Contacts of the helix formed by residues 137 - 154 (chain D) in PDB entry 5M8L
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 137 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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135D ASP 3.8 1.0 + - - -
136D LEU* 1.3 75.9 - - - +
138D LYS* 1.3 59.9 + - - +
139D GLU* 3.5 15.3 + - - +
140D GLU* 2.9 39.0 + - - +
141D LYS* 2.8 28.2 + - - +
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Residues in contact with LYS 138 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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137D SER* 1.3 74.2 - - - +
139D GLU* 1.3 82.5 + - - +
141D LYS* 3.6 12.6 + - - +
142D ASN* 3.2 22.5 + - + +
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Residues in contact with GLU 139 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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137D SER* 3.1 13.3 + - - +
138D LYS* 1.3 102.5 + - - +
140D GLU* 1.3 59.6 + - + +
142D ASN* 3.2 6.8 + - - +
143D HIS* 2.9 29.0 + - - +
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Residues in contact with GLU 140 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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131D ARG* 3.5 26.8 + - - -
136D LEU* 3.6 21.9 - - + +
137D SER* 2.9 34.4 + - - +
139D GLU* 1.3 76.5 - - + +
141D LYS* 1.3 63.1 + - - +
143D HIS* 3.3 9.3 + - + +
144D PHE* 3.1 23.7 + - - +
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Residues in contact with LYS 141 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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133D LEU* 3.5 18.4 - - + +
134D LEU* 3.8 23.3 + - - +
136D LEU* 3.5 28.9 + - + +
137D SER 2.8 22.0 + - - +
138D LYS* 3.8 9.9 - - - +
140D GLU* 1.3 78.5 - - - +
142D ASN* 1.3 60.6 + - - +
144D PHE* 3.4 5.8 + - - +
145D VAL* 3.2 28.4 + - - +
264D ASP* 4.3 21.7 + - + +
265D LEU* 3.8 31.4 - - + +
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Residues in contact with ASN 142 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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138D LYS* 3.2 14.4 + - + +
139D GLU* 3.2 7.2 + - - +
141D LYS* 1.3 77.0 - - - +
143D HIS* 1.3 65.4 + - - +
145D VAL* 3.4 7.8 + - - +
146D ARG* 3.0 59.8 + - - +
264D ASP* 5.0 4.2 + - - +
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Residues in contact with HIS 143 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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203B VAL* 5.5 6.2 - - + +
139D GLU 2.9 17.0 + - - +
140D GLU* 3.3 9.2 + - + +
142D ASN* 1.3 77.5 + - - +
144D PHE* 1.3 54.0 + - - +
146D ARG* 3.5 5.3 + - - +
147D ALA* 2.7 36.4 + - - +
239D LEU* 4.3 22.2 - - + +
241D GLU* 2.6 37.5 + - - -
244D PHE* 4.6 10.8 - + - -
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Residues in contact with PHE 144 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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133D LEU* 4.0 13.0 - - + -
136D LEU* 5.1 3.1 - - + -
140D GLU 3.1 15.7 + - - +
141D LYS* 3.7 4.7 - - - +
142D ASN 3.2 0.4 - - - -
143D HIS* 1.3 75.5 - - - +
145D VAL* 1.3 63.7 + - + +
147D ALA* 3.6 3.7 - - - +
148D LEU* 2.9 59.8 + - + +
244D PHE* 4.2 18.8 - + + -
245D SER 5.1 0.2 - - - -
246D LEU* 4.6 13.2 - - + -
247D PRO* 3.4 28.9 - - + -
266D MET* 3.3 33.4 - - + -
401D VAL* 4.9 4.9 - - + -
402D LEU* 3.7 26.0 - - + -
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Residues in contact with VAL 145 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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141D LYS 3.2 17.3 + - - +
142D ASN* 3.4 8.7 + - - +
143D HIS 3.4 0.2 - - - -
144D PHE* 1.3 78.0 - - + +
146D ARG* 1.3 63.0 + - + +
148D LEU* 3.4 3.9 + - - +
149D ASP* 3.0 26.0 + - - +
263D ASP 6.0 1.1 - - - +
264D ASP 3.7 15.3 - - - +
265D LEU* 3.6 25.8 - - + +
266D MET* 4.5 10.3 - - + -
281D SER* 5.8 0.7 - - - +
282D VAL* 3.8 25.6 - - + +
283D PHE* 3.9 17.3 - - + -
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Residues in contact with ARG 146 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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142D ASN* 3.0 42.9 + - - +
143D HIS* 4.0 5.8 - - - +
145D VAL* 1.3 75.1 - - + +
147D ALA* 1.3 61.4 + - - +
149D ASP* 3.3 6.5 + - - +
150D MET* 2.9 29.5 + - - +
153D ARG* 5.2 0.9 + - - -
282D VAL* 6.0 4.7 - - + -
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Residues in contact with ALA 147 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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143D HIS* 2.7 24.7 + - + +
144D PHE 3.6 4.3 - - - +
146D ARG* 1.3 70.1 - - - +
148D LEU* 1.3 66.4 + - - +
150D MET* 3.2 5.4 + - - +
151D ALA* 2.9 19.9 + - - +
235D MET* 3.7 17.0 - - + -
238D MET* 3.7 6.4 - - - +
239D LEU* 3.9 35.7 - - + -
244D PHE* 4.1 8.5 - - + -
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Residues in contact with LEU 148 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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144D PHE* 2.9 53.4 + - + +
145D VAL 3.6 5.2 - - - +
147D ALA* 1.3 76.4 - - - +
149D ASP* 1.3 62.3 + - - +
151D ALA* 3.2 4.0 + - - +
152D LYS* 3.1 18.2 + - - +
185D TYR* 3.9 31.5 - - + +
231D LEU* 5.1 0.4 - - + -
235D MET* 3.8 19.9 - - + +
266D MET* 4.6 2.2 - - - -
283D PHE* 4.0 17.0 - - + -
286D TRP* 3.5 10.7 - - + -
398D PRO* 3.8 27.6 - - + +
401D VAL* 4.6 9.2 - - + -
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Residues in contact with ASP 149 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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145D VAL 3.0 18.2 + - - +
146D ARG* 3.8 7.2 - - - +
147D ALA 3.2 0.2 - - - -
148D LEU* 1.3 75.7 - - - +
150D MET* 1.3 60.8 + - - +
152D LYS* 3.3 6.8 + - - +
153D ARG* 3.0 45.3 + - - +
282D VAL* 3.9 31.9 - - + +
285D GLN* 4.9 5.8 - - - +
286D TRP* 2.7 36.5 + - + +
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Residues in contact with MET 150 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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146D ARG 2.9 17.9 + - - +
147D ALA* 3.2 5.1 + - - +
149D ASP* 1.3 74.3 - - - +
151D ALA* 1.3 64.4 + - - +
153D ARG* 3.0 24.6 + - - +
154D THR* 2.8 42.4 + - + +
238D MET* 3.7 40.6 - - + +
239D LEU* 4.4 13.0 - - - -
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Residues in contact with ALA 151 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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147D ALA 2.9 13.3 + - - +
148D LEU* 3.5 11.9 - - - +
150D MET* 1.3 77.4 - - - +
152D LYS* 1.3 60.9 + - - +
153D ARG 3.4 0.3 + - - -
154D THR 3.7 2.3 - - - +
184D ILE* 3.3 32.9 + - + +
185D TYR* 2.9 29.9 + - + -
235D MET* 4.2 13.0 - - + -
238D MET* 3.5 17.6 - - + -
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Residues in contact with LYS 152 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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148D LEU 3.1 4.6 + - - -
149D ASP 3.5 8.5 - - - +
150D MET 3.1 0.4 - - - -
151D ALA* 1.3 77.0 - - - +
153D ARG* 1.3 60.7 + - + +
183D SER* 3.3 16.8 + - - -
185D TYR* 3.7 12.4 - - + +
186D ASN* 2.9 29.8 + - - +
286D TRP* 3.4 68.8 - - + +
287D ARG 2.6 35.1 + - - +
288D VAL* 4.5 0.2 - - - +
307D GLU* 3.2 13.7 + - - +
396D ASN* 4.4 8.5 + - - +
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Residues in contact with ARG 153 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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146D ARG 5.2 0.6 + - - -
149D ASP* 3.0 48.6 + - - +
150D MET* 3.0 27.0 + - - +
152D LYS* 1.3 85.0 - - + +
154D THR* 1.3 61.4 + - - +
155D THR* 3.7 2.9 + - - -
183D SER* 4.4 3.1 - - - -
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Residues in contact with THR 154 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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150D MET* 2.8 40.8 + - + +
151D ALA 3.7 0.5 + - - +
153D ARG* 1.3 78.5 + - - +
155D THR* 1.3 70.9 + - - +
157D PRO* 5.7 0.7 - - + -
183D SER* 3.2 2.9 - - - -
184D ILE* 2.9 39.5 + - + +
238D MET* 4.3 14.1 - - + -
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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