Contacts of the helix formed by residues 141 - 162 (chain A) in PDB entry 1YV5
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 141 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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58A ARG* 3.9 18.3 + - - +
137A GLY 4.9 4.7 - - - +
138A VAL 3.3 15.8 - - - +
140A LEU* 1.3 73.8 + - - +
142A ALA* 1.3 60.8 + - - +
143A ILE 2.9 7.4 + - - -
144A ASN* 2.9 20.5 + - + +
145A ASP* 3.2 13.4 + - - +
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Residues in contact with ALA 142 (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 VAL* 3.8 7.2 - - + +
119A ILE* 3.9 12.6 - - + -
132A TRP* 3.8 21.1 - - + -
133A TYR* 3.8 15.0 - - + -
138A VAL* 3.8 3.9 - - + +
139A GLY 3.0 19.1 + - - +
140A LEU 3.0 0.8 - - - -
141A ASP* 1.3 75.9 - - - +
143A ILE* 1.3 55.5 + - - +
145A ASP* 3.5 13.6 - - - +
146A ALA* 2.9 30.1 + - - +
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Residues in contact with ILE 143 (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* 6.5 0.4 - - - -
119A ILE* 4.1 19.1 - - + -
140A LEU* 3.0 41.2 + - + +
141A ASP 2.9 0.8 - - - -
142A ALA* 1.3 75.1 - - - +
144A ASN* 1.3 67.2 + - - +
145A ASP 3.2 0.3 + - - -
146A ALA* 3.5 6.1 + - - +
147A ASN* 3.3 30.7 + - - +
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Residues in contact with ASN 144 (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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141A ASP* 2.9 12.4 + - + +
143A ILE* 1.3 80.2 - - - +
145A ASP* 1.3 67.4 + - - +
147A ASN* 3.0 24.9 + - - +
148A LEU* 3.0 28.5 + - - +
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Residues in contact with ASP 145 (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 ARG* 2.6 51.4 + - - +
62A VAL* 3.5 24.9 - - + +
115A VAL* 5.4 1.1 - - + -
132A TRP* 3.0 24.1 + - + +
141A ASP 3.4 10.1 - - - +
142A ALA* 3.0 9.9 + - - +
144A ASN* 1.3 85.5 + - - +
146A ALA* 1.3 61.2 + - - +
148A LEU* 3.5 14.9 - - - +
149A LEU* 3.3 23.6 + - - +
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Residues in contact with ALA 146 (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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112A PHE* 3.0 39.0 - - + +
115A VAL* 3.8 19.0 - - + +
116A ALA* 4.7 9.2 - - + -
142A ALA 2.9 14.1 + - - +
143A ILE* 3.8 7.2 - - - +
145A ASP* 1.3 76.4 - - - +
147A ASN* 1.3 66.0 + - - +
149A LEU* 3.0 23.2 + - - +
150A GLU 3.1 3.3 + - - -
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Residues in contact with ASN 147 (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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112A PHE* 3.9 18.2 - - - -
143A ILE* 3.3 28.2 + - - +
144A ASN* 3.0 17.9 + - - +
146A ALA* 1.3 76.8 - - - +
148A LEU* 1.3 57.4 + - - +
150A GLU* 3.3 13.2 + - - +
151A ALA* 2.9 26.6 + - - +
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Residues in contact with LEU 148 (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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55A ALA* 5.4 4.7 - - + +
58A ARG* 5.6 2.7 - - + -
59A LEU* 4.4 38.4 - - + +
62A VAL* 5.5 2.2 - - + -
144A ASN* 3.0 27.8 + - - +
145A ASP* 3.5 23.6 - - - +
147A ASN* 1.3 75.3 - - - +
149A LEU* 1.3 63.9 + - - +
151A ALA* 3.3 10.9 + - + +
152A CYS* 3.0 30.0 + - - -
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Residues in contact with LEU 149 (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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59A LEU* 5.2 2.2 - - + -
62A VAL* 3.8 30.1 - - + +
63A LEU* 3.7 29.2 - - + -
66A ASN* 4.3 4.7 - - + -
67A ALA* 5.7 0.4 - - + -
108A LEU* 3.9 19.2 - - + +
111A ALA* 3.7 34.8 - - + +
112A PHE* 4.0 10.8 - - + +
115A VAL* 4.3 9.0 - - + -
145A ASP 3.3 12.3 + - - +
146A ALA* 3.0 12.5 + - - +
148A LEU* 1.3 74.3 - - - +
150A GLU* 1.3 67.6 + - - +
152A CYS* 3.3 18.3 + - - +
153A ILE* 3.6 9.5 + - - +
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Residues in contact with GLU 150 (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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109A LEU* 4.8 2.9 - - + -
112A PHE* 3.5 53.7 - - + +
146A ALA 3.1 3.0 + - - -
147A ASN* 3.3 16.5 - - - +
149A LEU* 1.3 75.8 - - - +
151A ALA* 1.3 66.0 + - - +
153A ILE* 3.0 32.2 + - + +
154A TYR* 3.4 24.6 + - + +
175A LEU* 5.8 3.1 - - - +
178A SER* 4.4 10.6 + - - -
182A GLU* 4.4 5.4 - - - +
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Residues in contact with ALA 151 (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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147A ASN 2.9 14.6 + - - +
148A LEU* 3.3 18.8 + - + +
150A GLU* 1.3 76.0 - - - +
152A CYS* 1.3 62.1 + - - +
154A TYR* 3.2 19.8 + - - +
155A ARG* 3.3 19.3 + - + +
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Residues in contact with CYS 152 (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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42A LEU* 3.8 24.7 - - + -
59A LEU* 3.8 30.3 - - - -
63A LEU* 4.5 3.1 - - - -
108A LEU* 3.7 17.5 - - + -
148A LEU* 3.0 25.7 + - - -
149A LEU* 3.5 11.7 - - - +
150A GLU 3.1 0.4 - - - -
151A ALA* 1.3 73.3 - - - +
153A ILE* 1.3 69.6 + - - +
154A TYR 3.2 0.2 - - - -
155A ARG* 3.3 12.9 + - - +
156A LEU* 3.1 24.6 + - - +
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Residues in contact with ILE 153 (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 CYS* 3.6 26.7 - - + +
108A LEU* 3.9 8.7 - - + +
109A LEU* 3.5 50.3 - - + +
149A LEU 3.8 6.5 - - - +
150A GLU* 3.0 21.3 + - + +
152A CYS* 1.3 80.0 - - - +
154A TYR* 1.3 72.1 + - + +
156A LEU* 3.1 3.1 + - - +
157A LEU* 3.0 40.7 + - + +
174A PHE* 3.8 24.7 - - + -
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Residues in contact with TYR 154 (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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109A LEU* 5.3 0.2 - - - +
150A GLU* 3.4 36.5 + - + +
151A ALA* 3.2 8.9 + - - +
153A ILE* 1.3 84.8 - - + +
155A ARG* 1.3 64.1 + - + +
156A LEU 3.3 0.2 - - - -
157A LEU* 4.0 14.9 - - + +
158A LYS* 3.1 24.3 + - - +
167A TYR* 4.8 1.6 + - - -
171A ILE* 4.1 21.3 - - + -
174A PHE* 3.5 39.5 + - + +
175A LEU* 3.4 35.9 - - + +
178A SER* 4.2 5.5 + - - -
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Residues in contact with ARG 155 (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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41A VAL 5.9 0.8 + - - -
42A LEU* 4.1 26.0 + - + +
45A ASP* 5.1 12.9 - - - +
59A LEU* 6.3 2.2 - - - -
151A ALA* 3.3 19.6 + - + +
152A CYS* 3.7 13.5 - - - +
153A ILE 3.3 0.2 - - - -
154A TYR* 1.3 79.8 - - + +
156A LEU* 1.3 56.8 + - - +
158A LYS* 3.6 5.2 + - - +
159A LEU* 2.9 45.6 + - + +
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Residues in contact with LEU 156 (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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38A ILE* 4.2 18.4 - - + -
41A VAL* 3.8 30.1 - - + -
42A LEU* 4.0 21.1 - - + -
101A THR* 3.9 16.4 - - + +
104A TRP* 5.1 0.2 - - + -
105A CYS* 3.8 19.7 - - - +
108A LEU* 3.8 29.4 - - + -
152A CYS 3.1 12.5 + - - +
153A ILE 3.5 6.7 - - - +
155A ARG* 1.3 74.5 - - - +
157A LEU* 1.3 67.1 + - - +
159A LEU* 4.3 3.6 - - + +
160A TYR* 3.0 41.0 + - + +
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Residues in contact with LEU 157 (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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101A THR* 6.1 0.4 - - + -
102A VAL* 3.9 27.6 - - + -
105A CYS* 4.2 11.0 - - - -
153A ILE* 3.0 34.8 + - + +
154A TYR* 4.0 20.0 - - + +
155A ARG 3.4 0.2 - - - -
156A LEU* 1.3 76.1 - - - +
158A LYS* 1.3 55.1 + - - +
161A CYS* 2.6 43.5 + - + +
162A ARG 3.4 1.4 + - - -
167A TYR* 3.7 15.0 - - + -
170A LEU* 4.2 16.4 - - + -
171A ILE* 4.4 17.9 - - + +
174A PHE* 4.2 19.1 - - + -
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Residues in contact with LYS 158 (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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154A TYR 3.1 18.0 + - - +
155A ARG* 3.8 5.8 - - - +
157A LEU* 1.3 77.4 - - - +
159A LEU* 1.3 62.8 + - + +
160A TYR 3.2 0.3 + - - -
162A ARG* 3.3 50.2 + - + +
167A TYR* 3.5 26.8 - - - +
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Residues in contact with LEU 159 (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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41A VAL* 4.4 35.0 - - + +
42A LEU* 5.0 2.7 - - + -
155A ARG* 2.9 42.1 + - + +
156A LEU* 3.3 4.9 + - + +
158A LYS* 1.3 78.6 - - + +
160A TYR* 1.3 76.6 + - + +
162A ARG* 4.6 10.3 + - - +
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Residues in contact with TYR 160 (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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34A HIS* 4.6 3.2 + - - -
37A GLN* 4.2 16.3 + - - +
38A ILE* 5.3 2.4 - - + +
41A VAL* 3.7 38.9 - - + +
97A GLN* 3.7 39.0 + - + -
98A ARG* 3.3 31.9 + - + +
101A THR* 3.7 33.2 - - + -
156A LEU* 3.0 22.7 + - + +
159A LEU* 1.3 92.2 - - + +
161A CYS* 1.3 69.7 + - - +
162A ARG 3.6 1.5 + - - -
163A GLU 5.4 0.2 + - - -
164A GLN* 4.6 2.1 + - - +
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Residues in contact with CYS 161 (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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98A ARG* 4.2 12.1 - - - -
101A THR* 6.0 0.9 - - - -
102A VAL* 4.2 23.1 - - - -
157A LEU* 2.6 30.8 + - + +
160A TYR* 1.3 84.8 - - - +
162A ARG* 1.3 63.2 + - - +
163A GLU 3.2 2.7 - - - -
164A GLN* 3.0 21.3 + - - +
166A TYR* 4.0 27.8 - - + -
167A TYR* 3.4 21.4 - - + +
170A LEU* 4.6 0.9 - - + -
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Residues in contact with ARG 162 (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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157A LEU 3.4 2.0 + - - -
158A LYS* 3.3 52.0 + - + +
159A LEU* 4.6 9.3 + - - +
160A TYR 3.6 2.2 - - - -
161A CYS* 1.3 78.2 - - - +
163A GLU* 1.3 95.8 + - - +
164A GLN 3.3 1.8 + - - +
167A TYR* 3.7 38.4 - - + +
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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
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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