Contacts of the helix formed by residues 86 - 109 (chain A) in PDB entry 2PWZ
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 ASP 86 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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84A GLY 3.9 1.7 + - - +
85A MET* 1.3 74.7 - - - +
87A ARG* 1.3 98.6 + - - +
88A SER* 3.5 4.2 + - - -
89A ASP* 2.8 48.1 + - - +
90A LEU* 2.9 15.6 + - - +
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Residues in contact with ARG 87 (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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86A ASP* 1.3 102.3 + - - +
88A SER* 1.3 78.7 + - - +
90A LEU* 3.4 12.2 + - - +
91A PHE* 2.9 29.5 + - - +
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Residues in contact with SER 88 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86A ASP* 3.6 5.8 - - - -
87A ARG* 1.3 97.2 - - - +
89A ASP* 1.3 63.8 + - - +
91A PHE* 3.7 8.4 + - - +
92A ASN* 3.2 34.5 + - - -
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Residues in contact with ASP 89 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84A GLY 3.8 6.2 - - - +
85A MET* 3.6 30.5 - - + +
86A ASP* 2.8 47.5 + - - +
88A SER* 1.3 72.2 + - - +
90A LEU* 1.3 64.9 - - - +
92A ASN* 3.3 11.9 + - - +
93A VAL* 3.1 25.3 + - - +
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Residues in contact with LEU 90 (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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79A VAL* 4.2 20.0 - - + +
80A ALA 3.6 22.0 - - - +
81A ARG* 4.1 9.6 - - - +
82A LYS* 3.8 33.4 - - + +
85A MET* 3.8 18.6 - - + +
86A ASP 2.9 20.8 + - - +
87A ARG* 3.6 11.7 - - - +
89A ASP* 1.3 73.0 - - - +
91A PHE* 1.3 61.1 + - - +
93A VAL* 3.4 6.6 + - - +
94A ASN* 2.9 37.3 + - - +
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Residues in contact with PHE 91 (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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87A ARG 2.9 18.2 + - - +
88A SER* 3.8 8.7 - - - +
89A ASP 3.3 0.2 - - - -
90A LEU* 1.3 75.7 - - - +
92A ASN* 1.3 74.4 + - - +
94A ASN* 3.2 5.3 + - - +
95A ALA* 2.8 53.0 + - + +
120A PRO* 3.9 27.1 - - + -
123A THR* 3.6 35.0 - - + -
124A THR* 5.4 1.1 - - + -
127A ILE* 4.7 2.2 - - + -
305A LEU* 3.9 29.8 - - + -
309A PHE* 4.2 11.9 - + + -
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Residues in contact with ASN 92 (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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88A SER* 3.2 24.5 + - - -
89A ASP* 3.3 11.0 + - - +
91A PHE* 1.3 90.5 - - - +
93A VAL* 1.3 61.6 + - + +
96A GLY* 3.1 19.9 + - - -
309A PHE* 3.9 23.1 - - + -
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Residues in contact with VAL 93 (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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79A VAL* 3.9 20.4 - - + -
82A LYS* 4.8 10.1 - - - +
85A MET* 3.8 30.5 - - + -
89A ASP 3.1 15.1 + - - +
90A LEU* 3.6 7.0 - - - +
91A PHE 3.3 0.2 - - - -
92A ASN* 1.3 75.1 - - + +
94A ASN* 1.3 56.7 + - - +
96A GLY* 3.2 2.6 + - - -
97A ILE* 2.9 52.1 + - + +
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Residues in contact with ASN 94 (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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78A GLY* 3.2 5.9 - - - -
79A VAL* 2.9 48.9 + - - +
90A LEU* 2.9 26.4 + - - +
91A PHE* 3.9 3.7 - - - +
93A VAL* 1.3 72.1 - - - +
95A ALA* 1.3 57.6 + - - +
97A ILE* 3.3 7.7 + - - +
98A VAL* 3.0 35.3 + - - +
118A THR* 3.8 13.1 - - + +
119A ASN* 3.4 28.6 + - - +
120A PRO* 5.2 1.9 - - + +
124A THR* 5.0 1.3 - - + -
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Residues in contact with ALA 95 (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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91A PHE* 2.8 36.8 + - + +
94A ASN* 1.3 72.7 - - - +
96A GLY* 1.3 57.9 + - - +
98A VAL* 3.6 3.5 + - - +
99A LYS* 2.9 30.7 + - - +
124A THR* 4.8 3.7 - - + +
127A ILE* 3.4 30.2 - - + +
309A PHE* 3.4 25.1 - - + -
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Residues in contact with GLY 96 (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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92A ASN 3.1 16.3 + - - -
93A VAL 3.6 3.1 - - - -
95A ALA* 1.3 72.8 - - - +
97A ILE* 1.3 64.2 + - - +
99A LYS* 3.4 3.9 + - - +
100A ASN* 3.0 25.9 + - - +
309A PHE* 3.5 13.8 - - - -
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Residues in contact with ILE 97 (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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77A ALA* 3.6 33.7 - - + +
78A GLY* 3.9 23.1 - - - +
79A VAL* 5.4 1.6 - - + -
93A VAL* 2.9 38.1 + - + +
94A ASN* 3.3 7.8 + - - +
96A GLY* 1.3 74.7 - - - +
98A VAL* 1.3 61.7 + - + +
100A ASN* 3.2 7.7 + - - +
101A LEU* 2.9 42.0 + - + +
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Residues in contact with VAL 98 (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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75A ILE* 4.8 7.2 - - + -
94A ASN 3.0 21.2 + - - +
95A ALA* 3.9 4.9 - - - +
97A ILE* 1.3 76.6 - - + +
99A LYS* 1.3 64.4 + - - +
101A LEU* 4.5 4.3 - - - +
102A VAL* 2.9 45.8 + - + +
116A ILE* 4.5 8.1 - - + -
118A THR* 3.7 33.9 - - + +
124A THR* 3.7 37.2 - - + +
127A ILE* 4.3 8.1 - - + -
128A ALA* 4.5 2.0 - - + -
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Residues in contact with LYS 99 (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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95A ALA 2.9 19.0 + - - +
96A GLY* 3.7 5.4 - - - +
98A VAL* 1.3 75.0 - - - +
100A ASN* 1.3 61.1 - - - +
103A GLN* 3.1 24.4 + - + +
127A ILE* 4.0 15.9 - - + +
131A VAL* 3.9 20.9 - - + +
309A PHE* 3.9 24.5 + - + -
310A VAL* 4.4 28.8 + - + +
312A LYS* 5.8 3.0 - - - +
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Residues in contact with ASN 100 (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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33A TYR* 5.5 0.9 + - - -
61A GLU 5.0 0.7 - - - +
96A GLY 3.0 18.4 + - - +
97A ILE* 3.5 5.5 - - - +
99A LYS* 1.3 74.7 - - - +
101A LEU* 1.3 75.8 + - - +
103A GLN* 3.3 7.4 + - - +
104A GLN* 3.1 45.7 + - - +
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Residues in contact with LEU 101 (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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6A LEU* 3.8 26.4 - - + +
33A TYR* 3.8 29.4 - - + +
63A ALA* 5.1 1.3 - - + -
75A ILE* 3.8 20.9 - - + -
77A ALA* 3.5 32.8 - - + -
97A ILE* 2.9 30.6 + - + +
98A VAL 4.1 1.6 - - - +
100A ASN* 1.3 86.9 - - - +
102A VAL* 1.3 57.7 + - - +
104A GLN* 3.3 13.7 + - - +
105A VAL* 3.0 31.4 + - - +
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Residues in contact with VAL 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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75A ILE* 3.7 23.1 - - + -
98A VAL* 2.9 26.8 + - + +
99A LYS 4.2 0.2 - - - +
101A LEU* 1.3 74.3 - - - +
103A GLN* 1.3 59.6 + - - +
105A VAL* 3.1 7.4 + - + +
106A ALA* 2.8 28.6 + - - +
114A ILE* 5.1 4.5 - - + -
116A ILE* 4.2 2.2 - - + -
128A ALA* 3.6 45.5 - - + +
131A VAL* 3.6 16.4 - - + -
132A LEU* 3.8 16.6 - - + -
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Residues in contact with GLN 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 LYS* 3.1 19.8 + - + +
100A ASN* 3.3 8.7 + - - +
102A VAL* 1.3 75.1 - - - +
104A GLN* 1.3 64.8 + - + +
106A ALA* 3.2 3.8 + - - +
107A LYS* 3.1 34.1 + - - +
131A VAL* 3.5 17.5 - - + +
134A LYS* 6.1 0.5 - - - +
135A ALA* 4.5 14.3 - - - +
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Residues in contact with GLN 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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33A TYR* 4.6 1.2 + - - -
61A GLU 3.0 21.3 + - - +
62A ASP* 3.6 10.8 - - - +
63A ALA* 2.6 33.9 + - + +
64A THR* 4.1 2.0 + - - +
67A LEU* 3.5 19.7 - - + +
100A ASN* 3.1 40.8 + - - +
101A LEU* 3.4 17.9 - - - +
103A GLN* 1.3 76.9 - - + +
105A VAL* 1.3 60.2 + - - +
107A LYS* 3.3 9.9 + - - +
108A THR* 3.2 21.1 + - - -
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Residues in contact with VAL 105 (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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6A LEU* 4.0 5.4 - - + -
67A LEU* 3.9 18.2 - - + -
73A VAL* 3.8 27.1 - - + -
75A ILE* 4.5 5.4 - - + -
101A LEU 3.0 20.1 + - - +
102A VAL* 3.1 12.3 + - + +
104A GLN* 1.3 75.2 - - - +
106A ALA* 1.3 59.9 + - - +
109A CYS* 2.9 54.5 + - - +
110A PRO* 5.1 0.4 - - + -
114A ILE* 3.7 34.5 - - + -
132A LEU* 4.8 1.3 - - + -
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Residues in contact with ALA 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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102A VAL 2.8 20.3 + - - +
103A GLN* 3.2 10.3 + - - +
105A VAL* 1.3 72.2 - - - +
107A LYS* 1.3 61.7 + - - +
110A PRO* 3.4 22.4 - - - +
131A VAL* 5.1 1.1 - - + -
132A LEU* 3.9 13.2 - - + -
135A ALA* 3.7 29.0 - - + +
137A VAL* 3.8 20.6 - - + +
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Residues in contact with LYS 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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64A THR* 5.2 9.1 + - - +
103A GLN* 3.1 24.0 + - - +
104A GLN* 3.6 10.5 - - - +
105A VAL 3.2 0.4 - - - -
106A ALA* 1.3 79.1 - - - +
108A THR* 1.3 70.0 + - - +
110A PRO* 4.3 3.5 - - - +
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Residues in contact with THR 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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64A THR* 3.7 25.8 + - + +
67A LEU* 3.8 15.0 - - + -
68A GLU* 3.6 45.5 - - + +
69A GLY 5.2 1.7 + - - -
104A GLN 3.2 13.8 + - - -
107A LYS* 1.3 87.7 - - - +
109A CYS* 1.3 59.8 + - - +
110A PRO* 3.4 6.1 - - - +
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Residues in contact with CYS 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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67A LEU* 3.4 39.9 - - - +
69A GLY* 5.1 1.8 - - - +
70A ALA* 3.8 19.3 - - - +
73A VAL* 3.7 29.6 - - - -
105A VAL* 2.9 27.1 + - - +
108A THR* 1.3 75.1 - - - +
110A PRO* 1.3 58.8 - - - +
111A LYS 3.0 11.0 + - - -
112A ALA* 3.1 13.0 + - - +
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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
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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