Contacts of the helix formed by residues 105 - 112 (chain A) in PDB entry 2P80
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 ALA 105 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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104A GLY* 1.3 72.6 - - - +
106A LEU* 1.3 68.8 + - - +
107A GLY 3.0 1.6 - - - -
108A GLY* 2.7 23.9 + - - +
109A GLY 3.1 6.9 + - - -
110A GLY* 3.3 7.7 + - - +
111A LEU* 3.2 40.8 - - + -
300B ILE 6.1 0.2 - - - -
301B TYR* 3.5 11.1 + - - -
326B TRP* 3.6 10.4 - - + -
331B MET* 3.5 5.2 - - - -
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Residues in contact with LEU 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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98A ASP* 2.8 28.8 - - + +
104A GLY 3.5 0.4 - - - -
105A ALA* 1.3 78.2 - - - +
107A GLY* 1.3 57.4 + - - +
109A GLY* 3.6 3.4 + - - +
110A GLY* 4.3 17.9 - - - +
139A PRO* 6.1 5.6 - - + -
257B ILE* 3.4 36.8 - - + +
258B GLY* 3.8 8.3 - - - -
300B ILE 3.5 25.5 + - - +
301B TYR* 3.9 12.2 - - - -
302B ALA* 4.0 6.1 - - + +
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Residues in contact with GLY 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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97A ILE 3.4 0.9 - - - +
98A ASP* 2.8 16.3 - - - -
99A PHE* 2.6 39.5 + - - +
100A HIS* 5.7 0.2 - - - -
102A ALA* 4.5 5.5 - - - +
104A GLY 3.6 5.8 + - - -
105A ALA 3.0 0.8 - - - -
106A LEU* 1.3 78.0 - - - +
108A GLY* 1.3 58.6 + - - +
122A LEU* 4.9 0.5 - - - +
258B GLY* 3.4 16.3 - - - -
331B MET* 4.0 8.5 - - - -
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Residues in contact with GLY 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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97A ILE 3.1 7.6 - - - -
104A GLY 3.5 5.5 + - - -
105A ALA* 2.7 14.5 + - - -
107A GLY* 1.3 71.4 - - - +
109A GLY* 1.3 53.3 + - - -
110A GLY 3.3 2.7 - - - -
111A LEU 3.3 5.9 + - - -
112A THR* 2.4 34.0 + - - +
122A LEU* 3.9 21.1 - - - -
331B MET* 3.7 12.5 - - - +
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Residues in contact with GLY 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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96A ASN* 3.8 21.9 + - - -
97A ILE 3.2 11.7 + - - -
98A ASP* 4.0 3.1 - - - +
105A ALA 3.1 3.2 + - - -
106A LEU* 3.6 11.5 + - - -
107A GLY 3.3 2.8 - - - -
108A GLY* 1.3 79.0 - - - +
110A GLY* 1.3 60.5 + - - +
111A LEU 3.2 1.0 + - - -
112A THR* 3.4 14.5 + - - -
113A GLU* 3.6 18.2 - - - +
139A PRO* 6.4 0.2 - - - -
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Residues in contact with GLY 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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105A ALA* 3.3 17.0 + - - -
106A LEU* 4.3 12.3 - - - +
109A GLY* 1.3 76.3 - - - +
111A LEU* 1.3 71.9 + - - +
112A THR 3.6 0.4 + - - -
113A GLU* 4.8 11.6 + - - +
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Residues in contact with LEU 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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105A ALA* 3.2 29.2 - - + -
108A GLY 3.3 3.6 + - - +
109A GLY 3.1 0.6 - - - -
110A GLY* 1.3 87.2 - - - +
112A THR* 1.3 67.8 + - - +
113A GLU 3.9 0.9 - - - -
120A THR* 4.1 7.3 + - - -
122A LEU* 4.5 10.8 - - + +
326B TRP* 4.2 13.5 - - + -
331B MET* 3.9 15.0 - - + -
333B SER* 4.1 34.9 + - - +
337B PRO* 4.3 10.0 - - - +
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Residues in contact with THR 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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85A LEU* 5.0 3.4 - - + +
96A ASN* 3.3 13.7 - - - +
97A ILE* 3.1 37.4 + - + -
108A GLY 2.4 25.4 + - - +
109A GLY* 3.4 6.0 + - - -
111A LEU* 1.3 83.4 - - - +
113A GLU* 1.3 65.4 + - - +
114A ILE* 3.1 15.6 + - - +
120A THR* 4.0 18.5 - - + +
122A LEU* 3.8 26.9 - - + -
337B PRO* 4.5 0.9 - - - -
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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