Contacts of the helix formed by residues 88 - 109 (chain E) in PDB entry 1PQ3
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 ASN 88 (chain E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35E GLN* 3.5 49.2 + - - +
37E GLN 5.0 4.4 + - - -
79E ASP* 2.9 34.8 + - - +
80E ASP 5.1 1.0 + - - -
87E VAL* 1.3 90.8 - - - +
89E PRO* 1.3 69.7 - - - +
91E SER* 3.8 9.0 - - - -
92E VAL* 3.0 21.5 + - - +
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Residues in contact with PRO 89 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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79E ASP* 3.3 11.0 - - - +
80E ASP 3.7 10.1 - - - +
82E TYR* 4.0 13.7 - - + -
86E ILE* 3.5 33.0 - - + +
87E VAL 3.1 5.6 - - - +
88E ASN* 1.3 90.3 - - - +
90E ARG* 1.3 59.6 + - - +
92E VAL* 3.2 0.7 + - - +
93E GLY 2.9 22.7 + - - -
159E LEU* 3.9 9.0 - - + -
178E LEU* 4.4 6.5 - - + -
179E PRO* 3.5 28.7 - - + +
181E PHE* 3.2 10.4 - - + -
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Residues in contact with ARG 90 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76E VAL* 3.6 24.3 - - + +
78E LYS 4.2 4.8 + - - -
79E ASP* 2.5 63.7 + - + +
80E ASP* 3.4 21.4 + - - +
82E TYR* 5.5 2.8 - - - +
89E PRO* 1.3 74.4 - - - +
91E SER* 1.3 60.1 + - - +
93E GLY 3.7 1.8 - - - +
94E LEU* 3.1 28.9 + - - +
179E PRO* 3.4 50.3 + - - +
180E GLY* 4.3 7.0 - - - -
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Residues in contact with SER 91 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33E PHE* 3.8 4.1 - - - -
35E GLN* 2.7 40.5 + - - -
74E THR 5.1 3.0 + - - +
75E PRO* 4.6 2.8 - - - +
76E VAL* 3.8 25.6 + - - -
79E ASP* 2.7 26.0 + - - -
88E ASN* 3.7 5.6 - - - -
90E ARG* 1.3 72.7 - - - +
92E VAL* 1.3 62.9 + - - +
94E LEU* 4.1 1.2 - - - +
95E ALA* 3.2 24.6 + - - +
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Residues in contact with VAL 92 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33E PHE* 3.6 18.4 - - + -
35E GLN* 3.1 29.8 - - + +
36E GLY* 4.0 4.0 - - - -
88E ASN 3.0 17.4 + - - +
89E PRO 3.6 3.4 - - - +
91E SER* 1.3 75.8 - - - +
93E GLY* 1.3 63.6 + - - +
95E ALA* 4.1 0.3 - - - +
96E ASN* 2.9 46.9 + - - +
121E SER* 3.9 14.4 - - - +
124E ILE* 4.5 1.8 - - + -
159E LEU* 3.7 24.5 - - + -
181E PHE* 3.9 10.5 - - + -
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Residues in contact with GLY 93 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89E PRO 2.9 15.2 + - - -
90E ARG 3.7 1.5 + - - -
91E SER 3.4 0.2 - - - -
92E VAL* 1.3 77.6 - - - +
94E LEU* 1.3 59.6 + - - +
96E ASN* 4.8 2.0 - - - -
97E GLN* 3.2 12.0 + - - +
180E GLY 3.5 22.4 - - - -
181E PHE* 3.8 14.3 - - - -
183E TRP* 3.1 23.2 + - - -
184E ILE* 5.7 0.2 - - - -
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Residues in contact with LEU 94 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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74E THR* 3.6 39.9 - - - +
75E PRO 5.0 0.4 - - - +
76E VAL* 4.0 14.6 - - + -
90E ARG 3.1 18.3 + - - +
91E SER 4.1 2.5 - - - +
93E GLY* 1.3 75.0 - - - +
95E ALA* 1.3 66.9 + - - +
97E GLN* 3.2 20.2 + - - +
98E GLU* 3.1 38.1 + - + +
180E GLY* 5.4 0.4 - - - -
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Residues in contact with ALA 95 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33E PHE* 3.6 31.6 - - + -
73E PHE* 3.2 41.2 - - + -
74E THR 5.4 1.0 + - - +
91E SER 3.2 16.2 + - - +
92E VAL 4.1 1.3 - - - +
94E LEU* 1.3 78.4 - - - +
96E ASN* 1.3 59.3 + - - +
98E GLU* 3.2 4.2 + - - -
99E LEU* 3.0 23.6 + - - +
122E LEU* 5.2 2.2 - - + -
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Residues in contact with ASN 96 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33E PHE* 5.2 1.6 - - - -
92E VAL* 2.9 40.4 + - - +
93E GLY* 4.1 1.1 - - - +
95E ALA* 1.3 79.3 - - - +
97E GLN* 1.3 57.3 + - - +
99E LEU* 4.3 4.9 - - - +
100E ALA* 2.8 31.0 + - - +
121E SER* 3.0 28.8 + - - +
122E LEU* 3.2 15.8 - - - +
124E ILE* 3.5 9.9 - - + +
125E GLY* 2.6 32.4 + - - +
183E TRP* 3.6 16.6 - - + -
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Residues in contact with GLN 97 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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93E GLY 3.2 17.6 + - - +
94E LEU* 3.2 21.1 + - + +
96E ASN* 1.3 76.5 - - - +
98E GLU* 1.3 61.8 + - + +
100E ALA* 3.6 2.8 - - - +
101E GLU* 3.4 35.7 + - + +
132E ARG* 4.8 1.3 + - - +
180E GLY 5.2 0.2 - - - +
183E TRP* 3.3 49.0 + - + +
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Residues in contact with GLU 98 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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71E LEU* 5.0 2.0 - - + -
72E SER 4.4 2.5 - - - +
73E PHE* 3.4 21.2 - - + +
74E THR* 2.5 41.6 + - - -
94E LEU* 3.1 26.6 + - + +
95E ALA* 3.5 6.0 - - - +
97E GLN* 1.3 77.5 - - + +
99E LEU* 1.3 64.5 + - - +
101E GLU* 3.1 20.5 + - - +
102E VAL* 3.3 18.2 + - + +
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Residues in contact with LEU 99 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29E ILE* 4.3 7.9 - - + -
31E ALA* 4.4 4.9 - - + -
71E LEU* 4.0 24.5 - - + -
73E PHE* 4.0 7.1 - - + -
95E ALA 3.0 16.2 + - - +
96E ASN* 3.8 5.6 - - - +
98E GLU* 1.3 75.7 - - - +
100E ALA* 1.3 63.3 + - - +
102E VAL* 3.2 1.9 + - - +
103E VAL* 3.0 43.4 + - + +
115E THR* 4.2 15.0 - - + -
122E LEU* 3.6 38.6 - - + +
126E THR* 3.5 31.2 - - + +
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Residues in contact with ALA 100 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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96E ASN 2.8 18.8 + - - +
97E GLN 3.6 7.6 - - - +
99E LEU* 1.3 77.7 - - - +
101E GLU* 1.3 56.7 + - - +
103E VAL* 3.6 0.8 + - - -
104E SER* 3.0 25.3 + - - -
125E GLY 3.4 23.1 + - - +
129E GLY* 3.2 15.7 - - - +
132E ARG* 3.7 15.0 + - - +
183E TRP* 3.9 17.0 - - + -
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Residues in contact with GLU 101 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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97E GLN* 3.4 27.1 + - + +
98E GLU* 3.1 12.3 + - - +
100E ALA* 1.3 74.7 - - - +
102E VAL* 1.3 66.9 + - + +
104E SER* 3.1 19.3 + - - -
105E ARG* 3.1 15.7 + - - +
132E ARG* 3.7 14.8 + - - +
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Residues in contact with VAL 102 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29E ILE* 3.5 28.5 - - + -
68E PHE* 3.7 23.0 - - + -
71E LEU* 3.9 28.9 - - + -
98E GLU* 3.6 14.1 - - + +
99E LEU 3.2 5.8 + - - +
101E GLU* 1.3 76.6 - - + +
103E VAL* 1.3 64.5 + - - +
105E ARG* 3.2 7.5 + - + +
106E ALA* 3.0 22.0 + - - +
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Residues in contact with VAL 103 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29E ILE* 3.9 15.9 - - + -
99E LEU* 3.0 38.8 + - + +
100E ALA 4.0 4.0 - - - +
102E VAL* 1.3 74.0 - - - +
104E SER* 1.3 60.2 + - - +
106E ALA* 3.2 2.1 + - - +
107E VAL* 2.9 39.3 + - + +
113E CYS* 4.1 12.3 - - + -
115E THR* 4.0 10.5 - - - +
126E THR* 3.7 35.7 - - + +
129E GLY* 4.6 0.9 - - - -
130E HIS* 3.9 10.3 - - + +
291E ALA* 5.5 2.2 - - + -
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Residues in contact with SER 104 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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100E ALA 3.0 13.8 + - - -
101E GLU* 3.1 13.9 + - - -
103E VAL* 1.3 77.8 - - - +
105E ARG* 1.3 60.9 + - - +
107E VAL* 4.4 2.2 - - - -
108E SER* 2.8 31.4 + - - -
129E GLY* 3.1 26.5 - - - -
132E ARG* 4.1 14.7 + - - -
133E HIS* 3.3 19.9 + - - -
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Residues in contact with ARG 105 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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68E PHE* 5.0 9.4 - - + -
101E GLU 3.1 12.9 + - - +
102E VAL* 3.3 12.8 - - - +
104E SER* 1.3 83.5 + - - +
106E ALA* 1.3 62.0 + - - +
108E SER* 3.3 8.0 + - - -
109E ASP* 3.0 37.0 + - - +
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Residues in contact with ALA 106 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27E ALA* 4.0 15.3 - - + -
29E ILE* 4.8 0.7 - - + -
68E PHE* 3.6 32.7 - - + -
102E VAL 3.0 10.7 + - - +
103E VAL 3.2 6.3 + - - +
105E ARG* 1.3 74.7 - - - +
107E VAL* 1.3 66.1 + - - +
109E ASP* 3.0 8.6 + - - -
111E TYR* 3.0 29.9 + - + +
113E CYS* 4.0 13.7 - - + -
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Residues in contact with VAL 107 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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103E VAL* 2.9 32.7 + - + +
104E SER* 4.0 5.6 - - - +
106E ALA* 1.3 75.5 - - - +
108E SER* 1.3 61.2 + - - +
110E GLY* 3.3 12.2 + - - -
111E TYR 3.6 13.4 - - - +
113E CYS* 4.1 14.4 - - + -
130E HIS* 3.9 35.9 - - + +
133E HIS* 4.1 12.7 - - + +
134E CYS* 3.9 17.9 - - - -
290E SER* 4.4 6.1 - - - +
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Residues in contact with SER 108 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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104E SER 2.8 20.8 + - - -
105E ARG* 3.3 11.4 - - - -
107E VAL* 1.3 75.3 - - - +
109E ASP* 1.3 60.4 + - - +
110E GLY 3.0 9.1 + - - -
133E HIS* 3.1 33.4 + - - -
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Residues in contact with ASP 109 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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66E LYS* 5.2 7.1 + - - -
68E PHE* 5.2 1.6 - - - -
105E ARG* 3.0 24.9 + - - +
106E ALA* 3.0 4.7 + - - +
108E SER* 1.3 77.8 - - - +
110E GLY* 1.3 60.2 + - - +
111E TYR* 3.3 31.7 + - + -
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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
------------------------------------------------------------
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