Contacts of the helix formed by residues 114 - 136 (chain H) in PDB entry 2W8B
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 THR 114 (chain H).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
292A GLU* 2.7 27.1 + - - -
335A GLN* 2.9 23.9 + - + +
336A ASP* 3.6 26.9 - - + +
349A VAL* 3.9 20.2 - - + -
378A GLU* 4.1 7.4 - - + -
113H GLY* 1.3 80.0 - - - +
115H PRO* 1.3 77.2 - - - +
117H TYR* 3.6 1.4 - - - +
118H ASN* 2.9 24.7 + - - +
150H LYS* 4.2 3.1 - - - -
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Residues in contact with PRO 115 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
203A MET* 3.8 5.0 - - + +
292A GLU* 5.1 0.2 - - - +
378A GLU* 3.2 28.7 - - - +
379A THR* 3.7 16.8 - - + -
423A PHE* 3.5 31.9 - - + -
114H THR* 1.3 89.6 - - - +
116H GLU* 1.3 63.5 + - + +
118H ASN* 3.4 1.9 + - - +
119H ILE* 3.4 22.0 + - - +
149H GLY* 4.9 1.2 - - - -
150H LYS* 4.1 13.7 - - + +
151H GLU* 3.1 24.3 - - - +
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Residues in contact with GLU 116 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
203A MET* 3.8 11.9 - - + +
204A SER* 2.8 32.3 + - - +
217A VAL* 4.0 4.0 - - - +
245A HIS* 2.7 31.6 + - - -
247A GLY* 3.8 3.6 - - - -
248A ALA* 2.8 36.5 + - + +
268A LEU* 3.9 9.7 - - - +
291A THR* 4.0 10.0 + - - +
292A GLU* 3.5 24.2 + - + +
114H THR 3.4 0.4 - - - -
115H PRO* 1.3 77.0 - - + +
117H TYR* 1.3 66.4 + - - +
119H ILE* 3.3 19.9 - - - +
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Residues in contact with TYR 117 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
268A LEU* 4.6 0.2 - - - +
289A ASN* 4.1 8.7 - - + -
291A THR* 3.9 14.4 - - + -
292A GLU* 3.2 14.2 + - - +
305A THR* 4.1 13.9 - - + -
307A ASP* 2.5 46.9 + - + +
312A PRO* 3.8 27.6 - - + +
333A GLN* 5.8 0.2 - - - -
335A GLN* 3.8 9.9 - - - +
114H THR* 3.4 18.1 + - - +
115H PRO 3.3 0.2 - - - -
116H GLU* 1.3 79.3 - - - +
118H ASN* 1.3 70.0 + - - +
120H SER* 2.9 50.7 + - - -
121H LEU* 4.4 17.1 - - + +
124H ARG* 3.1 11.8 + - - -
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Residues in contact with ASN 118 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
109H ALA* 3.7 9.9 - - + +
110H ASP 3.1 17.0 - - - +
112H ARG 2.8 23.7 + - - +
113H GLY* 3.5 7.3 - - - -
114H THR 2.9 35.7 + - - +
115H PRO 4.1 2.9 - - - +
116H GLU 3.3 0.2 - - - -
117H TYR* 1.3 88.6 - - - +
119H ILE* 1.3 64.3 + - - +
120H SER 3.1 0.4 - - - -
121H LEU* 3.1 29.1 + - - +
122H GLY 3.4 7.8 + - - -
149H GLY* 3.4 8.8 - - - -
150H LYS* 3.9 15.2 - - + +
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Residues in contact with ILE 119 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
203A MET* 4.3 13.0 - - + -
219A PHE* 4.5 0.9 - - + -
245A HIS* 3.5 56.1 - - + +
268A LEU* 4.4 7.0 - - + -
115H PRO 3.4 10.1 + - - +
116H GLU* 3.3 20.0 - - - +
117H TYR 2.9 0.2 + - - -
118H ASN* 1.3 78.0 - - - +
120H SER* 1.3 56.6 + - - +
121H LEU 3.2 0.3 + - - -
122H GLY 3.3 0.3 + - - -
123H GLU* 2.9 25.6 + - + +
147H SER* 2.7 47.4 + - - +
148H TYR* 3.9 4.5 - - - +
149H GLY* 3.7 14.1 - - - +
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Residues in contact with SER 120 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
268A LEU* 3.9 9.3 - - - +
289A ASN* 3.4 36.3 - - - -
117H TYR* 2.9 31.5 + - - -
119H ILE* 1.3 80.5 - - - +
121H LEU* 1.3 55.6 + - - +
123H GLU* 3.7 8.9 - - - +
124H ARG* 2.9 50.5 + - - +
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Residues in contact with LEU 121 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76H ASP* 4.4 9.6 - - - +
78H TYR* 3.3 27.1 - - + +
109H ALA* 3.8 9.0 - - + -
112H ARG 5.0 0.7 - - - +
117H TYR* 4.4 10.5 - - + +
118H ASN* 3.1 35.3 + - - +
120H SER* 1.3 76.1 - - - +
122H GLY* 1.3 66.6 + - - +
124H ARG* 3.2 30.1 + - - +
125H ARG* 3.2 38.4 + - - +
1175H ACT 3.7 29.8 - - + +
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Residues in contact with GLY 122 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
107H GLY* 3.5 10.6 - - - -
108H HIS 3.6 31.2 + - - -
118H ASN 3.4 5.2 + - - -
119H ILE 3.3 2.2 + - - -
121H LEU* 1.3 79.8 - - - +
123H GLU* 1.3 55.4 + - - -
125H ARG* 3.3 3.2 + - - +
126H ALA* 3.0 23.9 + - - +
147H SER* 3.4 18.2 - - - -
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Residues in contact with GLU 123 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
244A ARG* 3.5 21.7 + - - +
245A HIS* 3.6 10.0 + - - +
263A SER* 2.4 41.8 + - - +
266A GLY 4.7 3.5 - - - +
267A SER* 4.6 9.0 - - - -
268A LEU* 4.7 3.2 - - - +
289A ASN* 4.9 0.9 - - - +
119H ILE* 2.9 25.9 + - + +
120H SER* 3.7 8.2 - - - +
121H LEU 3.3 0.2 - - - -
122H GLY* 1.3 70.0 - - - +
124H ARG* 1.3 61.5 + - + +
126H ALA* 4.0 0.5 - - - +
127H ASN* 2.8 33.6 + - - +
145H ILE* 4.2 16.8 - - + +
147H SER* 3.3 22.7 + - - -
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Residues in contact with ARG 124 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
289A ASN* 3.9 13.3 - - - +
307A ASP* 3.7 11.3 + - - -
78H TYR* 3.6 52.6 + - + +
117H TYR* 3.1 17.4 + - - -
120H SER* 2.9 42.8 + - - +
121H LEU* 3.2 19.1 - - - +
122H GLY 3.4 0.4 - - - -
123H GLU* 1.3 74.8 - - + +
125H ARG* 1.3 58.1 + - - +
127H ASN* 3.8 5.8 - - - +
128H ALA* 3.0 29.6 + - - +
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Residues in contact with ARG 125 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73H PHE* 3.4 52.4 - - + +
74H ASP 3.3 13.7 + - - -
76H ASP* 3.7 5.5 - - - +
77H LYS 3.0 25.5 + - - +
78H TYR* 4.1 11.0 - - + -
108H HIS 2.9 27.7 + - - -
109H ALA* 3.4 5.1 - - - +
121H LEU* 3.2 14.9 + - - +
122H GLY* 3.6 7.0 - - - +
124H ARG* 1.3 73.5 - - - +
126H ALA* 1.3 66.8 + - - +
128H ALA* 3.1 4.9 + - - +
129H VAL* 3.1 24.4 + - - +
167H ARG* 3.7 10.7 - - - +
168H ARG 4.4 5.2 - - - +
169H ALA* 4.4 6.3 - - + -
1175H ACT 2.7 44.6 + - - -
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Residues in contact with ALA 126 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105H VAL* 3.4 42.3 - - + +
107H GLY 4.1 8.3 - - - +
122H GLY 3.0 16.5 + - - +
123H GLU 4.0 2.5 - - - +
125H ARG* 1.3 74.9 - - - +
127H ASN* 1.3 64.7 + - - +
129H VAL* 3.0 7.3 + - - +
130H LYS* 3.0 19.8 + - - +
145H ILE* 3.9 21.1 - - + +
146H VAL 5.0 0.9 - - - +
169H ALA* 4.4 2.8 - - - +
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Residues in contact with ASN 127 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
244A ARG* 2.8 39.7 - - - +
266A GLY 6.1 0.2 - - - -
123H GLU 2.8 23.4 + - - +
124H ARG* 3.8 6.7 - - - +
126H ALA* 1.3 71.3 - - - +
128H ALA* 1.3 52.7 + - - +
130H LYS* 2.8 16.2 + - - +
131H MET* 2.7 53.3 + - - +
145H ILE* 4.5 4.6 - - - +
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Residues in contact with ALA 128 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78H TYR* 3.1 28.5 - - + +
79H ASP* 4.7 1.6 - - - -
80H ILE* 3.7 17.0 - - + +
124H ARG 3.0 13.5 + - - +
125H ARG 3.1 4.5 + - - +
127H ASN* 1.3 77.1 - - - +
129H VAL* 1.3 62.9 + - - +
131H MET* 3.9 7.1 - - - +
132H TYR* 3.0 24.3 + - - +
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Residues in contact with VAL 129 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71H VAL* 4.1 15.7 - - + -
73H PHE* 4.8 0.4 - - + -
80H ILE* 3.7 20.4 - - + -
88H LEU* 4.1 20.6 - - + +
105H VAL* 3.8 25.1 - - + -
125H ARG 3.1 12.3 + - - +
126H ALA 3.0 8.8 + - - +
128H ALA* 1.3 77.7 - - - +
130H LYS* 1.3 62.7 + - - +
132H TYR* 3.3 3.2 + - - +
133H LEU* 3.0 33.2 + - + +
169H ALA* 4.0 20.4 - - + -
171H LEU* 4.1 8.1 - - + -
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Residues in contact with LYS 130 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
244A ARG* 4.3 7.2 - - - +
1432A SO4 3.1 30.2 + - - +
105H VAL* 5.6 0.2 - - + -
126H ALA 3.0 10.7 + - - +
127H ASN* 2.8 14.0 + - - +
129H VAL* 1.3 79.8 - - - +
131H MET* 1.3 66.6 + - - +
133H LEU* 3.4 2.3 + - - +
134H GLN* 2.9 45.2 + - - +
140H ALA* 3.2 21.2 + - - +
143H ILE* 2.8 56.3 + - + +
145H ILE* 4.0 12.8 - - + -
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Residues in contact with MET 131 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
127H ASN* 2.7 44.2 + - - +
128H ALA* 4.0 7.0 - - - +
130H LYS* 1.3 75.2 - - - +
132H TYR* 1.3 56.7 + - - +
134H GLN* 3.0 32.0 + - + +
135H GLY* 2.8 26.5 + - - -
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Residues in contact with TYR 132 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80H ILE* 4.2 26.9 - - + -
85H ALA* 3.3 34.2 + - + +
88H LEU* 3.6 28.5 - - + -
89H ASP* 2.9 31.3 + - - -
128H ALA 3.0 17.5 + - - +
129H VAL* 3.6 4.3 - - - +
130H LYS 3.3 0.2 - - - -
131H MET* 1.3 74.6 - - - +
133H LEU* 1.3 70.0 + - + +
135H GLY* 3.0 6.3 + - - +
136H LYS* 3.0 40.5 + - + +
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Residues in contact with LEU 133 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88H LEU* 3.6 37.2 - - + +
91H HIS* 4.2 4.9 - - + -
92H ALA* 3.8 19.3 - - + +
95H LEU* 4.2 16.4 - - + -
103H VAL* 4.3 9.6 - - + -
105H VAL* 5.1 1.1 - - + -
129H VAL* 3.0 34.4 + - + +
130H LYS* 5.0 0.4 - - - -
132H TYR* 1.3 78.3 - - + +
134H GLN* 1.3 58.3 + - - +
136H LYS* 2.8 18.0 + - - +
138H VAL* 3.0 26.6 + - + +
143H ILE* 3.8 26.5 - - + -
171H LEU* 4.4 8.1 - - + -
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Residues in contact with GLN 134 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
130H LYS* 2.9 36.2 + - - +
131H MET* 3.0 38.4 + - + +
133H LEU* 1.3 76.1 - - - +
135H GLY* 1.3 61.2 + - - +
137H GLY* 3.1 14.6 + - - -
138H VAL 3.8 19.6 + - - +
140H ALA* 3.3 30.4 + - - +
143H ILE* 4.4 10.1 - - + -
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Residues in contact with GLY 135 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
131H MET 2.8 13.0 + - - -
132H TYR* 3.0 8.3 + - - -
134H GLN* 1.3 77.2 - - - +
136H LYS* 1.3 68.3 + - - +
137H GLY 3.2 1.1 + - - -
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Residues in contact with LYS 136 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89H ASP* 3.6 27.7 + - - +
92H ALA* 3.3 28.3 - - + -
96H ARG* 2.7 35.3 + - - +
132H TYR* 3.0 37.3 + - + +
133H LEU 2.8 8.7 + - - +
135H GLY* 1.3 87.0 - - - +
137H GLY* 1.3 57.4 + - - +
138H VAL 3.5 0.4 + - - -
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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
------------------------------------------------------------
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) + - + + + + + -
------------------------------------------------------------
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