Contacts of the helix formed by residues 137 - 151 (chain D) in PDB entry 3DLX
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 PRO 137 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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135D LEU 4.3 0.2 - - - +
136D THR* 1.3 89.2 - - + +
138D GLN* 1.3 55.4 + - - +
139D GLY 3.3 0.4 - - - -
140D THR* 3.1 12.6 + - + +
141D LEU* 2.8 31.4 + - - +
159D THR* 3.7 27.8 - - + +
160D GLY* 5.0 1.1 - - - -
165D VAL* 3.8 40.6 - - + -
200D GLU* 5.6 0.2 - - - +
423D MET* 3.7 16.5 - - + -
424D GLY 3.9 0.4 - - - +
427D MET* 3.9 15.7 - - + -
428D ASP* 3.9 4.0 - - - +
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Residues in contact with GLN 138 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64D PHE* 3.3 21.8 - - - -
90D ASN* 3.4 26.9 - - - +
114D SER* 3.4 21.0 + - - -
115D TYR* 5.4 1.8 - - - +
136D THR 3.2 1.2 + - - -
137D PRO* 1.3 71.4 - - - +
139D GLY* 1.3 62.3 + - - +
141D LEU* 3.6 3.2 + - - +
142D ALA* 3.2 19.1 + - - +
230D PHE* 3.6 15.2 - - + -
344D GLU* 3.0 28.2 + - - +
382D SER* 5.1 0.2 + - - -
386D PHE* 3.3 21.9 - - + -
424D GLY* 3.0 24.1 + - - +
425D GLY* 3.6 10.8 - - - +
428D ASP* 3.8 0.4 + - - -
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Residues in contact with GLY 139 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
138D GLN* 1.3 77.2 - - - +
140D THR* 1.3 58.5 + - - +
142D ALA* 3.5 2.1 + - - +
143D GLU* 3.2 19.2 + - - +
386D PHE* 3.3 31.2 - - - +
390D ARG* 3.1 21.1 + - - -
428D ASP* 2.9 18.8 + - - -
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Residues in contact with THR 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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136D THR* 4.0 7.9 - - + -
137D PRO* 3.1 20.5 + - + +
139D GLY* 1.3 72.6 - - - +
141D LEU* 1.3 60.4 + - - +
143D GLU* 3.8 4.3 - - - +
144D ARG* 2.8 47.6 + - + +
155D PHE* 5.1 3.1 - - + -
157D THR* 3.8 20.0 + - + +
159D THR* 4.0 16.3 + - - +
200D GLU* 3.5 38.5 + - + +
390D ARG* 4.8 1.1 - - - +
428D ASP* 3.9 2.4 + - - -
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Residues in contact with LEU 141 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88D VAL* 3.9 11.2 - - + -
89D SER 4.5 0.7 - - - +
90D ASN* 3.9 36.3 - - - +
112D VAL* 3.7 22.9 - - + +
113D SER* 4.2 6.7 - - - -
114D SER* 4.1 14.6 - - - +
136D THR* 3.9 12.7 - - + +
137D PRO 2.8 19.0 + - - +
138D GLN* 3.6 6.3 - - - +
140D THR* 1.3 74.1 - - - +
142D ALA* 1.3 56.8 + - - +
144D ARG* 3.8 3.1 - - - +
145D ILE* 3.0 37.7 + - + +
203D ILE* 3.5 26.5 - - + -
230D PHE* 4.1 9.9 - - + -
234D MET* 6.1 0.2 - - + -
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Residues in contact with ALA 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 GLN 3.2 10.7 + - - +
139D GLY* 3.8 6.5 - - - +
140D THR 3.3 0.2 - - - -
141D LEU* 1.3 79.8 - - - +
143D GLU* 1.3 58.5 + - - +
145D ILE* 3.4 5.5 + - - +
146D ARG* 2.9 26.9 + - - +
230D PHE* 3.5 24.7 - - + -
233D PRO* 4.4 3.5 - - + +
382D SER* 3.9 6.7 - - - +
383D ASP* 3.7 34.0 - - + +
386D PHE* 4.9 0.4 - - + -
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Residues in contact with GLU 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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143C GLU* 4.9 1.2 - - - +
146C ARG* 3.0 43.8 + - - -
152C VAL* 4.8 4.4 - - + +
139D GLY 3.2 15.7 + - - +
140D THR 4.1 0.9 - - - +
142D ALA* 1.3 77.5 - - - +
144D ARG* 1.3 55.7 + - - +
146D ARG* 3.8 17.2 + - - +
147D ALA* 2.8 35.2 + - - +
155D PHE* 3.4 37.2 - - + +
383D ASP* 4.4 6.6 - - + +
390D ARG* 3.7 22.7 + - - +
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Residues in contact with ARG 144 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
112D VAL* 5.3 0.6 - - - +
134D GLU* 4.7 12.3 + - - -
136D THR* 3.5 28.0 + - - +
140D THR* 2.8 36.8 + - - +
141D LEU 3.8 0.2 - - - +
143D GLU* 1.3 73.5 - - - +
145D ILE* 1.3 64.5 + - - +
147D ALA* 4.3 0.2 - - - -
148D GLY 3.1 12.3 + - - -
155D PHE* 3.9 19.5 - - + -
187D ARG* 4.3 12.7 - - - +
200D GLU* 3.8 19.6 + - + -
201D GLU* 2.8 33.2 + - - +
202D ALA* 3.5 3.3 + - - -
203D ILE* 3.0 53.1 + - + +
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Residues in contact with ILE 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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60D LEU* 4.3 2.7 - - + -
88D VAL* 3.9 13.5 - - + -
141D LEU* 3.0 21.8 + - + +
142D ALA* 3.6 5.2 - - - +
144D ARG* 1.3 73.7 - - - +
146D ARG* 1.3 64.3 + - - +
148D GLY* 3.1 9.5 + - - -
149D GLY* 3.2 10.7 + - - -
203D ILE* 3.8 26.5 - - + -
230D PHE* 4.2 13.9 - - + -
233D PRO* 3.4 33.0 - - + +
234D MET* 3.5 38.6 - - + +
237D ALA* 3.3 17.5 - - + +
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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
----------------------------------------------------------
143C GLU* 2.9 36.5 + - - -
146C ARG* 3.3 44.9 - - - +
383C ASP* 4.1 17.8 + - - +
384C GLU* 5.3 5.7 + - - -
387C ALA* 4.3 9.2 - - - +
142D ALA 2.9 16.9 + - - +
143D GLU* 3.7 17.8 + - - +
145D ILE* 1.3 76.1 - - - +
147D ALA* 1.3 67.2 + - - +
149D GLY* 3.2 4.7 + - - +
150D ALA* 3.0 44.3 + - + +
152D VAL* 5.1 2.8 - - - +
233D PRO* 4.6 8.3 - - + +
236D LYS* 5.9 9.8 - - + +
383D ASP* 3.8 22.1 + - + +
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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
----------------------------------------------------------
143D GLU* 2.8 23.7 + - - +
144D ARG 3.7 4.9 - - - +
146D ARG* 1.3 76.6 - - - +
148D GLY* 1.3 63.0 + - - +
150D ALA* 3.1 3.3 + - - -
151D GLY 3.1 19.9 + - - -
152D VAL* 3.1 37.7 + - + +
155D PHE* 4.0 23.3 - - + -
202D ALA* 4.2 5.4 - - + -
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Residues in contact with GLY 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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391C GLY* 5.2 3.1 - - - +
144D ARG 3.1 12.7 + - - -
145D ILE 3.1 1.0 + - - -
147D ALA* 1.3 78.0 - - - +
149D GLY* 1.3 58.6 + - - +
150D ALA 3.5 0.3 + - - -
151D GLY* 3.8 6.5 + - - -
202D ALA* 3.6 14.8 - - - +
203D ILE 3.5 19.1 - - - -
204D THR* 3.7 21.4 - - - +
237D ALA* 4.4 1.9 - - - -
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Residues in contact with GLY 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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387C ALA* 3.3 9.7 - - - +
391C GLY* 3.4 4.5 - - - -
393C HIS* 2.9 23.7 + - - -
145D ILE 3.2 11.6 + - - -
146D ARG 3.2 4.4 + - - -
148D GLY* 1.3 75.7 - - - +
150D ALA* 1.3 56.4 + - - +
151D GLY 3.4 0.7 - - - -
236D LYS* 3.1 38.6 - - - +
237D ALA* 3.8 2.6 - - - +
265D TYR* 5.1 1.0 + - - -
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Residues in contact with ALA 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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387C ALA* 3.6 28.9 - - + +
390C ARG* 3.1 32.7 + - - +
391C GLY* 3.8 5.2 - - - -
146D ARG* 3.0 36.6 + - + +
147D ALA* 3.1 4.9 + - - +
149D GLY* 1.3 76.0 - - - +
151D GLY* 1.3 62.2 + - - +
152D VAL* 3.3 3.7 + - + -
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Residues in contact with GLY 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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158C PRO* 3.4 27.9 - - - +
197C PHE* 4.4 2.3 - - - -
390C ARG* 3.6 19.0 - - - -
391C GLY* 3.7 4.6 - - - -
147D ALA 3.1 3.5 + - - -
148D GLY 3.8 4.9 + - - -
149D GLY 3.4 3.2 - - - -
150D ALA* 1.3 79.5 - - - +
152D VAL* 1.3 60.9 + - - +
153D PRO* 3.7 3.4 - - - +
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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