Contacts of the helix formed by residues 141 - 157 (chain a) in PDB entry 5M32
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 141 (chain a).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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132H LEU* 5.3 8.1 - - + -
24N SER* 3.2 45.7 + - - -
25N TYR* 4.8 13.2 - + + -
9a THR* 4.3 9.6 + - - +
139a THR 3.7 0.2 + - - -
140a GLY* 1.3 70.5 - - - -
142a GLY* 1.3 59.9 + - - +
144a TYR* 2.9 30.7 + + + +
145a LEU* 2.8 36.4 + - + +
176a LEU* 4.2 2.5 - - - -
180a ASP* 3.3 30.1 - - - +
182a ARG* 6.4 0.2 - - + -
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Residues in contact with GLY 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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10a SER* 3.9 11.3 + - - -
138a ALA* 3.5 8.1 - - - -
139a THR 3.5 4.0 + - - -
140a GLY 3.1 1.4 - - - -
141a TYR* 1.3 77.9 - - - +
143a ALA* 1.3 56.3 + - - +
145a LEU 3.0 2.4 + - - -
146a ALA* 2.6 27.7 + - - +
147a GLN 2.9 10.2 + - - -
176a LEU* 3.7 31.8 - - - +
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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
----------------------------------------------------------
34Z SER* 3.6 18.7 + - - +
36Z HIS* 6.0 7.4 - - + +
124a TYR* 6.1 0.7 - - + +
138a ALA* 3.4 27.1 - - - +
139a THR* 4.5 0.2 - - - -
140a GLY 2.9 19.2 + - - +
142a GLY* 1.3 74.6 - - - +
144a TYR* 1.3 61.3 + - + +
147a GLN* 3.3 25.1 - - - +
148a PRO* 5.0 0.2 - - - +
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Residues in contact with TYR 144 (chain a).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
132H LEU* 2.9 57.2 - - + +
133H ALA* 4.0 1.0 + - - -
166H ASP* 5.7 3.6 - - - -
31Z GLU 5.7 0.5 + - - -
32Z GLY* 5.7 1.9 - - - -
33Z PHE* 5.3 9.6 + - + -
34Z SER* 3.7 32.3 - - - -
140a GLY 3.9 15.5 - - - -
141a TYR* 2.9 31.3 + + + +
143a ALA* 1.3 80.4 - - + +
145a LEU* 1.3 59.6 + - + +
148a PRO* 3.3 14.4 - - - +
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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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132H LEU* 3.3 38.8 - - + +
135H MET* 4.6 11.0 - - + -
136H ALA* 3.3 26.3 - - + +
25N TYR* 4.1 17.0 - - + -
141a TYR* 2.8 22.2 + - + +
144a TYR* 1.3 81.7 - - + +
146a ALA* 1.3 64.4 + - - +
147a GLN 3.3 1.1 - - - -
148a PRO* 3.3 9.2 - - - +
149a LEU* 4.4 2.3 + - - +
175a VAL* 4.7 9.5 - - + +
176a LEU* 3.7 24.7 - - + -
179a ARG* 3.7 28.5 - - + -
180a ASP* 4.4 3.6 - - + +
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Residues in contact with ALA 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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12a LEU* 3.7 29.6 - - + -
138a ALA* 4.3 6.1 - - + -
142a GLY* 2.6 22.1 + - - +
145a LEU* 1.3 76.0 - - - +
147a GLN* 1.3 61.7 + - - +
149a LEU* 3.2 7.7 + - - +
150a LEU* 3.2 28.6 + - + +
172a CYS* 3.9 19.4 - - + +
175a VAL* 5.9 0.9 - - - -
176a LEU* 4.4 7.0 - - + +
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Residues in contact with GLN 147 (chain a).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
165H ASN* 3.8 2.8 + - - +
34Z SER* 5.4 0.4 - - - +
35Z ILE 5.0 3.2 + - - +
36Z HIS* 4.8 7.0 + - - +
132a TYR* 5.6 1.2 + - - -
136a SER 3.6 15.9 + - - +
137a LEU* 4.1 4.2 - - - +
138a ALA* 3.8 29.8 + - + +
142a GLY 2.9 6.7 + - - +
143a ALA* 3.3 28.8 - - + +
146a ALA* 1.3 77.7 - - - +
148a PRO* 1.3 60.1 - - + +
150a LEU* 4.4 8.3 - - - +
151a ARG* 2.8 82.9 + - - +
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Residues in contact with PRO 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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132H LEU 4.2 1.6 - - - +
133H ALA* 3.8 30.3 - - - +
136H ALA* 5.1 3.1 - - + -
137H VAL* 5.0 6.3 - - + -
161H ALA* 4.6 10.2 - - + +
165H ASN* 3.2 24.0 - - - +
144a TYR 3.3 21.1 - - - +
145a LEU 3.3 15.0 - - - +
147a GLN* 1.3 89.4 - - + +
149a LEU* 1.3 62.0 + - - +
151a ARG 3.7 0.9 - - - +
152a GLU* 3.1 27.8 + - - +
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Residues in contact with LEU 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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136H ALA* 4.0 18.8 - - + +
137H VAL* 3.8 25.6 - - + -
140H ASP* 3.2 31.9 - - + +
145a LEU 4.6 2.7 - - - +
146a ALA 3.2 2.7 + - - +
148a PRO* 1.3 76.3 - - - +
150a LEU* 1.3 62.5 + - - +
152a GLU* 4.1 8.8 - - - +
153a VAL* 3.6 27.7 + - - +
168a LEU* 4.1 7.1 - - + +
171a ARG* 4.8 9.2 - - - +
172a CYS* 3.6 28.9 - - - -
175a VAL* 3.8 30.3 - - + -
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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
----------------------------------------------------------
12a LEU* 4.4 10.8 - - + -
13a GLY 4.3 1.8 - - - +
14a VAL* 4.2 10.8 - - + -
136a SER* 3.2 30.5 - - - +
137a LEU 3.8 18.6 - - - +
146a ALA* 3.2 31.7 + - + +
147a GLN* 3.9 10.1 - - - +
148a PRO 3.2 0.2 - - - -
149a LEU* 1.3 79.1 - - - +
151a ARG* 1.3 59.1 + - - +
152a GLU 3.2 4.5 + - - -
154a LEU* 3.3 32.5 + - - +
168a LEU* 3.7 31.4 - - + -
169a VAL* 4.6 5.8 - - + -
172a CYS* 4.0 8.5 - - - -
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Residues in contact with ARG 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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164H PHE* 4.2 5.4 + - - +
165H ASN* 3.3 31.4 + - - +
34Z SER* 5.1 0.6 + - - -
35Z ILE* 3.5 42.6 + - - +
36Z HIS 3.9 12.5 + - - -
37Z THR* 5.7 3.7 - - - +
38Z ARG* 4.8 11.2 - - - +
135a PRO* 6.2 4.7 - - + -
136a SER* 4.8 13.2 - - - +
147a GLN* 2.8 51.4 + - - +
148a PRO* 3.7 3.8 - - - -
150a LEU* 1.3 76.0 - - + +
152a GLU* 1.3 56.3 + - - +
154a LEU* 4.7 7.2 - - + -
155a GLU* 3.2 35.6 + - + +
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Residues in contact with GLU 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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137H VAL* 3.9 21.7 - - - +
140H ASP* 5.2 0.2 - - - +
141H LYS* 3.1 23.4 + - - -
157H GLU* 2.8 30.0 - - - +
161H ALA* 5.3 3.7 - - + +
148a PRO 3.1 16.3 + - - +
149a LEU* 4.1 10.7 - - - +
150a LEU 3.2 0.4 - - - -
151a ARG* 1.3 77.4 - - - +
153a VAL* 1.3 70.6 + - + +
154a LEU 3.3 1.1 - - - -
155a GLU* 3.4 7.6 + - - +
156a LYS* 3.3 18.9 + - - +
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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 LEU 3.6 18.8 + - - +
150a LEU 4.5 1.8 - - - +
152a GLU* 1.3 81.8 - - + +
154a LEU* 1.3 60.7 + - + +
156a LYS* 3.0 7.9 + - + +
157a GLN* 2.9 37.2 + - + +
160a LEU* 4.2 23.6 - - + -
168a LEU* 4.2 21.8 - - + -
171a ARG* 4.3 10.5 - - - +
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Residues in contact with LEU 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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14a VAL* 3.7 22.9 - - + -
15a LYS* 5.1 3.8 - - + +
135a PRO* 3.7 40.8 - - + +
136a SER* 3.8 12.8 - - - -
150a LEU 3.3 22.6 + - - +
151a ARG* 4.7 5.8 - - + -
153a VAL* 1.3 78.7 - - + +
155a GLU* 1.3 63.4 + - - +
157a GLN 3.4 15.4 - - - +
158a PRO* 3.8 23.5 - - + +
160a LEU* 3.7 19.7 - - + -
168a LEU* 4.2 10.3 - - + -
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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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164H PHE* 3.7 30.4 - - - +
38Z ARG* 3.7 21.7 + - - -
212Z LYS* 4.5 17.4 + - - +
151a ARG* 3.2 33.8 + - + +
152a GLU* 3.4 11.1 + - - +
153a VAL 3.2 0.6 - - - -
154a LEU* 1.3 76.1 - - - +
156a LYS* 1.3 65.1 + - - +
158a PRO* 5.1 2.4 - - - +
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Residues in contact with LYS 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 GLU 3.3 9.4 + - - +
153a VAL* 3.0 11.7 + - + +
155a GLU* 1.3 82.5 - - - +
157a GLN* 1.3 62.4 + - + +
158a PRO* 4.0 4.4 - - - +
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Residues in contact with GLN 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* 2.9 31.3 + - + +
154a LEU* 3.4 10.5 - - - +
156a LYS* 1.3 78.7 - - + +
158a PRO* 1.3 62.0 - - + +
159a VAL* 3.1 27.9 + - + +
160a LEU* 4.1 10.9 - - + +
164a GLU* 3.6 24.8 + - - -
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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