Contacts of the helix formed by residues 138 - 154 (chain A) in PDB entry 5INQ
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 ASN 138 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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136A GLY 3.4 2.0 + - - -
137A CYS* 1.3 83.3 - - - +
139A LEU* 1.3 63.7 + - - +
140A PRO* 3.3 6.9 - - - +
141A GLU* 3.2 10.9 + - + +
142A ARG* 2.9 29.7 + - - +
352A CYS* 3.5 35.2 - - + +
354A ARG* 3.2 31.2 + - - -
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Residues in contact with LEU 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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133A GLY* 3.9 13.0 - - - +
135A ASP 3.6 7.9 - - - +
136A GLY* 3.4 17.8 + - - +
137A CYS 3.1 2.2 - - - -
138A ASN* 1.3 76.0 - - - +
140A PRO* 1.3 68.0 - - + +
142A ARG* 3.2 32.1 + - + +
143A ALA* 2.8 28.1 + - - +
164A ILE* 3.7 29.6 - - + -
166A PRO* 5.4 1.1 - - + -
167A TYR* 3.7 33.7 - - + -
170A TYR* 4.4 13.5 - - + +
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Residues in contact with PRO 140 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
136A GLY 4.8 2.2 - - - +
138A ASN* 3.5 5.2 - - - +
139A LEU* 1.3 95.4 - - + +
141A GLU* 1.3 62.1 + - - +
143A ALA* 3.3 2.6 + - - +
144A ARG* 3.0 41.4 + - - +
170A TYR* 3.7 37.6 - - + +
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Residues in contact with GLU 141 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
138A ASN* 3.2 13.0 + - + +
140A PRO* 1.3 80.5 - - - +
142A ARG* 1.3 57.5 + - - +
144A ARG* 3.2 32.0 + - + +
145A GLY* 3.0 22.0 + - - -
350A LEU* 3.3 12.3 - - + +
351A ASP* 3.2 20.6 + - + +
352A CYS* 2.8 51.0 + - - +
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Residues in contact with ARG 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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131A ILE 3.2 17.2 + - - -
132A ASP* 2.8 34.2 + - - +
135A ASP* 2.7 36.4 + - - -
137A CYS 3.0 20.8 + - - -
138A ASN* 2.9 24.8 + - + +
139A LEU* 3.6 15.8 - - + +
141A GLU* 1.3 76.0 - - - +
143A ALA* 1.3 63.8 + - - +
145A GLY* 3.1 2.8 + - - -
146A VAL* 3.0 24.8 + - - +
167A TYR* 4.4 2.5 - - + -
314A ASN* 4.2 3.5 - - - +
350A LEU* 3.7 14.1 - - + -
352A CYS* 5.0 4.0 - - - -
354A ARG* 3.9 13.0 - - - +
355A PHE 3.5 20.3 + - - +
356A PRO* 2.9 23.6 + - - +
357A SER* 4.5 0.8 - - - +
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Residues in contact with ALA 143 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
139A LEU 2.8 19.8 + - - +
140A PRO 3.6 5.4 - - - +
142A ARG* 1.3 68.9 - - - +
144A ARG* 1.3 61.1 + - - +
146A VAL* 3.1 3.3 + - - +
147A CYS* 2.8 34.9 + - - -
167A TYR* 3.5 33.0 + - + -
170A TYR* 3.8 30.5 - - + -
174A ARG* 5.9 0.7 - - - -
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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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140A PRO* 3.0 30.9 + - - +
141A GLU* 3.2 39.7 + - + +
143A ALA* 1.3 74.6 - - + +
145A GLY* 1.3 57.4 + - - +
147A CYS* 3.7 7.2 - - - +
148A SER* 2.8 30.0 + - - -
174A ARG* 3.0 51.7 - - + +
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Residues in contact with GLY 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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129A TRP* 5.0 0.5 - - - -
141A GLU 3.0 13.5 + - - -
142A ARG 3.1 4.9 + - - -
144A ARG* 1.3 74.1 - - - +
146A VAL* 1.3 62.2 + - - +
148A SER* 2.7 23.7 + - - -
149A CYS* 3.2 9.4 + - - +
350A LEU* 4.1 24.2 - - - -
356A PRO* 4.5 8.4 - - - +
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Residues in contact with VAL 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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129A TRP* 3.9 26.2 - - + -
131A ILE* 3.7 22.2 - - + -
142A ARG 3.0 14.6 + - - +
143A ALA 3.1 6.7 + - - +
145A GLY* 1.3 74.4 - - - +
147A CYS* 1.3 68.3 + - - +
149A CYS* 3.1 6.9 + - - +
150A LEU* 3.0 35.2 + - + +
160A LEU* 4.9 7.2 - - + -
167A TYR* 3.2 27.8 - - + +
171A LEU* 5.1 3.1 - - + -
356A PRO* 3.9 18.1 - - + +
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Residues in contact with CYS 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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143A ALA* 2.8 21.7 + - - +
144A ARG* 3.8 4.5 - - - +
145A GLY 3.3 0.2 - - - -
146A VAL* 1.3 78.0 - - - +
148A SER* 1.3 56.3 + - - +
150A LEU* 3.3 10.1 + - - +
151A ALA* 3.0 28.2 + - - +
170A TYR 4.5 2.0 - - - -
171A LEU* 3.8 32.3 - - - -
174A ARG* 3.5 50.1 - - + +
175A ALA* 4.0 4.3 - - + -
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Residues in contact with SER 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 2.8 15.7 + - - -
145A GLY* 2.7 23.5 + - - -
147A CYS* 1.3 75.3 - - - +
149A CYS* 1.3 61.8 + - - +
151A ALA* 3.3 7.4 + - - +
152A LEU* 3.1 22.7 + - - +
350A LEU* 5.8 0.7 - - - +
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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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127A ILE* 4.0 9.4 - - - +
129A TRP* 4.0 14.8 - - + -
145A GLY 3.2 7.6 + - - +
146A VAL 3.1 9.8 + - - +
148A SER* 1.3 79.3 + - - +
150A LEU* 1.3 64.7 + - - +
152A LEU* 3.2 15.9 + - - +
153A TYR* 3.2 36.5 + - - +
345A VAL* 3.6 37.2 - - - -
346A GLY* 4.9 2.9 - - - +
348A GLU* 6.2 0.4 - - - +
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Residues in contact with LEU 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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127A ILE* 4.0 22.2 - - + -
129A TRP* 5.4 1.3 - - + -
146A VAL* 3.0 29.3 + - + +
147A CYS* 3.3 10.3 + - - +
149A CYS* 1.3 76.4 - - + +
151A ALA* 1.3 55.5 + - - +
154A SER* 2.7 35.0 + - - -
155A PRO* 3.5 5.8 - - + +
158A VAL* 3.8 39.3 - - + -
160A LEU* 6.0 0.4 - - + -
171A LEU* 4.8 4.3 - - + -
175A ALA* 4.3 22.4 - - + -
178A TYR* 4.2 17.3 + - + +
193A LEU* 4.3 12.6 - - + -
195A LYS* 5.5 0.3 + - - -
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Residues in contact with ALA 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 CYS 3.0 16.0 + - - +
148A SER* 3.6 8.5 - - - +
149A CYS 3.2 0.2 - - - -
150A LEU* 1.3 78.3 - - - +
152A LEU* 1.3 62.2 + - - +
153A TYR 3.6 0.2 + - - -
154A SER* 4.0 8.8 + - - +
174A ARG 6.0 1.1 - - - +
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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 SER 3.1 13.9 + - - +
149A CYS* 3.2 11.0 + - - +
151A ALA* 1.3 79.9 - - - +
153A TYR* 1.3 95.1 + - + +
154A SER* 5.3 0.3 - - - -
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Residues in contact with TYR 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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125A SER* 5.0 2.1 + - - -
127A ILE* 4.5 3.4 - - + -
149A CYS* 3.2 36.0 + - - +
152A LEU* 1.3 108.5 - - + +
154A SER* 1.3 73.3 + - - +
155A PRO* 3.2 10.4 - - + +
344A LEU 5.5 0.7 + - - -
345A VAL* 3.8 25.2 - - + +
363A LEU* 3.7 34.5 - - + +
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Residues in contact with SER 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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125A SER* 4.3 2.3 + - - -
150A LEU 2.7 16.5 + - - -
151A ALA* 4.0 8.3 + - - -
152A LEU 3.6 0.8 - - - -
153A TYR* 1.3 78.7 - - - +
155A PRO* 1.3 65.2 - - - +
156A ASP 3.7 0.2 + - - -
178A TYR* 3.8 3.6 - - - -
195A LYS* 3.4 14.1 + - - +
198A ARG* 2.7 45.7 + - - -
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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