -
106A GLY* 1.3 73.5 - - - +
108A TYR* 1.3 85.6 + - + +
111A GLY* 3.0 29.8 + - - -
158A PHE* 4.5 20.4 - - + -
161A LEU* 3.8 43.7 - - + +
162A PRO* 5.3 2.0 - - + -
164A ILE* 4.7 11.2 - - + +
165A ILE* 4.0 26.9 - - + -
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Residues in contact with TYR 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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80A LEU* 5.3 0.7 - - - +
83A VAL* 3.7 33.1 - - + +
84A PRO* 3.8 25.1 - - + +
104A LEU* 3.4 47.8 - - + -
105A THR* 3.3 7.6 + - + +
107A LEU* 1.3 96.1 - - + +
109A PHE* 1.3 61.4 + - + +
110A ILE 3.4 1.4 + - - -
111A GLY 4.4 0.3 + - - -
112A PHE* 3.3 47.2 + + - +
113A PHE* 6.0 0.3 - - - -
165A ILE* 5.7 3.1 - - + -
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Residues in contact with PHE 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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84A PRO* 3.5 43.3 - - + -
85A PHE* 5.4 0.9 - + - -
87A ALA* 6.1 1.1 - - + -
88A HIS* 3.8 23.8 - + + -
105A THR* 3.0 45.4 + - + +
106A GLY* 4.9 1.6 - - - +
108A TYR* 1.3 69.8 - - + +
110A ILE* 1.3 63.2 + - + +
113A PHE* 3.3 29.4 - + - -
194A GLN* 4.9 17.2 + - - +
283A GLU* 3.8 28.3 - - + -
287A MET* 3.7 32.5 - - + -
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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