Contacts of the helix formed by residues 137 - 151 (chain B) 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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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136B THR* 1.4 88.0 - - - +
138B GLN* 1.3 53.6 + - - +
139B GLY 3.3 0.4 - - - -
140B THR* 3.2 13.6 + - + +
141B LEU* 2.7 32.4 + - - +
159B THR* 3.6 20.4 - - + +
165B VAL* 3.9 28.9 - - + -
423B MET* 3.8 10.1 - - + -
424B GLY 3.8 6.1 - - - +
427B MET* 3.9 27.4 - - + -
428B ASP* 3.6 14.4 - - - +
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Residues in contact with GLN 138 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64B PHE* 3.4 28.7 - - - -
90B ASN* 3.3 21.9 - - - +
91B ASN* 5.8 0.2 - - - +
114B SER* 3.6 17.7 + - - +
115B TYR* 5.9 0.8 - - - +
136B THR 3.3 1.8 + - - -
137B PRO* 1.3 71.1 - - - +
139B GLY* 1.3 57.4 + - - +
141B LEU* 3.2 6.2 + - - +
142B ALA* 2.9 24.8 + - - +
230B PHE* 3.6 14.1 - - + -
344B GLU* 3.1 29.8 + - - +
382B SER* 4.8 0.7 + - - -
386B PHE* 3.3 28.2 - - + -
424B GLY* 2.9 22.5 + - - +
425B GLY* 3.7 4.8 - - - +
428B ASP* 3.7 0.6 + - - -
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Residues in contact with GLY 139 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
138B GLN* 1.3 74.3 - - - +
140B THR* 1.3 61.0 + - - +
142B ALA* 3.9 1.7 - - - +
143B GLU* 3.0 19.1 + - - +
386B PHE* 3.2 32.0 - - - -
390B ARG* 2.9 21.8 + - - -
428B ASP* 2.9 19.0 + - - -
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Residues in contact with THR 140 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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136B THR* 3.4 17.3 - - - +
137B PRO* 3.2 24.6 + - + +
139B GLY* 1.3 74.1 - - - +
141B LEU* 1.3 65.7 + - - +
143B GLU* 4.5 3.4 - - - +
144B ARG* 2.8 38.4 + - + +
155B PHE* 5.0 2.7 - - + -
157B THR* 3.8 20.0 + - + +
159B THR* 4.1 10.2 + - - +
200B GLU* 3.4 36.1 - - + +
390B ARG* 4.8 1.1 - - - +
428B ASP* 3.8 2.6 + - - -
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Residues in contact with LEU 141 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88B VAL* 4.1 9.6 - - + -
89B SER 4.4 1.8 - - - +
90B ASN* 3.8 39.9 - - - +
112B VAL* 4.1 11.2 - - + +
113B SER* 4.3 5.2 - - - -
114B SER* 4.2 13.9 - - - +
136B THR* 3.5 21.3 + - + -
137B PRO 2.7 17.6 + - - +
138B GLN* 3.3 9.2 - - - +
140B THR* 1.3 75.8 - - - +
142B ALA* 1.3 61.4 + - - +
144B ARG* 3.4 3.6 + - - +
145B ILE* 3.2 31.2 + - + +
203B ILE* 3.7 24.0 - - + -
230B PHE* 4.0 11.9 - - + -
234B MET* 6.0 0.4 - - + -
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Residues in contact with ALA 142 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
138B GLN 2.9 18.4 + - - +
139B GLY* 3.9 6.3 - - - +
140B THR 3.4 0.2 - - - -
141B LEU* 1.3 73.6 - - - +
143B GLU* 1.3 57.3 + - - +
145B ILE* 3.6 4.3 + - - +
146B ARG* 3.1 27.7 + - - +
230B PHE* 3.6 19.6 - - + -
233B PRO* 4.7 3.8 - - + +
382B SER* 3.7 10.1 - - - +
383B ASP* 3.7 35.6 - - + +
386B PHE* 4.6 1.6 - - + -
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Residues in contact with GLU 143 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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143A GLU* 5.0 0.2 - - - +
146A ARG* 3.1 40.4 + - - -
152A VAL* 4.6 9.0 - - + -
139B GLY 3.0 19.5 + - - +
142B ALA* 1.3 74.3 - - - +
144B ARG* 1.3 60.0 + - - +
146B ARG* 3.4 21.4 + - - +
147B ALA* 2.8 32.7 + - - +
155B PHE* 3.5 35.6 - - + -
383B ASP* 4.4 7.1 - - - +
390B ARG* 3.7 19.8 + - - +
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Residues in contact with ARG 144 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
112B VAL* 5.3 1.2 - - - +
134B GLU* 4.6 14.6 + - - -
136B THR* 3.4 23.4 + - - +
140B THR* 2.8 43.6 + - - +
141B LEU 3.8 2.5 - - - +
143B GLU* 1.3 71.8 - - - +
145B ILE* 1.3 57.0 + - - +
147B ALA* 3.4 1.2 + - - -
148B GLY 3.0 17.8 + - - -
155B PHE* 3.7 20.9 - - + -
187B ARG* 3.7 20.8 - - - +
200B GLU* 3.8 12.6 + - + -
201B GLU* 2.7 32.0 + - - +
202B ALA* 3.4 4.6 + - - -
203B ILE* 2.9 52.7 + - + +
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Residues in contact with ILE 145 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60B LEU* 4.3 2.9 - - + -
88B VAL* 4.3 5.6 - - + -
141B LEU* 3.2 26.2 + - + +
142B ALA 3.8 3.8 - - - +
144B ARG* 1.3 73.5 - - - +
146B ARG* 1.3 66.6 + - - +
148B GLY 3.3 0.5 + - - -
149B GLY* 3.0 17.8 + - - -
203B ILE* 3.6 28.5 - - + -
230B PHE* 4.0 16.8 - - + -
233B PRO* 3.5 32.3 - - + +
234B MET* 3.7 37.2 - - + +
237B ALA* 3.1 23.5 - - + +
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Residues in contact with ARG 146 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
143A GLU* 2.8 41.8 + - - -
146A ARG* 3.4 45.9 - - - +
383A ASP* 4.2 17.8 + - - -
384A GLU* 5.4 4.4 + - - +
387A ALA* 4.3 10.3 - - - +
142B ALA 3.1 18.6 + - - +
143B GLU* 3.4 17.4 + - - +
145B ILE* 1.3 76.4 - - - +
147B ALA* 1.3 61.1 + - - +
149B GLY* 3.2 3.0 + - - -
150B ALA* 2.9 41.9 + - + +
152B VAL* 5.5 2.4 - - - +
233B PRO* 4.6 8.9 - - + +
236B LYS* 5.7 12.3 - - + +
383B ASP* 3.7 21.8 + - + +
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Residues in contact with ALA 147 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
143B GLU* 2.8 26.8 + - - +
144B ARG 3.6 5.8 - - - +
146B ARG* 1.3 74.4 - - - +
148B GLY* 1.3 58.5 + - - +
150B ALA* 3.1 3.6 + - - +
151B GLY 3.0 10.7 + - - -
152B VAL* 3.0 53.0 + - + +
155B PHE* 4.1 20.4 - - + -
202B ALA* 4.1 4.9 - - + -
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Residues in contact with GLY 148 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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391A GLY* 5.3 2.4 - - - +
144B ARG 3.0 10.7 + - - -
145B ILE 3.3 0.2 + - - -
146B ARG 3.2 0.6 - - - -
147B ALA* 1.3 78.4 - - - +
149B GLY* 1.3 60.5 + - - +
151B GLY* 3.8 7.0 + - - -
152B VAL 4.6 0.2 - - - -
202B ALA* 3.6 14.5 - - - +
203B ILE 3.5 18.4 - - - -
204B THR* 3.7 22.4 - - - +
237B ALA* 4.4 1.1 - - - -
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Residues in contact with GLY 149 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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387A ALA* 3.5 4.0 - - - +
391A GLY* 3.5 9.7 - - - -
393A HIS* 2.9 24.1 + - - -
145B ILE 3.0 12.4 + - - -
146B ARG 3.6 3.8 - - - -
148B GLY* 1.3 78.3 - - - +
150B ALA* 1.3 55.7 + - - +
151B GLY 3.5 0.4 - - - -
236B LYS* 3.2 36.1 - - - +
237B ALA* 3.8 1.8 - - - +
265B TYR* 5.3 0.7 + - - -
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Residues in contact with ALA 150 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
387A ALA* 3.4 30.3 - - + -
390A ARG* 3.1 39.4 + - - +
391A GLY* 3.8 4.7 - - - -
146B ARG* 2.9 34.0 + - + +
147B ALA* 3.1 4.2 + - - +
149B GLY* 1.3 76.0 - - - +
151B GLY* 1.3 57.5 + - - +
152B VAL* 3.4 4.3 - - + -
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Residues in contact with GLY 151 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
158A PRO* 3.5 26.7 - - - +
197A PHE* 4.1 3.4 - - - -
390A ARG* 3.6 18.3 - - - -
391A GLY* 3.8 5.0 - - - -
147B ALA 3.0 3.2 + - - -
148B GLY 3.8 5.0 + - - -
149B GLY 3.5 3.2 - - - -
150B ALA* 1.3 78.8 - - - +
152B VAL* 1.3 60.5 + - - +
153B PRO* 3.6 5.0 - - - +
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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