Contacts of the helix formed by residues 140 - 158 (chain A) in PDB entry 5A5J
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 SER 140 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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133A ASN* 3.4 21.3 - - - +
138A LYS 3.5 5.0 + - - -
139A ARG* 1.3 74.8 - - - +
141A ILE* 1.3 60.0 + - - +
142A GLU* 3.4 9.5 + - - +
143A ASP* 3.0 49.8 + - - +
144A ARG* 3.4 16.8 + - - +
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Residues in contact with ILE 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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131A LEU* 3.9 33.2 - - + +
133A ASN* 3.4 22.0 + - - +
136A MET* 3.7 23.8 - - + -
140A SER* 1.3 72.2 - - - +
142A GLU* 1.3 66.8 + - - +
144A ARG* 3.2 17.6 + - + +
145A VAL* 3.3 13.6 + - + +
177A VAL* 5.6 0.2 - - + -
181A ILE* 3.9 24.7 - - + -
440A LEU* 3.2 31.6 - - + -
443A MET* 4.0 16.4 - - + -
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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
----------------------------------------------------------
133A ASN* 5.1 0.4 + - - -
140A SER* 3.3 9.0 + - - +
141A ILE* 1.3 76.0 - - - +
143A ASP* 1.3 72.3 + - - +
144A ARG 3.0 0.7 + - - -
145A VAL* 3.3 1.7 + - - +
146A GLN* 3.2 32.4 + - - +
338A CYS* 3.6 13.7 - - - +
339A MET* 2.9 47.5 + - + +
340A GLN* 4.8 0.3 + - - +
443A MET* 3.6 22.9 - - + +
447A LEU* 4.5 6.5 - - + +
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Residues in contact with ASP 143 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
139A ARG* 3.6 30.9 + - + +
140A SER* 3.0 40.5 + - - +
142A GLU* 1.3 78.0 - - - +
144A ARG* 1.3 61.8 + - - +
146A GLN* 3.1 24.0 + - - +
147A GLU* 3.1 8.5 + - - +
150A ARG* 5.1 1.4 + - - -
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Residues in contact with ARG 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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136A MET* 4.2 12.3 + - - +
139A ARG* 4.0 45.6 + - - +
140A SER 3.4 19.0 + - - +
141A ILE* 3.2 15.7 + - + +
142A GLU 3.0 1.2 + - - -
143A ASP* 1.3 75.3 - - - +
145A VAL* 1.3 63.1 + - - +
146A GLN 3.0 5.1 + - - -
147A GLU* 3.2 4.2 + - - +
148A GLU* 3.2 20.6 + - - +
177A VAL* 5.0 10.1 - - + +
180A SER* 2.6 54.5 + - - +
181A ILE* 4.3 21.4 - - - +
184A HIS* 3.5 24.6 + - - +
261A GLN 3.2 23.8 + - - -
262A ASP* 4.8 2.2 - - - +
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Residues in contact with VAL 145 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
141A ILE 3.3 14.7 + - - +
142A GLU 3.3 0.4 + - - +
144A ARG* 1.3 75.9 - - - +
146A GLN* 1.3 53.2 + - - +
148A GLU* 4.6 0.2 - - - -
149A ALA* 2.8 33.5 + - - +
177A VAL* 3.9 24.7 - - + -
440A LEU* 4.0 9.6 - - + -
443A MET* 3.9 8.5 - - + +
444A GLU* 3.7 39.7 - - + -
447A LEU* 3.9 22.4 - - + -
448A PHE* 3.3 22.9 - - + -
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Residues in contact with GLN 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* 3.2 31.6 + - - +
143A ASP* 3.1 15.8 + - - +
144A ARG 3.0 0.4 - - - -
145A VAL* 1.3 76.5 - - - +
147A GLU* 1.3 62.0 + - - +
148A GLU 3.2 0.2 - - - -
149A ALA* 3.3 8.7 + - + +
150A ARG* 3.1 44.5 + - - +
336A SER* 3.2 20.3 + - - +
337A PRO 2.8 27.0 + - - +
338A CYS* 3.6 18.0 - - - +
447A LEU* 4.5 8.8 - - + +
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Residues in contact with GLU 147 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
139A ARG* 3.0 39.0 + - - +
143A ASP 3.1 4.9 + - - +
144A ARG* 3.2 6.0 + - - +
146A GLN* 1.3 77.0 - - - +
148A GLU* 1.3 57.2 + - - +
150A ARG* 3.4 19.5 + - - +
151A CYS* 3.0 35.7 + - - -
180A SER* 6.1 0.9 - - - -
186A ARG* 3.3 35.7 + - - +
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Residues in contact with GLU 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 ARG 3.2 15.2 + - - +
145A VAL 3.9 3.6 - - - +
147A GLU* 1.3 73.2 - - - +
149A ALA* 1.3 68.7 + - - +
150A ARG 3.0 2.2 - - - -
151A CYS* 2.9 2.8 + - - +
152A LEU* 2.7 27.0 + - - +
173A ALA* 3.8 26.2 - - + +
176A ASN* 3.1 26.1 + - - +
177A VAL* 4.3 7.0 - - + +
180A SER* 6.0 0.2 - - - -
186A ARG* 3.1 28.5 + - - +
189A TYR* 2.2 45.9 + - - +
448A PHE* 4.2 7.4 - - + -
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Residues in contact with ALA 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 VAL 2.8 20.9 + - - +
146A GLN* 3.3 14.1 - - + +
148A GLU* 1.3 76.8 - - - +
150A ARG* 1.3 61.7 + - + +
152A LEU* 3.5 6.3 + - - +
153A VAL* 3.3 25.7 + - - +
447A LEU* 4.8 6.7 - - + -
448A PHE* 3.7 21.3 - - + -
451A SER* 3.8 22.0 - - - +
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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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143A ASP 5.1 1.0 + - - -
146A GLN* 3.1 24.4 + - - +
147A GLU* 3.8 24.5 - - - +
148A GLU 3.0 0.8 - - - -
149A ALA* 1.3 72.9 - - + +
151A CYS* 1.3 60.2 + - - +
152A LEU 2.7 10.8 + - - -
153A VAL* 2.9 15.4 + - - +
154A GLU* 3.1 17.2 + - + +
336A SER* 3.2 35.1 + - - -
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Residues in contact with CYS 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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147A GLU* 3.0 29.7 + - - +
148A GLU* 2.9 9.2 + - - +
150A ARG* 1.3 74.6 - - - +
152A LEU* 1.3 55.8 + - - +
154A GLU* 3.8 10.6 - - - +
155A GLU* 3.4 26.3 + - - +
186A ARG* 3.3 47.3 - - - +
189A TYR* 4.2 4.2 + - - +
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Residues in contact with LEU 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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148A GLU 2.7 14.5 + - - +
149A ALA 3.5 4.7 - - - +
150A ARG 2.7 1.6 + - - -
151A CYS* 1.3 77.1 - - - +
153A VAL* 1.3 64.4 + - + +
155A GLU* 3.5 5.1 + - - +
156A LEU* 3.2 34.4 + - + +
169A ILE* 3.5 30.7 - - + +
170A LEU* 4.4 12.8 - - + -
173A ALA* 4.2 10.3 - - + -
189A TYR* 4.1 12.6 - - - +
448A PHE* 3.8 45.3 - - + -
451A SER* 6.1 0.4 - - - -
452A ILE* 4.8 10.5 - - + -
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Residues in contact with VAL 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 ALA 3.3 12.7 + - - +
150A ARG* 2.9 8.7 + - - +
152A LEU* 1.3 77.8 - - + +
154A GLU* 1.3 67.0 + - - +
156A LEU* 2.9 15.7 + - - +
157A ARG* 3.0 23.8 + - - +
451A SER* 4.0 33.4 - - - +
452A ILE* 4.5 3.8 - - + +
455A ASN* 3.8 23.6 - - + +
456A PHE* 3.5 25.4 - - + -
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Residues in contact with GLU 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* 3.1 18.6 + - + +
151A CYS* 3.8 10.1 - - - +
153A VAL* 1.3 79.3 - - - +
155A GLU* 1.3 64.0 + - + +
157A ARG* 3.1 36.9 + - - +
158A LYS* 3.5 16.7 + - - +
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Residues in contact with GLU 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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151A CYS 3.4 14.7 + - - +
152A LEU 3.5 4.9 + - - +
153A VAL 3.2 0.8 - - - -
154A GLU* 1.3 80.7 - - + +
156A LEU* 1.3 60.5 + - - +
158A LYS* 3.1 51.6 + - - +
159A THR* 4.0 3.6 - - - +
169A ILE* 4.0 24.5 - - + +
189A TYR* 3.5 43.0 - - + +
190A LYS* 4.6 7.1 + - - +
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Residues in contact with LEU 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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152A LEU* 3.2 39.0 + - + +
153A VAL* 2.9 7.2 + - - +
155A GLU* 1.3 76.0 - - - +
157A ARG* 1.3 57.9 + - - +
158A LYS 3.4 0.2 - - - -
159A THR* 3.4 25.1 + - + +
160A LYS 4.7 0.5 + - - -
164A CYS* 5.0 1.1 - - - -
166A PRO* 5.8 2.2 - - + -
169A ILE* 3.5 28.3 - - + -
170A LEU* 5.4 3.4 - - + -
452A ILE* 4.1 18.8 - - + -
456A PHE* 3.9 19.3 - - + -
487A PHE* 3.8 60.9 - - + +
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Residues in contact with ARG 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 VAL* 3.0 23.3 + - - +
154A GLU* 3.1 30.3 + - - +
156A LEU* 1.3 74.3 - - - +
158A LYS* 1.3 63.0 + - + +
159A THR 3.1 3.8 + - - -
160A LYS* 3.2 25.9 + - - +
455A ASN* 2.9 38.0 + - - +
456A PHE* 3.9 13.9 - - + -
489A PRO* 4.2 27.8 - - + +
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Residues in contact with LYS 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 GLU* 3.8 15.3 - - - +
155A GLU* 3.1 49.3 + - - +
157A ARG* 1.3 78.0 - - + +
159A THR* 1.3 56.5 + - + +
160A LYS* 3.1 23.3 - - - +
188A ASP* 5.6 3.2 + - - -
190A LYS* 3.6 23.6 - - - +
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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