Contacts of the helix formed by residues 100 - 121 (chain A) in PDB entry 1H27
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 100 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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97A THR* 4.7 4.7 - - - +
98A GLY 3.7 4.3 - - - +
99A ILE* 1.3 86.5 - - + +
101A LEU* 1.3 68.1 + - - +
102A PRO* 3.1 11.9 - - + -
103A LEU* 2.7 27.0 + - + +
104A ILE 3.0 8.7 + - - -
295A HIS* 3.7 37.7 - - + +
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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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99A ILE 3.3 4.2 + - - -
100A PRO* 1.3 71.7 - - - +
102A PRO* 1.3 61.3 - - + +
104A ILE* 3.0 18.7 + - + +
105A LYS* 2.8 55.1 + - - +
197A VAL* 6.1 0.7 - - + -
254A PRO 6.2 0.2 - - - +
255A LEU* 4.9 10.8 - - + -
256A ASP* 4.6 12.6 - - + +
285A PHE* 4.3 23.8 - - + -
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Residues in contact with PRO 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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100A PRO* 3.1 12.3 - - + -
101A LEU* 1.3 99.8 - - + +
103A LEU* 1.3 55.7 + - - +
105A LYS* 3.3 9.8 + - + +
106A SER* 2.9 28.9 + - - -
289A VAL* 5.4 0.3 - - - +
290A THR* 4.5 5.4 + - - +
292A PRO* 4.2 18.3 - - + +
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Residues in contact with LEU 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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90A PHE* 4.2 12.6 - - + -
99A ILE* 4.0 7.6 - - + -
100A PRO* 2.7 23.6 + - + +
102A PRO* 1.3 72.5 - - - +
104A ILE* 1.3 66.5 + - - +
106A SER* 3.3 5.3 + - - -
107A TYR* 2.9 56.2 + - + +
292A PRO* 3.4 39.9 - - + +
293A VAL 4.3 3.4 - - - +
294A PRO* 3.9 15.7 - - + -
295A HIS* 3.6 30.5 - - + +
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Residues in contact with ILE 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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99A ILE* 3.2 37.9 - - + +
100A PRO 3.0 4.4 + - - +
101A LEU* 3.2 18.6 - - + +
103A LEU* 1.3 77.8 - - - +
105A LYS* 1.3 58.2 + - - +
107A TYR* 3.1 3.6 + - - +
108A LEU* 2.9 28.1 + - - +
193A PHE* 4.0 28.0 - - + -
196A MET* 3.4 50.9 - - + +
197A VAL* 4.1 15.0 - - + +
285A PHE* 5.0 3.1 - - + -
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Residues in contact with LYS 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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101A LEU* 2.8 37.2 + - - +
102A PRO* 3.4 12.2 - - + +
104A ILE* 1.3 75.7 - - - +
106A SER* 1.3 62.1 + - - +
108A LEU* 3.5 0.4 + - - -
109A PHE* 3.1 26.5 + - - +
256A ASP* 5.5 2.6 + - - -
285A PHE* 3.2 61.9 + - + +
286A PHE* 3.5 18.9 - - + -
288A ASP* 3.2 35.2 + - - +
289A VAL* 3.9 13.2 - - + -
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Residues in contact with SER 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 PRO 2.9 13.5 + - - -
103A LEU* 3.6 6.5 - - - -
105A LYS* 1.3 70.4 - - - +
107A TYR* 1.3 63.7 + - - +
109A PHE* 3.5 1.8 + - - +
110A GLN* 3.0 48.6 + - - +
139A GLY 4.4 1.2 + - - -
289A VAL* 3.9 6.8 - - - +
290A THR 2.5 28.5 + - - -
291A LYS* 3.1 11.3 - - - +
292A PRO* 3.2 17.2 + - - +
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Residues in contact with TYR 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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87A LEU* 4.0 13.0 - - + -
90A PHE* 4.3 9.2 - + - -
99A ILE* 5.4 2.7 - - + -
103A LEU* 2.9 43.0 + - + +
104A ILE 3.1 5.3 + - - +
106A SER* 1.3 75.9 - - - +
108A LEU* 1.3 62.3 + - - +
110A GLN* 3.4 6.0 + - - -
111A LEU* 2.8 35.1 + - + +
135A ILE* 2.8 45.9 - - + +
139A GLY 3.7 18.8 - - - -
141A ILE* 3.6 32.6 - - + +
196A MET* 4.0 25.6 - - + -
294A PRO* 3.7 16.5 - - - +
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Residues in contact with LEU 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 ILE 2.9 16.4 + - - +
105A LYS* 4.7 0.9 - - - -
107A TYR* 1.3 78.4 - - - +
109A PHE* 1.3 59.2 + - - +
111A LEU* 3.2 9.1 + - + +
112A LEU* 2.8 41.2 + - + +
189A LEU* 4.2 26.9 - - + +
193A PHE* 3.8 45.1 - - + -
196A MET* 4.4 11.2 - - + +
262A LEU* 3.7 17.9 - - + -
266A MET* 4.5 5.2 - - + -
285A PHE* 4.3 1.3 - - + -
286A PHE* 3.7 25.8 - - + -
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Residues in contact with PHE 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 LYS 3.1 19.5 + - - +
106A SER 3.8 4.0 - - - +
107A TYR 3.1 0.2 - - - -
108A LEU* 1.3 78.4 - - - +
110A GLN* 1.3 61.5 + - + +
112A LEU* 3.4 3.5 + - - +
113A GLN* 3.1 52.4 + - - +
281A LEU* 3.3 45.6 - - + +
286A PHE* 3.4 36.1 - + + -
289A VAL* 3.9 26.2 - - + -
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Residues in contact with GLN 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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62A ASN* 3.2 31.7 + - - +
106A SER* 3.0 36.6 + - - +
107A TYR* 4.0 4.2 - - - -
109A PHE* 1.3 73.0 - - + +
111A LEU* 1.3 65.1 + - - +
113A GLN* 3.2 18.0 + - - +
114A GLY 3.1 17.7 + - - -
139A GLY 3.0 22.8 + - - -
140A ALA* 3.1 9.1 - - - +
141A ILE* 2.9 36.2 + - + +
291A LYS* 3.6 17.0 + - + +
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Residues in contact with LEU 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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62A ASN* 5.5 1.1 - - - -
87A LEU* 5.1 0.2 - - + -
107A TYR 2.8 28.0 + - - +
108A LEU* 3.5 10.1 - - + +
110A GLN* 1.3 77.1 - - - +
112A LEU* 1.3 57.7 + - - +
114A GLY* 3.1 2.8 + - - -
115A LEU* 2.9 28.9 + - - +
133A LEU* 3.9 33.7 - - + -
141A ILE* 4.0 28.9 - - + -
142A LYS* 4.9 3.6 - - - +
143A LEU* 3.7 29.1 - - + +
189A LEU* 4.0 25.1 - - + +
192A ILE* 4.7 3.6 - - + -
196A MET* 4.6 13.5 - - + -
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Residues in contact with LEU 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 LEU* 2.8 24.8 + - + +
109A PHE* 3.7 4.9 - - - +
111A LEU* 1.3 77.4 - - - +
113A GLN* 1.3 56.0 + - - +
115A LEU* 4.4 1.6 - - - -
116A ALA* 2.9 31.9 + - - +
186A ILE* 4.6 2.7 - - + -
189A LEU* 3.8 22.7 - - + -
262A LEU* 4.8 1.6 - - + -
266A MET* 4.4 10.3 - - + -
277A ALA* 3.7 31.2 - - + +
280A ALA* 3.8 20.9 - - + +
281A LEU* 3.8 12.6 - - + +
286A PHE* 3.4 40.2 - - + -
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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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60A HIS* 3.9 17.0 + - + +
61A PRO* 5.6 2.1 - - - +
62A ASN* 3.8 14.4 + - - +
109A PHE* 3.1 51.7 + - + +
110A GLN* 3.2 15.6 + - - +
112A LEU* 1.3 76.4 - - - +
114A GLY* 1.3 61.2 + - - +
116A ALA* 3.9 2.1 - - - +
117A PHE* 3.2 22.0 + - - +
281A LEU* 3.6 24.2 - - + -
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Residues in contact with GLY 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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60A HIS* 3.9 19.5 + - - -
62A ASN* 4.0 9.4 - - - -
63A ILE* 3.6 14.4 - - - +
110A GLN 3.1 13.8 + - - -
111A LEU 3.1 3.3 + - - -
113A GLN* 1.3 76.6 - - - +
115A LEU* 1.3 61.2 + - - +
117A PHE* 3.4 5.2 + - - +
118A CYS* 3.1 17.2 + - - -
143A LEU* 3.8 8.5 - - - -
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Residues in contact with LEU 115 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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111A LEU 2.9 15.8 + - - +
112A LEU* 3.9 4.3 - - - +
114A GLY* 1.3 74.7 - - - +
116A ALA* 1.3 59.9 + - - +
118A CYS* 3.1 9.1 + - + +
119A HIS* 2.9 64.9 + - + +
125A HIS* 4.8 4.0 - - + -
128A LEU* 3.8 26.9 - - + -
143A LEU* 3.8 14.7 - - + +
185A ASP* 3.8 24.2 - - + +
186A ILE* 4.1 12.6 - - + -
189A LEU* 3.8 21.5 - - + -
277A ALA* 4.3 3.1 - - + -
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Residues in contact with ALA 116 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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112A LEU 2.9 18.2 + - - +
113A GLN 3.9 4.0 - - - +
115A LEU* 1.3 73.6 - - - +
117A PHE* 1.3 61.3 + - - +
120A SER* 2.9 35.0 + - - +
277A ALA* 3.8 12.9 - - + +
278A LYS* 3.9 21.5 - - + +
281A LEU* 4.7 7.4 - - + -
178B TYR* 3.8 15.3 - - + +
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Residues in contact with PHE 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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57A GLU 4.1 2.5 - - - -
58A LEU* 3.8 20.6 - - + -
59A ASN 3.5 40.8 - - - -
60A HIS* 3.6 31.0 - + + +
63A ILE* 4.2 3.8 - - + -
113A GLN 3.2 12.3 + - - +
114A GLY 3.4 9.9 - - - +
116A ALA* 1.3 74.2 - - - +
118A CYS* 1.3 65.8 + - - +
120A SER* 3.1 5.1 + - - -
121A HIS* 2.8 60.2 + + - -
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Residues in contact with CYS 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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58A LEU* 4.2 12.8 - - - -
63A ILE* 3.5 26.7 - - - -
114A GLY 3.1 8.3 + - - -
115A LEU* 3.1 13.6 + - + +
117A PHE* 1.3 78.2 - - - +
119A HIS* 1.3 66.4 + - - +
121A HIS 3.0 9.9 + - - -
123A VAL* 3.0 38.3 + - + +
125A HIS* 5.6 3.8 - - - +
143A LEU* 4.0 10.3 - - - -
146A PHE* 3.7 28.0 - - - -
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Residues in contact with HIS 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 LEU* 2.9 42.9 + - + +
118A CYS* 1.3 77.9 - - - +
120A SER* 1.3 62.1 + - - +
122A ARG* 3.2 11.1 + - - -
123A VAL 3.3 14.3 + - - -
124A LEU* 4.2 1.5 - - + +
152A PHE* 3.8 5.7 - - - -
182A THR* 3.4 44.6 + - + +
185A ASP* 3.0 31.4 - - + +
186A ILE* 4.8 4.8 - - + +
276A SER* 6.3 0.2 - - - -
277A ALA* 4.7 4.7 - - + -
178B TYR* 3.5 39.0 - + + +
182B ILE* 3.5 16.8 - - - +
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Residues in contact with SER 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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116A ALA* 2.9 22.9 + - - +
117A PHE* 3.4 8.1 - - - -
119A HIS* 1.3 77.3 - - - +
121A HIS* 1.3 69.6 + - - +
122A ARG 3.4 1.3 - - - -
278A LYS* 4.7 1.4 - - - -
178B TYR* 3.4 11.2 - - - -
181B ASP* 2.9 45.6 + - - +
182B ILE* 3.7 13.2 - - - +
185B TYR* 4.3 3.8 - - - +
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Residues in contact with HIS 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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57A GLU* 4.3 5.4 - - - +
58A LEU* 3.9 13.9 - - + -
117A PHE* 2.8 67.9 + + - +
118A CYS 3.0 8.0 + - - +
120A SER* 1.3 88.3 - - - +
122A ARG* 1.3 88.3 + - - +
123A VAL* 3.2 4.7 + - - +
182B ILE* 4.9 0.2 - - - -
185B TYR* 3.4 52.1 - + + +
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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