Contacts of the helix formed by residues 100 - 110 (chain A) in PDB entry 3PEY
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 100 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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98A GLY 3.9 1.2 + - - -
99A LEU* 1.3 75.6 - - - +
101A PRO* 1.3 76.4 - - + +
102A GLU* 3.2 13.5 - - - +
103A LEU* 3.0 30.0 + - + +
104A LEU* 3.0 11.1 + - - +
154A THR* 5.5 2.9 + - + +
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Residues in contact with PRO 101 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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99A LEU 3.8 2.0 - - - +
100A ALA* 1.3 89.7 - - + +
102A GLU* 1.3 71.3 + - + +
104A LEU* 3.3 14.8 + - + +
105A LYS* 3.1 34.1 + - - +
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Residues in contact with GLU 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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100A ALA* 3.5 20.1 - - - +
101A PRO* 1.3 83.5 - - + +
103A LEU* 1.3 60.1 + - + +
105A LYS* 3.5 11.6 + - - +
106A GLY* 3.1 20.1 + - - -
185A MET 4.6 1.4 - - - +
188A PHE* 3.5 35.2 + - + +
189A THR* 3.8 23.7 - - + +
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Residues in contact with LEU 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 LEU* 4.5 9.4 - - + -
100A ALA* 3.0 24.4 + - + +
102A GLU* 1.3 75.6 - - - +
104A LEU* 1.3 59.4 + - - +
106A GLY* 3.1 2.5 + - - +
107A ILE* 2.9 35.2 + - - +
150A LEU* 4.2 20.9 - - + +
153A LEU* 4.0 38.6 - - + +
154A THR* 3.5 28.7 - - - +
185A MET 4.0 11.4 - - - +
186A GLY* 4.4 0.4 - - - -
189A THR* 4.0 24.0 - - + -
191A ILE* 5.5 0.7 - - + -
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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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94A PHE* 3.5 40.6 - - + +
95A ASP* 3.7 28.0 - - + +
99A LEU* 4.1 27.8 - - + +
100A ALA 3.0 14.8 + - - +
101A PRO* 3.3 12.8 + - + +
103A LEU* 1.3 77.2 - - - +
105A LYS* 1.3 63.4 + - + +
107A ILE* 3.3 4.0 + - + +
108A TYR* 2.9 41.0 + - + +
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Residues in contact with LYS 105 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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101A PRO* 3.1 25.9 + - - +
102A GLU* 3.6 16.4 - - + +
103A LEU 3.2 0.2 - - - -
104A LEU* 1.3 76.2 - - + +
106A GLY* 1.3 58.7 - - - +
108A TYR* 3.8 4.1 - - - +
109A ALA* 2.9 32.2 + - - +
188A PHE* 3.6 35.9 - - + -
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Residues in contact with GLY 106 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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102A GLU 3.1 8.3 + - - -
103A LEU 3.1 4.2 + - - -
105A LYS* 1.3 77.7 - - - +
107A ILE* 1.3 61.0 + - - +
109A ALA* 3.5 2.8 + - - +
110A MET* 3.3 31.7 + - - +
184A GLU 4.5 3.4 - - - +
185A MET* 3.5 25.8 - - - -
187A LYS* 5.3 0.2 - - - -
188A PHE* 3.5 15.7 - - - -
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Residues in contact with ILE 107 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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94A PHE* 3.6 20.6 - - + -
99A LEU* 3.6 31.2 - - + -
103A LEU 2.9 24.7 + - - +
104A LEU* 3.6 10.8 - - + +
106A GLY* 1.3 74.2 - - - +
108A TYR* 1.3 68.1 + - + +
110A MET* 3.2 12.4 + - - +
112A PHE* 3.1 53.2 + - + +
150A LEU* 3.7 18.2 - - + -
185A MET* 3.6 26.2 - - + -
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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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93A SER* 3.4 7.2 - - - -
94A PHE* 2.9 28.9 + + + +
95A ASP* 2.7 31.1 + - - -
104A LEU* 2.9 32.5 + - + +
105A LYS* 4.3 3.6 - - - +
107A ILE* 1.3 79.5 - - + +
109A ALA* 1.3 65.0 + - - +
110A MET 3.1 1.6 - - - -
111A LYS* 3.0 18.6 + - - +
112A PHE 3.3 27.1 - - - +
113A GLN* 3.8 14.1 - - - -
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Residues in contact with ALA 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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105A LYS 2.9 18.8 + - - +
106A GLY 3.7 5.2 - - - +
108A TYR* 1.3 76.8 - - - +
110A MET* 1.3 60.2 + - + +
111A LYS* 3.2 10.1 + - - +
184A GLU* 5.1 2.7 - - - +
187A LYS* 4.3 16.2 - - - +
188A PHE* 4.0 19.7 - - + -
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Residues in contact with MET 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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106A GLY 3.3 15.4 + - - +
107A ILE 3.2 9.8 + - - +
108A TYR 3.1 0.8 - - - -
109A ALA* 1.3 75.4 - - + +
111A LYS* 1.3 68.9 + - - +
112A PHE* 3.3 37.0 + - + -
181A VAL* 4.5 15.0 - - + -
184A GLU* 3.7 48.0 - - + +
185A MET* 3.4 39.0 - - + +
1000A ADP 5.3 1.6 - - - +
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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