Contacts of the helix formed by residues 103 - 124 (chain A) in PDB entry 3PA3
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 PRO 103 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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102A MET* 1.3 92.5 - - + +
104A GLU* 1.3 67.4 + - - +
105A PRO* 4.0 2.9 - - + -
106A ASP* 3.0 31.9 + - - +
107A ALA 3.1 9.0 + - - -
271A LYS* 3.6 35.2 - - + +
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Residues in contact with GLU 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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102A MET 3.3 3.2 + - - -
103A PRO* 1.3 70.9 - - - +
105A PRO* 1.3 70.5 - - + +
107A ALA* 3.2 1.6 + - - +
108A GLN* 2.9 22.3 + - - +
202A LEU* 4.0 21.4 - - + +
235A ASP* 3.6 26.4 + - - +
238A PRO* 4.0 9.6 - - - +
264A TRP* 2.8 41.4 + - + +
267A LYS* 5.0 4.0 + - - -
269A LEU* 3.8 16.3 - - + +
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Residues in contact with PRO 105 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103A PRO* 3.3 11.7 - - + -
104A GLU* 1.3 93.4 - - + +
106A ASP* 1.3 63.1 + - - +
108A GLN* 3.5 3.5 + - - +
109A ARG* 3.1 23.4 + - - +
269A LEU* 4.0 20.0 - - + +
270A LYS* 3.7 44.2 - - - +
271A LYS* 3.8 13.9 - - + +
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Residues in contact with ASP 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 MET* 4.0 13.4 - - + +
103A PRO* 3.0 20.6 + - - +
105A PRO* 1.3 75.5 - - - +
107A ALA* 1.3 67.7 + - - +
109A ARG* 3.2 9.3 + - - +
110A PHE* 2.9 39.6 + - + -
271A LYS* 2.8 40.5 + - - +
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Residues in contact with ALA 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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102A MET* 3.7 12.7 - - + -
103A PRO 3.1 10.5 + - - +
104A GLU 3.2 4.2 + - - +
106A ASP* 1.3 78.2 - - - +
108A GLN* 1.3 56.1 + - - +
110A PHE 3.4 0.2 + - - -
111A PHE* 2.9 30.7 + - - +
198A LEU* 4.7 1.8 - - + -
201A MET* 3.4 30.9 - - + +
202A LEU* 3.6 32.5 - - + -
264A TRP* 4.5 2.0 - - + -
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Residues in contact with GLN 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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104A GLU 2.9 17.0 + - - +
105A PRO 3.8 4.6 - - - +
107A ALA* 1.3 77.0 - - - +
109A ARG* 1.3 58.4 + - - +
111A PHE* 3.1 2.6 + - - +
112A HIS* 2.8 57.6 + - + +
264A TRP* 2.9 52.7 + - + +
265A TYR* 3.5 7.7 + - - -
267A LYS 2.8 28.1 + - - +
269A LEU* 3.5 24.4 + - + +
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Residues in contact with ARG 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 PRO 3.1 17.4 + - - +
106A ASP* 3.7 8.2 - - - +
108A GLN* 1.3 78.0 + - - +
110A PHE* 1.3 78.1 + - - +
112A HIS* 3.3 14.3 + - + +
113A GLN* 3.1 38.3 + - + +
141A ARG 3.3 15.0 + - - -
142A ASP* 2.8 34.9 + - - +
143A ASN* 3.3 22.2 + - - -
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Residues in contact with PHE 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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92A LEU* 3.6 20.0 - - + -
95A ARG* 4.6 13.5 - - + -
102A MET* 3.6 26.5 - - + -
106A ASP* 2.9 29.5 + - + +
107A ALA 3.8 3.4 - - - +
109A ARG* 1.3 89.3 - - - +
111A PHE* 1.3 57.9 + - - +
113A GLN* 3.2 10.1 + - - +
114A LEU* 2.8 30.0 + - - +
138A LEU* 3.4 33.7 - - + -
142A ASP* 3.4 29.8 - - + -
144A LEU* 3.7 15.4 - - + +
201A MET* 3.8 13.5 - - - -
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Residues in contact with PHE 111 (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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107A ALA 2.9 19.2 + - - +
108A GLN* 3.1 7.2 + - - +
110A PHE* 1.3 75.5 - - - +
112A HIS* 1.3 65.9 + + - +
114A LEU* 3.3 12.4 + - + +
115A MET* 2.9 51.1 + - + +
194A CYS* 3.7 24.7 - - + -
198A LEU* 4.0 27.4 - - + -
201A MET* 4.1 8.0 - - + +
241A LEU* 3.9 8.5 - - + -
245A ILE* 4.1 21.5 - - + -
259A ILE* 3.9 12.8 - - + -
264A TRP* 4.3 9.4 - + + -
265A TYR* 3.8 30.7 - + - -
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Residues in contact with HIS 112 (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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108A GLN* 2.8 52.3 + - + +
109A ARG* 3.3 11.9 + - + +
111A PHE* 1.3 72.9 - + - +
113A GLN* 1.3 61.9 + - + +
115A MET* 3.3 3.5 + - - +
116A ALA* 3.0 26.3 + - - +
265A TYR* 2.8 64.9 + + - +
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Residues in contact with GLN 113 (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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66A ASN* 3.5 30.4 - - - +
109A ARG* 3.1 51.3 + - + +
110A PHE* 3.7 8.7 - - - +
111A PHE 3.2 0.2 - - - -
112A HIS* 1.3 79.0 - - + +
114A LEU* 1.3 65.3 + - - +
116A ALA* 3.2 6.6 + - - +
117A GLY* 3.0 19.1 + - - -
142A ASP 3.8 3.3 - - - +
143A ASN* 3.4 14.4 + - - -
144A LEU* 2.8 37.7 + - + +
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Residues in contact with LEU 114 (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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110A PHE 2.8 17.4 + - - +
111A PHE* 3.6 17.7 - - + +
113A GLN* 1.3 76.1 - - - +
115A MET* 1.3 57.4 + - + +
117A GLY* 3.2 2.3 + - - -
118A VAL* 2.9 46.4 + - + +
131A ILE* 4.2 6.1 - - + -
136A LEU* 3.8 33.0 - - + -
144A LEU* 3.8 13.8 - - + +
146A ILE* 4.3 6.7 - - + -
194A CYS* 3.7 37.9 - - + -
197A VAL* 4.3 21.3 - - + -
201A MET* 5.6 0.9 - - + -
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Residues in contact with MET 115 (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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111A PHE* 2.9 40.1 + - + +
112A HIS 3.6 0.2 - - - +
114A LEU* 1.3 80.4 - - + +
116A ALA* 1.3 57.0 + - - +
118A VAL* 4.0 4.4 - - + +
119A VAL* 2.8 37.5 + - + +
191A VAL* 6.1 1.3 - - - -
194A CYS* 3.6 39.7 - - + -
256A ILE* 4.0 32.5 - - + -
259A ILE* 4.2 17.7 - - + -
260A LYS* 5.2 2.7 - - - -
265A TYR* 3.5 37.2 - - + +
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Residues in contact with ALA 116 (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 HIS* 3.8 12.4 + - + +
66A ASN* 3.5 15.5 - - - +
112A HIS 3.0 15.2 + - - +
113A GLN* 3.2 9.4 + - - +
115A MET* 1.3 77.1 - - - +
117A GLY* 1.3 61.7 + - - +
119A VAL* 3.8 6.1 - - - +
120A TYR* 3.1 22.9 + - - +
260A LYS* 6.0 2.5 - - - +
265A TYR* 5.2 0.2 + - - -
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Residues in contact with GLY 117 (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 HIS* 4.1 7.4 - - - -
66A ASN* 3.9 17.9 - - - +
67A VAL* 4.4 2.0 - - - +
113A GLN 3.0 11.7 + - - -
114A LEU 3.7 2.2 - - - -
116A ALA* 1.3 78.1 - - - +
118A VAL* 1.3 55.7 + - - +
120A TYR* 3.3 4.0 + - - +
121A LEU* 3.0 31.9 + - - +
146A ILE* 3.6 17.9 - - - -
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Residues in contact with VAL 118 (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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114A LEU* 2.9 26.9 + - + +
115A MET* 4.0 4.7 - - + +
117A GLY* 1.3 73.5 - - - +
119A VAL* 1.3 65.2 + - - +
121A LEU* 3.2 8.3 + - + +
122A HIS* 2.9 56.4 + - + +
131A ILE* 3.9 24.2 - - + -
146A ILE* 4.0 7.4 - - + -
190A ASP* 4.5 8.1 - - + +
191A VAL* 5.8 0.2 - - + -
194A CYS* 3.9 17.0 - - - -
256A ILE* 3.6 16.6 - - + -
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Residues in contact with VAL 119 (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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115A MET 2.8 25.2 + - - +
116A ALA* 3.8 5.4 - - - +
118A VAL* 1.3 71.1 - - - +
120A TYR* 1.3 59.6 + - - +
122A HIS* 3.5 4.2 + - - +
123A GLY* 2.9 27.5 + - - -
256A ILE* 3.4 37.0 - - + -
260A LYS* 3.7 24.7 - - - +
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Residues in contact with TYR 120 (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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61A MET 3.4 13.9 + - - -
62A LEU* 4.5 3.1 - - + -
63A ASN* 2.8 45.2 + - - +
64A HIS* 3.5 40.8 - + + +
67A VAL* 4.1 6.7 - - + -
116A ALA 3.1 14.2 + - - +
117A GLY 3.4 7.4 - - - +
119A VAL* 1.3 78.0 - - - +
121A LEU* 1.3 81.3 + - + +
123A GLY* 3.1 9.8 + - - -
124A ILE* 3.2 43.6 + - + +
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Residues in contact with LEU 121 (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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62A LEU* 3.7 30.3 - - + -
67A VAL* 4.3 5.6 - - + -
117A GLY 3.0 19.4 + - - +
118A VAL* 3.7 10.3 - - + +
120A TYR* 1.3 86.1 - - + +
122A HIS* 1.3 67.1 + - + +
124A ILE* 3.0 13.6 + - - +
126A ILE* 2.9 39.5 + - + +
128A HIS* 4.4 15.9 - - + +
146A ILE* 4.0 22.2 - - + -
149A PHE* 3.8 30.1 - - + -
190A ASP* 6.1 0.4 - - - +
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Residues in contact with HIS 122 (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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118A VAL* 2.9 40.1 + - + +
119A VAL* 4.0 4.7 - - - +
121A LEU* 1.3 78.6 - - + +
123A GLY* 1.3 52.0 + - - +
125A GLY* 3.0 7.4 + - - -
126A ILE 3.3 17.7 - - - -
127A THR* 4.4 0.4 + - - -
155A PHE* 3.6 11.5 - + + -
156A ARG* 2.8 35.0 + - - -
187A GLU* 3.5 46.5 + - + +
190A ASP* 2.8 36.8 + - + +
191A VAL* 5.1 0.9 - - + -
256A ILE* 4.1 12.7 - - + +
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Residues in contact with GLY 123 (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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119A VAL 2.9 16.7 + - - -
120A TYR* 3.1 4.7 + - - -
121A LEU 3.1 0.6 - - - -
122A HIS* 1.3 76.5 - - - +
124A ILE* 1.3 62.4 + - - +
125A GLY 3.2 1.0 + - - -
156A ARG* 3.6 11.1 + - - -
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Residues in contact with ILE 124 (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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61A MET* 4.0 32.2 - - + +
62A LEU* 3.9 28.5 - - + -
120A TYR* 3.2 43.0 + - + +
121A LEU* 3.0 17.1 + - - +
123A GLY* 1.3 78.1 - - - +
125A GLY* 1.3 58.9 + - - +
126A ILE* 3.6 13.9 + - + -
156A ARG* 4.6 3.9 - - - +
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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