Contacts of the helix formed by residues 131 - 149 (chain M) in PDB entry 5IYB
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 131 (chain M).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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99B TRP 5.4 2.5 - - - +
100B GLU* 5.0 1.1 - - - +
101B ARG* 3.5 42.2 - - + +
911B LEU* 6.4 0.2 - - + -
913B GLN 4.4 7.4 - - - +
914B GLU 3.1 22.0 - - - +
915B GLY* 3.9 7.2 - - - -
129M ASN 3.8 2.9 - - - +
130M LEU* 1.3 91.4 - - + +
132M ARG* 1.3 65.7 + - - +
133M ASN* 3.1 11.3 + - - +
134M ILE* 3.1 26.2 + - + +
135M VAL* 3.8 2.8 + - - +
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Residues in contact with ARG 132 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
913B GLN 4.4 1.4 + - - +
914B GLU* 3.0 37.6 + - + +
916B TYR* 5.7 1.1 - - + -
75M LEU* 6.1 1.2 - - - +
122M THR* 4.5 22.1 - - - +
130M LEU 3.7 1.7 + - - -
131M PRO* 1.3 70.3 - - - +
133M ASN* 1.3 61.7 + - - +
135M VAL* 3.1 19.6 + - - +
136M ASP* 3.0 48.4 + - - +
139M ASN* 4.7 9.9 - - - +
61Y A 5.2 12.3 + - - -
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Residues in contact with ASN 133 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
820B LYS* 5.9 1.0 - - - +
914B GLU* 2.8 19.3 + - - +
915B GLY* 4.3 8.2 + - - -
916B TYR* 3.5 43.3 + - + +
131M PRO* 3.6 8.5 - - - +
132M ARG* 1.3 77.5 - - - +
134M ILE* 1.3 77.8 + - - +
136M ASP* 3.4 3.3 + - - +
137M ARG* 3.0 28.4 + - - +
171M GLU* 2.8 36.7 + - - +
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Residues in contact with ILE 134 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101B ARG* 5.1 2.0 - - + +
130M LEU* 3.7 32.8 - - + -
131M PRO* 3.1 29.3 + - + +
133M ASN* 1.3 87.6 + - - +
135M VAL* 1.3 61.8 + - - +
137M ARG* 3.1 9.1 + - + +
138M THR* 2.8 33.7 + - - +
164M LEU* 4.9 0.4 - - + -
167M ALA* 4.2 28.5 - - + +
168M CYS* 4.4 4.9 - - - -
171M GLU* 4.0 22.4 - - + -
173M VAL* 4.2 14.8 - - + -
175M ARG* 4.7 1.3 - - - +
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Residues in contact with VAL 135 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121M ILE* 3.7 22.9 - - + -
122M THR* 3.8 25.1 - - + -
125M ALA* 3.8 23.6 - - + -
130M LEU* 4.8 9.0 - - + +
131M PRO 4.0 10.5 - - - +
132M ARG* 3.1 25.8 + - - +
134M ILE* 1.3 74.9 - - - +
136M ASP* 1.3 56.4 + - - +
138M THR* 3.3 8.2 + - - -
139M ASN* 2.9 34.3 + - - +
164M LEU* 5.6 2.0 - - + -
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Residues in contact with ASP 136 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
820B LYS* 5.6 4.7 - - + -
821B LYS* 5.5 10.8 - - - +
822B GLY 5.8 3.7 - - - +
916B TYR* 3.8 21.4 + - - +
75M LEU* 5.1 5.0 - - - +
132M ARG* 3.0 42.3 + - - +
133M ASN 3.7 7.6 - - - +
135M VAL* 1.3 73.5 - - - +
137M ARG* 1.3 60.3 + - - +
139M ASN* 3.2 17.9 + - - +
140M ASN* 2.9 26.9 + - - +
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Residues in contact with ARG 137 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
820B LYS* 5.8 9.4 - - + +
133M ASN* 3.0 14.4 + - - +
134M ILE* 3.3 11.0 - - - +
136M ASP* 1.3 75.4 - - - +
138M THR* 1.3 58.8 + - - +
140M ASN* 3.0 11.7 + - + +
141M LEU* 2.8 32.3 + - + +
167M ALA* 4.3 18.6 - - + -
170M GLN* 3.2 49.4 + - - +
171M GLU* 3.3 27.7 + - - +
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Residues in contact with THR 138 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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121M ILE* 4.0 27.4 - - + -
134M ILE 2.8 19.3 + - - -
135M VAL* 3.5 10.1 - - - -
137M ARG* 1.3 68.6 - - - +
139M ASN* 1.3 67.4 + - - +
141M LEU* 3.1 4.9 + - - +
142M PHE* 2.9 22.9 + - - +
160M ALA 4.4 0.2 - - - +
163M CYS* 3.8 8.1 - - + -
164M LEU* 3.4 42.0 - - + +
167M ALA* 3.2 20.5 - - - +
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Residues in contact with ASN 139 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75M LEU* 3.7 31.8 - - + +
118M PHE* 3.0 44.0 - - + +
121M ILE* 3.5 14.7 - - - +
122M THR* 5.9 1.7 - - - +
132M ARG* 4.7 8.1 - - - +
135M VAL* 2.9 25.9 + - - +
136M ASP* 3.2 20.5 + - - +
138M THR* 1.3 74.6 - - - +
140M ASN* 1.3 62.2 + - - +
142M PHE* 3.9 2.7 - - - +
143M LYS* 3.0 25.5 + - - +
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Residues in contact with ASN 140 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
820B LYS* 4.3 11.7 - - + +
822B GLY 4.0 6.2 + - - +
823B PHE* 3.1 52.3 + - - +
75M LEU* 5.1 2.4 - - - +
136M ASP 2.9 13.4 + - - +
137M ARG* 3.0 16.0 + - + +
139M ASN* 1.3 78.6 - - - +
141M LEU* 1.3 62.9 + - + +
143M LYS* 3.4 4.8 + - - +
144M GLN* 2.9 39.8 + - - +
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Residues in contact with LEU 141 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
137M ARG* 2.8 21.4 + - + +
138M THR 3.1 6.0 + - - +
140M ASN* 1.3 72.8 - - + +
142M PHE* 1.3 60.7 + - - +
144M GLN* 3.4 14.1 + - - +
145M VAL* 3.2 27.4 + - + +
163M CYS* 3.8 32.8 - - + +
166M ILE* 3.9 16.4 - - + -
167M ALA* 3.8 24.7 - - + +
170M GLN* 4.2 19.7 - - - +
198M ILE* 6.4 0.7 - - + -
202M LEU* 3.6 29.4 - - + -
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Residues in contact with PHE 142 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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113M ALA 5.1 0.4 - - - -
114M MET* 4.7 12.1 - - + -
117M ALA* 3.4 25.4 - - + -
118M PHE* 4.7 8.5 - + + -
121M ILE* 4.5 10.8 - - + -
138M THR 2.9 20.2 + - - +
139M ASN* 3.9 4.3 - - - +
141M LEU* 1.3 69.9 - - - +
143M LYS* 1.3 70.1 + - - +
144M GLN 3.2 0.2 + - - -
145M VAL* 3.3 1.4 + - - +
146M TYR* 2.9 47.5 + + + +
156M ASN* 3.1 29.6 - - - -
159M ILE* 4.0 13.0 - - + -
160M ALA* 3.6 39.3 - - + -
163M CYS* 3.5 16.9 - - + -
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Residues in contact with LYS 143 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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823B PHE* 3.9 48.1 - - + -
73M PRO 5.8 0.2 - - - -
74M LEU 4.2 14.1 - - - +
75M LEU* 4.7 17.0 - - + +
76M SER* 5.0 3.4 - - - +
114M MET* 4.6 20.6 - - - +
118M PHE* 5.5 2.7 - - + -
139M ASN 3.0 17.9 + - - +
140M ASN* 3.7 6.1 - - - +
141M LEU 3.4 0.2 - - - -
142M PHE* 1.3 79.2 - - - +
144M GLN* 1.3 58.2 + - + +
146M TYR* 3.8 5.1 - - - +
147M GLU* 3.0 50.6 + - + +
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Residues in contact with GLN 144 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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823B PHE* 5.4 1.7 + - + -
140M ASN* 2.9 41.1 + - - +
141M LEU* 3.6 16.3 - - - +
142M PHE 3.2 0.6 - - - -
143M LYS* 1.3 78.9 - - + +
145M VAL* 1.3 57.2 + - - +
147M GLU* 3.2 11.9 + - - +
148M GLN* 2.9 33.4 + - - +
202M LEU* 3.6 30.0 - - + +
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Residues in contact with VAL 145 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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141M LEU* 3.2 18.2 + - + +
142M PHE* 3.9 5.4 - - - +
144M GLN* 1.3 72.3 - - - +
146M TYR* 1.3 65.1 - - - +
148M GLN* 3.4 13.0 + - - +
149M LYS* 3.3 16.8 + - - -
150M SER* 4.4 3.1 + - - +
151M LEU* 3.6 38.9 - - + +
159M ILE* 3.8 17.9 - - + -
163M CYS* 4.6 4.5 - - - -
198M ILE* 3.8 31.0 - - + +
201M ALA* 6.3 2.0 - - + -
202M LEU* 4.7 13.5 - - + -
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Residues in contact with TYR 146 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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110M SER 3.4 21.9 + - - -
111M ASP* 5.1 7.1 - - - -
113M ALA* 5.9 6.9 - - + +
114M MET* 4.3 32.2 + - + -
142M PHE* 2.9 42.0 + + + +
143M LYS* 3.8 4.7 - - - +
145M VAL* 1.3 76.3 - - - +
147M GLU* 1.3 63.2 + - - +
149M LYS* 3.0 49.0 + - + +
151M LEU* 5.9 0.9 - - - -
159M ILE* 5.7 1.1 - - - +
23X G 5.9 6.9 - - - -
24X G 3.8 15.9 + - - -
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Residues in contact with GLU 147 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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143M LYS* 3.0 42.9 + - + +
144M GLN* 3.2 13.7 + - - +
146M TYR* 1.3 82.3 - - + +
148M GLN* 1.3 58.0 + - + +
149M LYS* 4.4 6.3 - - - +
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Residues in contact with GLN 148 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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144M GLN* 2.9 17.4 + - + +
145M VAL* 3.7 11.6 - - - +
146M TYR 3.3 0.4 - - - -
147M GLU* 1.3 76.2 - - + +
149M LYS* 1.3 66.2 + - - +
150M SER* 2.9 34.6 + - - +
201M ALA* 3.0 36.2 + - - +
202M LEU* 4.1 15.8 + - + +
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Residues in contact with LYS 149 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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145M VAL 3.3 5.5 + - - -
146M TYR* 3.0 43.4 + - + +
147M GLU* 4.4 4.9 - - - +
148M GLN* 1.3 78.3 - - - +
150M SER* 1.3 55.7 + - - +
151M LEU* 3.1 11.6 + - - -
152M LYS* 3.5 41.0 + - + +
24X G 3.3 26.9 + - - -
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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
------------------------------------------------------------
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) + - + + + + + -
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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