Contacts of the helix formed by residues 132 - 149 (chain A) 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 A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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130A GLY 4.2 0.4 + - - +
131A MET* 1.3 76.2 - - - +
133A ASP* 1.3 65.9 + - - +
134A ARG* 3.5 11.0 + - - +
135A TRP* 3.0 16.3 + - - +
136A ARG* 3.0 21.0 + - - +
192A GLU* 2.8 40.6 + - - +
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Residues in contact with ASP 133 (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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131A MET 3.8 3.0 + - - +
132A THR* 1.3 73.3 - - - +
134A ARG* 1.3 55.6 + - - +
136A ARG* 3.3 43.7 + - - +
137A ALA* 2.9 27.5 + - - +
106B HIS* 5.4 1.6 - - - +
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Residues in contact with ARG 134 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
132A THR* 3.1 10.7 + - - +
133A ASP* 1.3 75.8 - - - +
135A TRP* 1.3 66.8 + - - +
137A ALA* 3.3 14.4 + - - +
138A ARG* 3.6 6.1 + - - +
192A GLU* 5.8 0.2 - - - +
195A GLN* 3.0 24.7 + - - +
99B GLU* 2.9 36.5 + - - -
102B SER* 3.7 9.4 - - - -
103B ALA* 4.4 16.6 - - - +
106B HIS* 3.5 46.3 - - + +
108B THR* 4.9 10.2 + - + -
141B CYS* 4.9 0.5 - - - -
144B GLU* 3.0 33.4 + - - +
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Residues in contact with TRP 135 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
127A ILE* 3.8 19.5 - - + -
128A THR* 4.5 7.4 - - + -
131A MET* 3.4 38.8 - - + -
132A THR* 3.0 20.2 + - - +
134A ARG* 1.3 73.8 - - - +
136A ARG* 1.3 72.1 + - - +
138A ARG* 3.1 25.6 + - - +
139A ALA* 2.9 38.1 + - + -
183A ASP* 3.4 26.6 + - + -
184A MET* 3.6 24.9 - - + -
186A GLU* 3.0 41.7 + - - +
187A ARG* 4.1 8.7 - - + -
192A GLU* 3.7 15.7 + - + +
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Residues in contact with ARG 136 (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 ALA 5.3 1.1 - - - +
124A TRP* 3.6 24.5 - - + +
128A THR* 3.8 25.4 - - + -
131A MET* 5.6 1.6 - - + +
132A THR 3.0 14.1 + - - +
133A ASP* 3.4 44.0 + - - +
135A TRP* 1.3 88.0 - - + +
137A ALA* 1.3 56.5 + - - +
139A ALA* 4.2 1.8 - - - -
140A ALA* 2.8 31.0 + - + +
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Residues in contact with ALA 137 (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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133A ASP 2.9 13.5 + - - +
134A ARG 3.6 9.9 - - - +
135A TRP 3.1 0.6 - - - -
136A ARG* 1.3 78.1 - - - +
138A ARG* 1.3 62.3 + - - +
140A ALA* 3.5 4.1 + - - +
141A CYS* 3.0 29.1 + - - -
106B HIS* 4.1 13.2 - - + +
137B ALA* 4.1 21.4 - - + +
141B CYS* 3.9 13.7 - - - -
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Residues in contact with ARG 138 (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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134A ARG 3.6 4.3 + - - +
135A TRP* 3.1 26.9 + - - +
137A ALA* 1.3 75.6 - - - +
139A ALA* 1.3 67.1 + - - +
141A CYS* 3.2 5.9 + - + +
142A ASN* 2.9 34.3 + - - +
183A ASP* 2.8 29.7 + - - +
186A GLU* 2.8 27.9 + - - -
193A VAL* 5.6 0.2 - - - +
198A MET* 3.9 29.3 - - - +
199A HIS* 5.9 8.6 + - - -
207A ARG* 4.4 6.7 - - - +
141B CYS* 3.5 22.7 - - + -
144B GLU* 5.9 2.0 + - - +
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Residues in contact with ALA 139 (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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124A TRP* 4.0 13.2 - - + -
127A ILE* 5.3 0.4 - - + -
135A TRP* 2.9 51.0 + - + +
136A ARG 3.8 3.6 - - - +
138A ARG* 1.3 77.4 - - - +
140A ALA* 1.3 61.3 + - - +
142A ASN* 3.3 3.3 + - - +
143A TRP* 3.0 30.6 + - + -
183A ASP* 3.5 19.0 - - + +
184A MET* 5.7 0.7 - - + -
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Residues in contact with ALA 140 (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 ALA* 3.6 30.4 - - - +
106A HIS* 3.7 23.4 + - + +
124A TRP* 3.7 11.1 - - + -
136A ARG* 2.8 24.1 + - + +
137A ALA* 3.8 3.8 - - - +
139A ALA* 1.3 72.7 - - - +
141A CYS* 1.3 58.0 + - - +
143A TRP* 3.2 3.9 + - - +
144A GLU* 2.9 29.3 + - - +
137B ALA* 5.6 0.2 - - + -
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Residues in contact with CYS 141 (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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106A HIS* 4.3 7.4 - - - -
137A ALA 3.0 21.7 + - - +
138A ARG* 3.2 8.3 + - + +
140A ALA* 1.3 78.5 - - - +
142A ASN* 1.3 60.2 + - - +
144A GLU* 3.4 11.8 + - - +
145A TYR* 2.9 26.9 + - - +
134B ARG 4.8 1.3 - - - -
137B ALA* 3.8 10.5 - - - -
138B ARG* 3.5 46.4 - - + -
141B CYS* 5.0 2.7 - - + -
199B HIS* 5.2 2.3 + - - -
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Residues in contact with ASN 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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138A ARG* 2.9 30.7 + - - +
139A ALA 3.8 1.1 - - - +
140A ALA 3.3 0.2 - - - -
141A CYS* 1.3 75.9 - - - +
143A TRP* 1.3 65.4 + - - +
145A TYR* 3.4 14.1 - - - +
146A TYR* 3.1 19.8 + - - +
179A GLU* 3.6 32.9 + - + +
180A SER* 3.7 15.3 + - - +
183A ASP* 2.9 38.3 + - - +
207A ARG* 4.3 2.0 - - - +
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Residues in contact with TRP 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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72A LEU* 3.5 31.4 - - + -
75A PHE* 4.1 8.3 - + - -
76A TYR* 3.6 33.4 - + - -
105A ALA* 4.2 14.8 - - + -
120A PHE* 3.5 33.4 - + - -
123A LEU* 5.6 0.2 - - + -
124A TRP* 3.5 27.5 - + - -
127A ILE* 4.2 14.9 - - + +
139A ALA* 3.0 25.8 + - + +
140A ALA 3.2 7.4 + - - +
142A ASN* 1.3 75.0 - - - +
144A GLU* 1.3 59.4 + - - +
146A TYR* 3.2 18.8 + + - +
147A PHE* 2.9 57.1 + + + -
180A SER* 3.9 17.4 + - - -
183A ASP* 6.0 0.2 - - - -
184A MET* 5.6 3.8 - - - +
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Residues in contact with GLU 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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102A SER* 3.4 16.4 + - - +
105A ALA* 5.2 0.6 - - - +
106A HIS* 2.8 26.1 + - + +
140A ALA 2.9 15.0 + - - +
141A CYS* 3.6 10.8 - - - +
143A TRP* 1.3 78.2 - - - +
145A TYR* 1.4 51.5 + - - +
147A PHE* 3.9 0.2 - - - -
148A ALA* 2.8 38.8 + - - +
134B ARG* 3.0 37.8 + - - +
138B ARG* 6.0 0.4 + - - -
195B GLN* 3.3 24.3 - - + +
199B HIS* 4.5 10.2 + - - +
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Residues in contact with TYR 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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141A CYS 2.9 15.1 + - - +
142A ASN* 3.4 23.8 - - - +
144A GLU* 1.4 76.7 - - - +
146A TYR* 1.3 63.7 + - - +
148A ALA* 3.3 1.2 + - - +
149A CYS* 3.2 37.8 + - - -
170A THR 4.4 1.4 + - - -
173A ARG* 3.5 18.9 - - - +
174A GLY* 3.5 34.8 + - - -
179A GLU* 4.2 23.1 - - + -
199B HIS* 3.5 31.8 + + + -
204B ARG* 3.6 40.0 + - - -
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Residues in contact with TYR 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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75A PHE* 4.8 1.6 - + - -
76A TYR* 3.6 32.2 + + - +
79A PHE* 3.3 25.8 - + - +
80A ASP* 4.8 3.1 + - - +
142A ASN 3.1 10.4 + - - +
143A TRP* 3.4 24.9 - + + +
145A TYR* 1.3 81.5 - - - +
147A PHE* 1.3 88.8 + + - +
149A CYS* 3.4 6.9 + - - +
150A HIS* 2.8 45.6 + + - -
174A GLY 3.6 25.2 - - - +
175A THR 3.5 15.5 - - - -
177A ALA* 3.6 25.8 - - + -
180A SER* 5.3 2.2 - - - +
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Residues in contact with PHE 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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75A PHE* 4.4 5.8 - + - -
79A PHE* 4.1 11.9 - + - -
98A CYS* 3.3 32.4 - - + +
101A LEU* 3.6 42.8 - - + -
102A SER* 3.6 30.7 - - - +
120A PHE* 3.7 31.0 - + - -
143A TRP* 2.9 55.0 + + + +
146A TYR* 1.3 95.4 - + - +
148A ALA* 1.3 62.8 + - - +
150A HIS* 3.1 15.8 + - - -
151A PRO* 3.8 0.3 - - - +
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Residues in contact with ALA 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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144A GLU 2.8 18.9 + - - +
145A TYR 3.9 0.4 - - - +
146A TYR 3.2 0.2 - - - -
147A PHE* 1.3 78.2 - - - +
149A CYS* 1.3 59.4 + - - +
150A HIS 3.2 0.4 - - - -
151A PRO* 3.4 12.8 - - - +
152A ALA* 4.9 1.2 + - - +
195B GLN* 3.4 45.7 - - + +
196B HIS* 3.5 17.4 - - - +
199B HIS* 3.5 20.6 - - + +
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Residues in contact with CYS 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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145A TYR* 3.2 33.7 + - - +
146A TYR 3.9 4.9 - - - +
147A PHE 3.2 1.2 + - - -
148A ALA* 1.3 76.9 - - - +
150A HIS* 1.3 65.5 + - - +
151A PRO 3.4 0.7 - - - -
152A ALA* 3.3 7.0 + - - +
153A GLU* 3.2 17.0 + - - +
170A THR 5.3 2.2 - - - -
171A LEU* 3.6 18.6 - - + +
174A GLY* 3.7 22.0 - - - -
175A THR* 3.8 21.5 - - + +
199B HIS* 3.7 22.9 - - - -
204B ARG* 5.1 0.9 - - - -
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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
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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