Contacts of the helix formed by residues 137 - 159 (chain A) in PDB entry 4UML
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 TYR 137 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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132A LYS 5.3 4.0 - - - +
134A LYS* 2.8 36.6 + - + +
136A ARG* 1.3 126.5 + - + +
138A ARG* 1.3 56.8 + - - +
139A THR 3.4 2.7 - - - -
140A ALA* 3.2 17.7 + - + -
141A ALA* 2.8 27.9 + - + +
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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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133A TYR* 3.5 27.4 + - + +
134A LYS 3.3 4.2 + - - -
135A SER* 3.3 16.7 + - - +
136A ARG 3.5 1.8 + - - -
137A TYR* 1.3 76.0 - - - +
139A THR* 1.3 59.3 + - - +
141A ALA* 3.3 5.8 + - - +
142A GLU* 2.8 54.6 + - - +
180A ASP* 4.9 10.5 + - - -
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Residues in contact with THR 139 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
137A TYR 3.4 0.6 - - - -
138A ARG* 1.3 77.7 - - - +
140A ALA* 1.3 58.4 + - - +
142A GLU* 3.3 15.9 + - - +
143A SER* 3.0 30.1 + - - -
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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
----------------------------------------------------------
131A PRO* 5.5 0.2 - - - -
137A TYR* 3.2 21.7 + - + +
139A THR* 1.3 79.6 - - - +
141A ALA* 1.3 56.8 + - - +
143A SER* 3.4 7.1 + - - -
144A SER* 2.9 32.6 + - - +
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Residues in contact with ALA 141 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
131A PRO* 3.5 26.6 - - + +
132A LYS 5.4 0.2 - - - +
133A TYR* 3.6 36.3 - - + -
134A LYS 5.1 0.4 - - - +
137A TYR* 2.8 21.1 + - + +
138A ARG* 3.3 4.5 + - - +
140A ALA* 1.3 72.5 - - - +
142A GLU* 1.3 57.1 + - - +
144A SER 3.3 0.3 + - - -
145A LEU* 2.9 28.9 + - - +
176A TYR* 3.6 8.4 - - + -
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Residues in contact with GLU 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* 2.8 51.8 + - + +
139A THR* 3.6 15.6 + - - +
141A ALA* 1.3 76.3 - - - +
143A SER* 1.3 56.9 + - - +
145A LEU* 3.4 1.7 + - - +
146A TYR* 2.9 32.0 + - - +
176A TYR* 3.2 21.8 - - - +
180A ASP* 5.9 2.9 - - - +
184A ILE* 4.2 15.2 - - + +
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Residues in contact with SER 143 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
139A THR* 3.0 19.3 + - - -
140A ALA* 3.7 7.9 - - - -
142A GLU* 1.3 77.5 - - - +
144A SER* 1.3 56.4 + - - +
146A TYR* 3.5 8.7 + - - +
147A SER* 3.0 35.7 + - - -
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Residues in contact with SER 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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109A THR* 3.7 24.5 + - - +
110A GLY* 3.7 4.8 - - - -
131A PRO* 3.8 20.5 - - - +
140A ALA* 2.9 19.8 + - - +
141A ALA 3.7 3.6 - - - -
143A SER* 1.3 73.5 + - - +
145A LEU* 1.3 64.9 + - - +
147A SER* 3.2 8.2 + - - -
148A CYS* 3.0 27.1 + - - -
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Residues in contact with LEU 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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130A GLY* 4.9 0.2 - - - -
131A PRO* 4.1 16.3 - - + +
141A ALA 2.9 19.7 + - - +
142A GLU 4.0 2.5 - - - +
144A SER* 1.3 73.9 - - - +
146A TYR* 1.3 64.8 + - - +
148A CYS* 3.2 13.1 + - - +
149A TYR* 3.2 38.8 + - + -
169A ILE* 4.0 21.1 - - + -
170A ASN* 4.4 14.4 - - + +
176A TYR* 3.7 24.5 - - + -
181A ALA* 3.8 37.7 - - + +
184A ILE* 4.1 11.0 - - + -
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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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142A GLU 2.9 19.7 + - - +
143A SER* 3.6 9.6 - - - +
145A LEU* 1.3 77.7 - - - +
147A SER* 1.3 64.2 + - - +
149A TYR* 3.3 3.5 + - - +
150A ARG* 2.9 49.4 + - + +
184A ILE* 3.9 14.5 - - + +
187A ARG* 5.6 6.3 - - - +
188A THR* 3.4 36.1 - - + -
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Residues in contact with SER 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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110A GLY* 3.3 18.2 - - - -
143A SER* 3.0 21.4 + - - -
144A SER* 3.2 6.3 + - - -
146A TYR* 1.3 79.6 - - - +
148A CYS* 1.3 61.0 + - - +
150A ARG* 4.1 9.1 - - - +
151A ASN* 2.8 43.7 + - - +
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Residues in contact with CYS 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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110A GLY* 3.4 11.8 + - - -
128A THR* 3.5 19.2 + - - +
129A VAL 3.1 33.7 - - - -
130A GLY* 3.8 9.6 - - - -
144A SER 3.0 19.4 + - - -
145A LEU* 3.2 10.5 + - - +
147A SER* 1.3 75.6 - - - +
149A TYR* 1.3 61.7 + - - +
151A ASN* 3.9 1.4 - - - +
152A VAL* 3.0 30.8 + - - +
169A ILE* 3.9 21.1 - - + -
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Residues in contact with TYR 149 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
145A LEU* 3.2 39.8 + - + -
146A TYR 3.8 2.9 - - - +
148A CYS* 1.3 79.4 - - + +
150A ARG* 1.3 63.5 + - - +
152A VAL* 3.4 1.7 + - - +
153A LEU* 3.1 29.8 + - + +
166A PHE* 3.5 40.6 - + + -
167A CYS 4.0 3.1 + - - -
169A ILE* 3.3 43.6 + - + +
170A ASN* 4.3 5.4 + - - -
181A ALA 5.1 0.2 - - - -
184A ILE* 4.8 2.2 - - + -
185A ALA* 3.3 47.1 - - + +
188A THR* 3.8 22.4 - - + +
189A VAL* 4.6 3.1 - - + -
205A PHE* 4.9 4.7 - + - -
215A TYR* 4.2 6.4 + - - -
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Residues in contact with ARG 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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146A TYR* 2.9 45.5 + - + +
147A SER* 3.7 7.4 - - - +
149A TYR* 1.3 76.5 - - - +
151A ASN* 1.3 81.6 + - - +
153A LEU* 3.4 6.4 + - - +
154A GLN* 2.5 61.3 + - - +
188A THR* 4.0 7.0 - - + +
192A PHE* 5.7 0.8 - - - -
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Residues in contact with ASN 151 (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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110A GLY 2.9 23.3 + - - +
111A GLU* 3.9 8.1 - - - +
112A ALA* 3.9 21.2 - - + +
147A SER* 2.8 27.9 + - - +
148A CYS 4.1 0.7 - - - +
150A ARG* 1.3 103.8 + - - +
152A VAL* 1.3 65.1 + - - +
154A GLN* 2.9 11.4 - - + +
155A LEU* 3.0 27.9 + - - +
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Residues in contact with VAL 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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72A VAL* 3.7 28.0 - - + -
112A ALA* 4.2 5.6 - - + -
126A ILE* 3.8 29.9 - - + +
128A THR* 4.5 4.5 - - - -
148A CYS 3.0 24.5 + - - +
149A TYR 3.7 4.5 - - - +
151A ASN* 1.3 74.8 - - - +
153A LEU* 1.3 60.0 + - - +
155A LEU* 3.2 5.0 + - - +
156A ALA* 2.9 26.3 + - - +
164A VAL* 4.0 11.0 - - + -
166A PHE* 3.5 32.1 - - + -
169A ILE* 4.5 3.6 - - + -
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Residues in contact with LEU 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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149A TYR 3.1 22.0 + - - +
150A ARG* 3.7 5.6 - - - +
152A VAL* 1.3 83.1 - - + +
154A GLN* 1.3 56.2 + - - +
156A ALA* 3.3 4.5 + - - +
157A LYS* 3.0 29.3 + - - +
164A VAL* 5.3 6.3 - - + -
166A PHE* 3.9 23.6 - - + -
188A THR* 4.3 7.6 - - + +
189A VAL* 4.2 23.8 - - + -
192A PHE* 3.7 58.9 - - + -
200A ILE* 5.0 4.7 - - + -
203A VAL* 4.9 12.6 - - + -
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Residues in contact with GLN 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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150A ARG* 2.5 59.5 + - - +
151A ASN* 2.9 13.5 - - - +
152A VAL 3.3 0.2 - - - -
153A LEU* 1.3 68.7 - - - +
155A LEU* 1.3 62.1 + - + +
157A LYS* 3.4 5.9 + - - +
158A GLU* 2.9 56.8 + - + +
192A PHE* 4.7 2.6 - - - -
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Residues in contact with LEU 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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112A ALA* 3.7 35.4 - - + +
113A LYS* 3.8 7.2 - - - +
114A LEU* 4.0 20.9 - - + +
126A ILE* 3.8 28.0 - - + -
151A ASN 3.0 10.5 + - - +
152A VAL 3.5 7.9 - - - +
154A GLN* 1.3 75.4 - - + +
156A ALA* 1.3 67.0 + - - +
158A GLU* 3.3 20.9 + - - +
159A GLN* 2.9 35.4 + - + +
161A MET* 4.5 3.4 - - + -
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Residues in contact with ALA 156 (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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126A ILE* 4.6 0.9 - - + +
152A VAL 2.9 12.4 + - - +
153A LEU* 3.6 11.0 - - + +
154A GLN 3.3 0.4 - - - -
155A LEU* 1.3 77.7 - - - +
157A LYS* 1.3 59.7 + - - +
159A GLN 3.4 0.5 + - - -
160A SER 3.2 2.9 + - - -
161A MET* 2.9 48.8 + - + +
164A VAL* 3.5 32.3 - - + -
200A ILE* 4.7 11.2 - - + -
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Residues in contact with LYS 157 (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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153A LEU 3.0 17.5 + - - +
154A GLN* 3.8 5.8 - - - +
156A ALA* 1.3 76.8 - - - +
158A GLU* 1.3 63.0 + - - +
160A SER* 2.9 17.3 + - - +
192A PHE* 3.9 12.1 - - + -
196A HIS* 3.4 49.8 - - + +
199A THR* 4.5 18.2 + - + +
200A ILE* 5.3 2.4 - - - +
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Residues in contact with GLU 158 (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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154A GLN* 2.9 47.5 + - + +
155A LEU* 3.6 22.2 - - + +
157A LYS* 1.3 76.9 - - - +
159A GLN* 1.3 67.7 + - + +
160A SER* 3.3 4.1 + - - -
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Residues in contact with GLN 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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114A LEU* 4.1 23.6 - - + +
123A ARG* 5.7 2.6 + - - -
124A PHE* 4.0 18.6 - - + -
155A LEU* 2.9 26.0 + - + +
157A LYS 3.2 0.2 - - - -
158A GLU* 1.3 83.5 + - + +
160A SER* 1.3 70.0 + - - +
161A MET* 3.2 29.4 + - + +
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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