Contacts of the helix formed by residues 85 - 94 (chain D) in PDB entry 1P27
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 85 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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83D GLU 3.5 4.7 + - - -
84D ALA* 1.3 76.4 + - - +
86D GLU* 1.3 70.8 + - + +
87D GLU* 3.2 30.3 - - + +
88D ASP* 3.1 32.0 + - - +
89D ILE* 3.2 10.4 + - - +
104D LEU* 3.9 4.3 - - - -
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Residues in contact with GLU 86 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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85D THR* 1.3 77.3 - - + +
87D GLU* 1.3 58.0 + - - +
89D ILE* 3.1 4.4 + - - +
90D HIS* 2.8 33.4 + - - +
102D ILE* 3.3 44.0 + - + +
104D LEU* 3.4 31.5 - - + +
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Residues in contact with GLU 87 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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85D THR* 3.2 14.5 - - + +
86D GLU* 1.3 76.2 - - - +
88D ASP* 1.3 62.9 + - - +
90D HIS* 3.3 14.9 + - - +
91D ASP* 3.4 23.1 + - + +
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Residues in contact with ASP 88 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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83D GLU 4.5 0.5 - - - +
84D ALA* 3.8 9.1 - - + -
85D THR* 3.1 36.3 + - - +
87D GLU* 1.3 74.8 - - - +
89D ILE* 1.4 66.9 + - - +
91D ASP* 3.2 22.1 - - - +
92D LYS* 3.6 9.9 + - - +
139D LEU* 4.6 16.9 - - + +
140D MET* 3.9 15.3 - - - +
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Residues in contact with ILE 89 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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77D VAL* 6.4 0.9 - - + -
80D VAL* 4.1 7.4 - - + -
84D ALA* 3.9 21.5 - - + -
85D THR 3.2 22.7 + - - +
86D GLU* 3.1 6.7 + - - +
88D ASP* 1.4 77.1 - - - +
90D HIS* 1.3 60.7 + - - +
92D LYS* 2.6 31.1 + - - +
93D PHE* 2.9 36.8 + - + -
102D ILE* 4.4 23.8 - - + -
104D LEU* 3.7 27.6 - - + -
117D THR* 4.4 10.8 - - + +
119D VAL* 4.5 8.7 - - + -
139D LEU* 4.4 15.5 - - + -
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Residues in contact with HIS 90 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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86D GLU* 2.8 21.1 + - - +
87D GLU* 3.6 10.8 - - - +
88D ASP 3.2 0.6 - - - -
89D ILE* 1.3 77.1 - - - +
91D ASP* 1.3 54.7 + - + +
93D PHE 3.3 0.5 + - - -
94D ALA* 2.7 57.8 + - + +
99D ILE* 3.7 19.5 + - + +
102D ILE* 4.0 26.7 - - + -
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Residues in contact with ASP 91 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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87D GLU* 3.4 18.8 + - + +
88D ASP* 3.2 11.1 - - - +
90D HIS* 1.3 79.0 - - + +
92D LYS* 1.3 72.6 + - - +
94D ALA* 4.1 10.7 + - - +
95D GLU* 4.3 14.6 + - - +
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Residues in contact with LYS 92 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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88D ASP 3.8 11.0 - - - +
89D ILE* 2.6 21.4 + - - +
91D ASP* 1.3 82.2 + - - +
93D PHE* 1.4 67.7 + - + +
94D ALA 3.7 0.3 + - - -
95D GLU* 4.2 5.7 + - - +
96D TYR* 3.8 19.6 - - - -
134D LEU* 3.8 20.6 - - + +
137D GLN* 4.9 16.0 - - - +
138D ASP 3.4 27.5 + - - +
139D LEU* 4.5 19.5 - - + +
144D ILE* 5.3 4.7 - - + -
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Residues in contact with PHE 93 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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75D LEU* 4.7 1.8 - - + -
77D VAL* 3.6 36.8 - - + -
89D ILE* 2.9 36.6 + - + +
92D LYS* 1.4 78.4 - - + +
94D ALA* 1.3 62.1 + - - +
95D GLU 3.2 2.9 - - - -
96D TYR* 3.3 10.4 + - - +
99D ILE* 3.4 19.5 - - + -
117D THR* 6.4 0.2 - - - -
119D VAL* 3.9 17.5 - - + -
121D TYR* 2.3 39.6 + + - +
130D ALA* 4.2 6.1 - - + -
134D LEU* 3.6 28.9 - - + -
139D LEU* 5.9 1.6 - - + -
144D ILE* 4.1 17.3 - - + -
146D VAL* 4.0 21.1 - - + -
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Residues in contact with ALA 94 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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90D HIS* 2.7 47.5 + - + +
91D ASP* 4.1 7.0 - - - +
92D LYS 3.4 1.0 - - - -
93D PHE* 1.3 71.9 - - - +
95D GLU* 1.4 64.9 + - + +
97D GLY* 3.1 23.4 + - - +
99D ILE* 4.1 3.8 - - + +
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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