Contacts of the helix formed by residues 93 - 115 (chain B) in PDB entry 1PD3
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 SER 93 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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89B ILE* 4.1 5.1 - - - +
90B THR* 2.6 41.9 + - - -
92B ASN* 1.3 79.9 - - - +
94B PHE* 1.3 65.1 + - - +
95B GLU* 4.0 11.8 - - - +
96B GLN* 3.3 11.8 + - - +
97B ILE* 3.0 23.0 + - - +
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Residues in contact with PHE 94 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82A GLU* 3.6 40.6 - - + -
83A VAL* 5.0 1.3 - - - -
86A ARG* 3.4 56.5 - - - +
92B ASN 3.7 1.8 + - - -
93B SER* 1.3 71.8 - - - +
95B GLU* 1.3 62.6 + - - +
97B ILE* 3.3 11.3 + - + +
98B THR* 2.8 59.5 + - + -
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Residues in contact with GLU 95 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83A VAL* 3.0 43.9 - - - +
86A ARG* 3.7 24.3 - - - +
87A LEU* 4.2 16.1 - - - +
87B LEU* 4.6 2.0 - - + -
89B ILE* 4.1 27.6 - - + +
93B SER* 4.0 11.2 - - - +
94B PHE* 1.3 86.8 - - - +
96B GLN* 1.3 51.5 + - - +
98B THR 3.7 0.2 - - - -
99B PHE* 2.8 49.5 + - + -
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Residues in contact with GLN 96 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84B ARG* 2.7 44.7 + - - +
89B ILE* 4.0 6.5 - - + +
90B THR 3.2 23.1 - - - +
91B GLU* 3.5 26.1 - - - +
93B SER* 3.2 7.8 + - - +
95B GLU* 1.3 76.1 - - - +
97B ILE* 1.3 67.4 + - - +
99B PHE* 3.5 3.6 + - - +
100B MET* 3.0 57.5 + - + +
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Residues in contact with ILE 97 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91B GLU 4.6 9.0 - - - +
92B ASN* 3.5 29.2 - - - +
93B SER 3.0 19.0 + - - +
94B PHE* 3.6 10.8 - - + +
96B GLN* 1.3 81.8 - - - +
98B THR* 1.3 60.2 + - - +
100B MET* 3.1 12.0 + - + +
101B GLN* 2.9 53.8 + - + +
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Residues in contact with THR 98 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79A LEU* 3.5 36.0 - - + +
82A GLU* 3.9 12.7 + - + +
83A VAL* 3.2 24.5 - - + -
94B PHE* 2.8 47.2 + - - -
97B ILE* 1.3 71.8 - - - +
99B PHE* 1.3 64.9 + - - +
100B MET 3.1 0.5 + - - -
101B GLN* 3.3 13.0 + - - +
102B ALA* 3.2 21.9 + - - +
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Residues in contact with PHE 99 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80A ILE* 6.0 1.8 - - + -
83A VAL* 3.5 34.2 - - + +
87A LEU* 5.7 0.2 - - + -
99A PHE* 4.0 4.5 - + - -
80B ILE* 3.7 41.3 - - + -
83B VAL* 3.7 23.3 - - + -
84B ARG* 3.8 34.3 - - + +
87B LEU* 3.5 27.8 - - + -
95B GLU* 2.8 36.4 + - + +
96B GLN* 3.7 6.3 - - - +
98B THR* 1.3 72.3 - - - +
100B MET* 1.3 63.2 + - + +
102B ALA* 3.5 5.9 + - + +
103B LEU* 3.1 30.5 + - + +
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Residues in contact with MET 100 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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91B GLU* 4.6 8.1 - - + +
96B GLN* 3.0 55.0 + - + +
97B ILE* 3.1 10.7 + - + +
99B PHE* 1.3 76.5 - - + +
101B GLN* 1.4 66.9 + - - +
103B LEU* 4.0 11.5 - - + +
104B GLN* 3.0 37.3 + - + +
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Residues in contact with GLN 101 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79A LEU* 3.7 30.1 - - + +
97B ILE* 2.9 36.7 + - + +
98B THR* 3.3 9.3 + - - +
100B MET* 1.4 75.4 - - + +
102B ALA* 1.3 51.4 + - - +
104B GLN* 3.3 11.7 + - - +
105B LEU* 2.8 39.4 + - + +
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Residues in contact with ALA 102 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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76A ILE* 4.6 9.5 - - + +
79A LEU* 3.8 25.6 - - + +
80A ILE* 4.2 20.4 - - + -
80B ILE* 5.3 6.5 - - + -
98B THR 3.2 16.2 + - - +
99B PHE* 3.8 7.6 - - + +
101B GLN* 1.3 73.6 - - - +
103B LEU* 1.4 59.8 + - + +
105B LEU* 3.3 3.8 + - - +
106B LEU* 2.9 33.8 + - - +
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Residues in contact with LEU 103 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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77B ARG* 3.8 23.5 - - + +
80B ILE* 3.7 28.9 - - + -
81B GLU* 3.5 39.9 - - + +
84B ARG* 5.6 5.6 - - + -
99B PHE* 3.1 30.0 + - + +
100B MET* 4.1 11.2 - - + +
102B ALA* 1.4 74.9 - - - +
104B GLN* 1.3 65.3 + - + +
106B LEU* 3.4 7.3 + - + +
107B LEU* 3.1 34.6 + - + +
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Residues in contact with GLN 104 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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100B MET* 3.0 30.5 + - + +
101B GLN* 3.6 10.0 + - - +
103B LEU* 1.3 77.7 - - + +
105B LEU* 1.3 62.9 + - - +
107B LEU* 3.2 7.7 + - + +
108B GLU* 3.0 25.2 + - - +
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Residues in contact with LEU 105 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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72A LYS* 4.2 22.7 - - + +
75A GLU* 3.6 32.5 - - + -
76A ILE* 3.7 18.8 - - + -
79A LEU* 4.1 15.7 - - + -
101B GLN* 2.8 19.3 + - + +
102B ALA 3.3 1.5 + - - +
104B GLN* 1.3 70.0 - - + +
106B LEU* 1.3 68.8 + - - +
107B LEU 3.3 0.2 + - - -
108B GLU* 3.4 27.6 + - - +
109B VAL* 3.0 25.5 + - - +
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Residues in contact with LEU 106 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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76A ILE* 3.9 26.4 - - + +
106A LEU* 4.7 2.7 - - + -
73B PHE* 4.3 22.7 - - + +
76B ILE* 3.8 22.9 - - + -
77B ARG* 3.8 32.5 - - + -
80B ILE* 3.6 31.0 - - + -
102B ALA 2.9 19.7 + - - +
103B LEU* 3.9 7.6 - - + +
105B LEU* 1.3 78.4 - - - +
107B LEU* 1.4 57.1 + - - +
109B VAL* 3.7 2.4 + - + +
110B GLU* 3.2 29.6 + - - +
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Residues in contact with LEU 107 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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77B ARG* 3.7 40.8 - - - +
103B LEU* 3.1 27.6 + - + +
104B GLN* 3.9 7.4 - - + +
106B LEU* 1.4 71.8 - - - +
108B GLU* 1.3 65.4 + - - +
110B GLU* 3.3 11.7 + - + +
111B GLN* 3.1 27.9 + - - +
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Residues in contact with GLU 108 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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72A LYS* 3.1 35.0 + - - +
104B GLN* 3.0 17.6 + - - +
105B LEU* 3.7 16.5 - - - +
107B LEU* 1.3 77.4 - - - +
109B VAL* 1.3 62.7 + - - +
111B GLN* 3.2 8.4 + - - +
112B GLU* 2.9 32.5 + - + +
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Residues in contact with VAL 109 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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69A LEU* 3.8 15.0 - - + -
72A LYS* 3.7 37.2 - - + -
73A PHE* 3.7 29.2 - - + -
76A ILE* 4.2 11.4 - - + -
73B PHE* 3.7 14.4 - - + -
105B LEU* 3.0 23.1 + - + +
106B LEU* 3.9 6.1 - - + +
108B GLU* 1.3 72.9 - - - +
110B GLU* 1.3 58.1 + - - +
112B GLU* 3.3 8.6 + - - +
113B ILE* 2.9 27.6 + - + +
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Residues in contact with GLU 110 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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70B GLY* 3.9 8.7 - - - +
73B PHE* 3.6 38.8 - - + +
74B GLU* 2.5 36.7 + - - +
77B ARG* 3.3 18.9 + - - +
106B LEU* 3.2 19.3 + - - +
107B LEU* 3.3 14.9 + - + +
109B VAL* 1.3 75.3 - - - +
111B GLN* 1.3 63.7 + - + +
113B ILE* 3.6 3.6 + - - +
114B ARG* 3.3 22.8 + - - +
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Residues in contact with GLN 111 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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107B LEU* 3.1 18.4 + - - +
108B GLU* 3.6 7.0 - - - +
109B VAL 3.1 0.4 - - - -
110B GLU* 1.3 82.7 - - + +
112B GLU* 1.3 58.9 + - - +
114B ARG* 2.9 35.9 + - - +
115B THR* 2.8 32.9 + - + +
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Residues in contact with GLU 112 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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65A TRP* 3.5 28.2 + - + +
68A GLN* 5.7 2.1 - - - +
69A LEU* 3.8 22.2 + - + +
72A LYS* 3.0 36.9 + - - +
108B GLU* 2.9 24.2 + - + +
109B VAL* 3.5 9.9 - - - +
111B GLN* 1.3 72.3 - - - +
113B ILE* 1.3 70.5 + - - +
114B ARG 3.1 0.2 + - - -
115B THR* 3.9 6.5 - - - +
116B PHE* 3.2 22.3 + - - +
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Residues in contact with ILE 113 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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65A TRP* 4.3 12.1 - - + -
69A LEU* 3.9 33.0 - - + -
113A ILE* 4.9 2.7 - - + -
65B TRP* 5.1 5.9 - - + -
66B ARG* 3.8 42.9 + - + +
69B LEU* 4.1 22.9 - - + -
70B GLY* 5.0 3.1 - - - +
73B PHE* 3.9 27.8 - - + -
109B VAL 2.9 24.7 + - - +
110B GLU 3.6 4.9 + - - +
111B GLN 3.3 0.2 - - - -
112B GLU* 1.3 76.4 - - - +
114B ARG* 1.3 65.7 + - - +
116B PHE* 3.8 9.5 - - - +
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Residues in contact with ARG 114 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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66B ARG* 4.0 18.6 + - - +
110B GLU* 3.3 15.7 + - - +
111B GLN* 2.9 46.3 + - - +
112B GLU 3.1 0.2 - - - -
113B ILE* 1.3 83.9 - - + +
115B THR* 1.3 86.1 + - - +
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Residues in contact with THR 115 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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66B ARG* 3.4 4.9 + - - -
111B GLN* 2.8 25.6 + - + +
112B GLU* 3.9 4.3 - - - +
114B ARG* 1.3 108.3 - - - +
116B PHE* 1.3 74.0 + - - +
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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