Contacts of the helix formed by residues 132 - 149 (chain B) in PDB entry 5I1U
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 132 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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130B GLY 4.2 0.2 + - - -
131B MET* 1.3 76.3 - - - +
133B ASP* 1.3 59.3 + - - +
134B ARG* 3.5 11.9 + - - +
135B TRP* 3.0 14.6 + - - +
136B ARG* 2.9 25.9 + - - +
192B GLU* 2.7 40.5 + - - +
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Residues in contact with ASP 133 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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106A HIS* 5.1 2.6 + - - +
131B MET 3.8 0.7 + - - +
132B THR* 1.3 73.8 - - - +
134B ARG* 1.3 57.0 + - - +
136B ARG* 3.2 35.1 + - - +
137B ALA* 2.9 27.9 + - - +
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Residues in contact with ARG 134 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99A GLU* 2.9 42.8 + - - -
102A SER* 3.7 7.7 - - - -
103A ALA* 4.4 16.2 - - - +
106A HIS* 3.5 47.5 - - + +
108A THR* 5.0 9.6 + - + -
141A CYS* 4.8 0.5 - - - -
144A GLU* 3.0 34.0 + - - +
132B THR* 3.1 10.5 - - - +
133B ASP* 1.3 76.4 - - - +
135B TRP* 1.3 64.7 + - - +
137B ALA* 3.4 15.4 + - - +
138B ARG* 3.7 6.2 + - - +
192B GLU* 5.7 0.4 - - - +
195B GLN* 3.0 19.2 + - - +
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Residues in contact with TRP 135 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
127B ILE* 3.7 17.7 - - + -
128B THR* 4.7 1.3 - - + -
131B MET* 3.4 27.6 - - + -
132B THR* 3.0 20.8 + - - +
134B ARG* 1.3 76.8 - - - +
136B ARG* 1.3 76.3 + - + +
138B ARG* 3.1 24.8 + - - +
139B ALA* 2.9 37.7 + - + -
183B ASP* 3.4 28.9 + - + -
184B MET* 3.5 25.1 - - + -
186B GLU* 3.0 43.7 + - + +
187B ARG* 4.1 10.5 - - + -
192B GLU* 3.6 24.2 + - + +
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Residues in contact with ARG 136 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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124B TRP* 4.1 7.7 - - + +
125B ARG* 4.2 17.0 - - - +
128B THR* 3.6 45.6 + - + +
131B MET 3.7 13.0 + - - +
132B THR 2.9 19.8 + - - +
133B ASP* 3.2 29.3 + - - +
135B TRP* 1.3 93.2 - - + +
137B ALA* 1.3 55.9 + - - +
139B ALA* 3.9 2.2 - - - +
140B ALA* 2.8 33.9 + - - +
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Residues in contact with ALA 137 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
106A HIS* 4.1 12.3 - - + +
137A ALA* 4.1 22.3 - - + +
140A ALA* 5.6 0.2 - - + -
141A CYS* 3.8 15.0 - - - -
133B ASP 2.9 12.2 + - - +
134B ARG 3.5 10.5 - - - +
135B TRP 3.1 0.4 - - - -
136B ARG* 1.3 77.1 - - - +
138B ARG* 1.3 62.4 + - - +
140B ALA* 3.8 3.6 - - - +
141B CYS* 3.1 29.3 + - - -
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Residues in contact with ARG 138 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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141A CYS* 3.5 21.2 - - + -
144A GLU* 6.0 1.0 + - - -
134B ARG 3.7 4.6 + - - +
135B TRP* 3.1 24.1 + - - +
137B ALA* 1.3 75.8 - - - +
139B ALA* 1.3 67.0 + - - +
141B CYS* 3.1 6.3 + - + +
142B ASN* 2.9 34.0 + - - +
183B ASP* 2.8 29.1 + - - -
186B GLU* 2.8 30.1 + - - -
198B MET* 3.9 23.5 - - - +
199B HIS* 5.8 11.0 + - - -
207B ARG* 3.8 11.8 - - - +
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Residues in contact with ALA 139 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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124B TRP* 3.9 13.5 - - + -
127B ILE* 5.3 0.2 - - + -
135B TRP* 2.9 51.5 + - + +
136B ARG 3.9 3.1 - - - +
138B ARG* 1.3 77.4 - - - +
140B ALA* 1.3 61.4 + - - +
142B ASN* 3.2 2.9 + - - +
143B TRP* 3.0 30.0 + - + +
183B ASP* 3.5 18.0 + - + +
184B MET* 5.7 0.4 - - + -
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Residues in contact with ALA 140 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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137A ALA* 5.7 0.2 - - + -
105B ALA* 3.7 29.2 - - - +
106B HIS* 3.7 24.9 + - + +
124B TRP* 3.6 11.3 - - + -
136B ARG 2.8 21.6 + - - +
137B ALA* 3.8 4.3 - - - +
139B ALA* 1.3 69.8 - - - +
141B CYS* 1.3 60.4 + - - +
143B TRP* 3.2 4.2 + - - +
144B GLU* 2.9 28.9 + - - +
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Residues in contact with CYS 141 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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134A ARG 4.9 0.7 - - - -
137A ALA* 3.9 7.9 - - - -
138A ARG* 3.5 47.6 - - + -
141A CYS* 5.0 3.4 - - + -
199A HIS* 5.1 2.1 + - - -
106B HIS* 4.3 6.7 - - - -
137B ALA 3.1 23.0 + - - +
138B ARG* 3.1 8.5 + - + +
140B ALA* 1.3 76.9 - - - +
142B ASN* 1.3 59.7 + - - +
144B GLU* 3.4 13.6 + - - +
145B TYR* 3.0 27.0 + - - +
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Residues in contact with ASN 142 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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138B ARG* 2.9 28.8 + - - +
139B ALA 3.7 2.0 - - - +
141B CYS* 1.3 77.3 - - - +
143B TRP* 1.3 65.9 - - - +
145B TYR* 3.4 14.1 - - - +
146B TYR* 3.1 20.1 + - - +
179B GLU* 3.6 33.6 + - + +
180B SER* 3.6 13.7 + - - +
183B ASP* 2.8 39.2 + - - +
207B ARG* 4.9 0.2 - - - +
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Residues in contact with TRP 143 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72B LEU* 3.5 30.5 - - + -
75B PHE* 4.1 11.2 - + - -
76B TYR* 3.5 34.3 - + - -
105B ALA* 4.1 13.9 - - + -
120B PHE* 3.5 27.6 - + - -
123B LEU* 5.9 0.2 - - + -
124B TRP* 3.6 29.3 - + - -
127B ILE* 4.2 13.9 - - + +
139B ALA* 3.0 26.4 + - + +
140B ALA 3.2 7.2 + - - +
142B ASN* 1.3 74.2 - - - +
144B GLU* 1.3 59.9 + - - +
146B TYR* 3.2 15.0 + + - +
147B PHE* 2.9 64.0 + + + -
180B SER* 3.9 16.8 + - - -
183B ASP* 6.0 0.2 - - - -
184B MET* 5.8 3.2 - - - +
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Residues in contact with GLU 144 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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134A ARG* 3.0 37.4 + - - +
138A ARG* 5.9 2.1 + - - +
195A GLN* 3.3 24.1 - - + +
199A HIS* 4.6 9.5 + - - +
102B SER* 3.5 16.3 + - - +
105B ALA* 5.3 0.6 - - + +
106B HIS* 2.8 25.3 + - + +
140B ALA 2.9 15.9 + - - +
141B CYS* 3.5 12.8 - - - +
143B TRP* 1.3 76.5 - - - +
145B TYR* 1.3 50.6 + - - +
147B PHE 3.4 0.7 + - - -
148B ALA* 2.8 38.8 + - - +
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Residues in contact with TYR 145 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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199A HIS* 3.5 32.0 + + + -
204A ARG* 3.5 38.3 + - - -
141B CYS 3.0 14.9 + - - +
142B ASN* 3.4 24.9 - - - +
144B GLU* 1.3 75.0 - - - +
146B TYR* 1.3 62.6 + - - +
148B ALA* 3.3 1.6 + - - +
149B CYS* 3.2 37.8 + - - -
170B THR 4.4 2.3 + - - -
173B ARG* 3.5 19.6 - - - +
174B GLY* 3.5 34.8 + - - -
179B GLU* 4.1 23.3 - - + -
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Residues in contact with TYR 146 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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75B PHE* 4.9 0.9 - + - -
76B TYR* 3.5 27.0 + + - -
79B PHE* 3.4 11.9 - + - -
80B ASP* 2.8 29.6 + - - -
142B ASN 3.1 11.0 + - - +
143B TRP* 3.4 22.9 - + + +
145B TYR* 1.3 81.1 - - - +
147B PHE* 1.3 82.7 + + - +
149B CYS* 3.4 8.3 + - - +
150B HIS* 2.8 47.1 + + - -
174B GLY 3.6 24.1 - - - +
175B THR 3.5 18.2 - - - -
177B ALA* 3.6 24.9 - - + -
180B SER* 5.3 2.2 - - - +
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Residues in contact with PHE 147 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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75B PHE* 4.5 5.6 - + - -
79B PHE* 4.0 22.9 - + - -
98B CYS* 3.3 28.2 - - + +
101B LEU* 3.7 34.3 - - + -
102B SER* 3.6 30.5 - - - +
120B PHE* 3.8 27.4 - + - -
143B TRP* 2.9 57.3 + + + +
146B TYR* 1.3 94.2 - + - +
148B ALA* 1.3 63.8 + - - +
150B HIS* 3.1 20.4 + - - +
151B PRO* 3.8 0.5 - - - +
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Residues in contact with ALA 148 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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195A GLN* 3.4 47.0 - - + +
196A HIS* 3.5 16.3 - - - +
199A HIS* 3.6 20.1 - - + +
144B GLU 2.8 23.5 + - - +
145B TYR 3.9 0.7 - - - +
146B TYR 3.3 0.2 - - - -
147B PHE* 1.3 73.6 - - - +
149B CYS* 1.3 58.1 + - - +
150B HIS 3.2 0.4 - - - -
151B PRO* 3.4 13.2 - - - +
152B ALA* 5.0 1.6 + - - +
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Residues in contact with CYS 149 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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199A HIS* 3.7 22.9 - - - -
204A ARG* 5.1 1.1 - - - -
145B TYR* 3.2 32.4 + - - +
146B TYR 3.8 6.3 - - - +
147B PHE 3.2 0.8 + - - -
148B ALA* 1.3 76.4 - - - +
150B HIS* 1.3 64.6 + - - +
151B PRO 3.5 0.4 - - - -
152B ALA* 3.4 6.3 + - - +
153B GLU* 3.2 17.2 + - - +
170B THR 5.2 0.4 - - - -
171B LEU* 3.5 21.1 - - + +
174B GLY* 3.7 22.0 - - - -
175B THR* 4.0 20.0 - - + +
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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
------------------------------------------------------------
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