Contacts of the helix formed by residues 137 - 151 (chain A) 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 A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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135A LEU 4.5 0.2 - - - +
136A THR* 1.3 88.2 - - + +
138A GLN* 1.3 56.2 + - - +
139A GLY 3.3 0.4 - - - -
140A THR* 3.0 15.6 + - + +
141A LEU* 2.8 31.4 + - - +
159A THR* 3.6 28.5 - - + -
160A GLY* 5.1 0.2 - - - -
165A VAL* 4.0 29.8 - - + -
200A GLU* 5.3 0.2 - - - +
423A MET* 3.6 16.8 - - + -
424A GLY 4.5 0.4 - - - +
427A MET* 4.0 25.8 - - + -
428A ASP* 3.8 4.0 - - - +
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Residues in contact with GLN 138 (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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64A PHE* 3.3 21.9 - - - -
90A ASN* 3.4 26.7 - - - +
91A ASN* 5.5 1.2 - - - +
114A SER* 3.4 21.9 + - - +
115A TYR* 5.6 1.2 - - - +
136A THR 3.2 1.8 + - - -
137A PRO* 1.3 70.7 - - - +
139A GLY* 1.3 57.3 + - - +
141A LEU* 3.3 6.0 + - - +
142A ALA* 2.9 28.2 + - - +
230A PHE* 3.7 10.8 - - + -
344A GLU* 3.0 28.9 + - - +
345A ASN* 4.9 0.2 - - - -
382A SER* 5.1 0.2 + - - -
386A PHE* 3.4 25.9 - - + -
424A GLY* 3.0 24.0 + - - +
425A GLY 3.7 6.9 - - - +
428A ASP* 3.7 0.4 + - - -
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Residues in contact with GLY 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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138A GLN* 1.3 76.0 - - - +
140A THR* 1.3 60.7 + - - +
142A ALA* 3.7 2.7 - - - +
143A GLU* 3.1 18.5 + - - +
386A PHE* 3.3 32.6 - - - -
390A ARG* 2.9 21.8 + - - -
428A ASP* 3.0 17.7 + - - -
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Residues in contact with THR 140 (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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136A THR* 4.1 7.9 - - + -
137A PRO* 3.0 18.9 + - + +
139A GLY* 1.3 75.6 - - - +
141A LEU* 1.3 66.3 + - - +
143A GLU* 3.3 3.7 + - - +
144A ARG* 2.9 40.1 + - + +
155A PHE* 5.0 2.9 - - + -
157A THR* 3.9 10.9 + - + +
159A THR* 3.8 27.0 + - - +
200A GLU* 3.4 40.6 - - + +
390A ARG* 4.8 1.3 + - - +
428A ASP* 4.0 1.8 + - - -
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Residues in contact with LEU 141 (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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88A VAL* 3.9 9.9 - - + -
89A SER 4.5 0.7 - - - -
90A ASN* 3.8 39.9 - - - +
112A VAL* 3.7 42.0 - - + +
113A SER* 4.2 1.3 - - - -
114A SER* 4.1 11.0 - - - +
136A THR* 3.8 12.5 - - + +
137A PRO 2.8 16.2 + - - +
138A GLN* 3.5 8.5 - - - +
140A THR* 1.3 72.3 - - - +
142A ALA* 1.3 63.1 + - - +
144A ARG* 3.9 4.2 - - - +
145A ILE* 3.1 37.4 + - + +
203A ILE* 3.8 15.9 - - + -
230A PHE* 4.1 7.2 - - + -
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Residues in contact with ALA 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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138A GLN 2.9 19.5 + - - +
139A GLY* 3.7 8.5 - - - +
140A THR 3.3 0.2 - - - -
141A LEU* 1.3 73.9 - - - +
143A GLU* 1.3 57.2 + - - +
145A ILE* 3.7 4.4 - - - +
146A ARG* 3.1 27.2 + - - +
230A PHE* 3.7 19.8 - - + -
233A PRO* 4.5 3.1 - - + +
382A SER* 3.8 9.4 - - - +
383A ASP* 3.7 33.8 - - - +
386A PHE* 4.6 1.6 - - + -
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Residues in contact with GLU 143 (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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139A GLY 3.1 17.5 + - - +
140A THR 4.1 0.7 - - - +
142A ALA* 1.3 74.2 - - - +
144A ARG* 1.3 56.4 + - - +
146A ARG* 3.6 16.1 + - - -
147A ALA* 2.8 36.4 + - - +
155A PHE* 3.4 34.4 - - + -
383A ASP* 4.4 6.8 - - - +
390A ARG* 3.7 24.1 + - - +
143B GLU* 5.0 0.5 - - - +
146B ARG* 2.8 43.1 + - - -
152B VAL* 4.6 5.9 - - + +
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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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112A VAL* 5.0 3.4 - - - +
134A GLU* 5.0 9.3 + - - -
136A THR* 3.7 26.1 + - - +
140A THR* 2.9 36.3 + - - +
141A LEU 3.9 3.1 - - - +
143A GLU* 1.3 72.5 - - - +
145A ILE* 1.3 60.7 + - - +
147A ALA* 4.1 1.3 - - - -
148A GLY 2.8 23.6 + - - -
155A PHE* 3.7 21.3 - - + -
187A ARG* 4.8 8.6 - - - +
200A GLU* 3.7 20.0 + - + -
201A GLU* 2.7 33.1 + - - +
202A ALA* 3.4 3.9 + - - -
203A ILE* 2.9 50.0 + - + +
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Residues in contact with ILE 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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60A LEU* 4.6 2.5 - - + -
88A VAL* 4.0 12.6 - - + -
141A LEU* 3.1 32.3 + - + +
142A ALA* 3.7 3.4 - - - +
144A ARG* 1.3 73.9 - - - +
146A ARG* 1.3 66.5 + - - +
148A GLY 3.1 2.4 + - - -
149A GLY 3.0 17.3 + - - -
203A ILE* 3.7 27.1 - - + -
230A PHE* 4.2 9.2 - - + -
233A PRO* 3.5 35.0 - - + +
234A MET* 3.6 37.9 - - + +
237A ALA* 3.2 19.4 - - + +
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Residues in contact with ARG 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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142A ALA 3.1 17.5 + - - +
143A GLU* 3.6 13.4 + - - +
144A ARG 3.4 0.2 - - - -
145A ILE* 1.3 76.8 - - - +
147A ALA* 1.3 51.3 + - - +
149A GLY* 3.0 5.1 + - - +
150A ALA* 2.8 55.3 + - + +
152A VAL* 5.6 2.0 - - - +
233A PRO* 4.4 12.3 - - + -
236A LYS* 5.7 10.0 - - + +
383A ASP* 3.9 24.6 + - + +
143B GLU* 3.1 31.5 + - - -
146B ARG* 3.4 52.6 - - - +
383B ASP* 4.3 17.2 + - - -
384B GLU* 5.3 5.9 + - - +
387B ALA* 4.4 10.0 - - + +
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Residues in contact with ALA 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 GLU* 2.8 24.0 + - - +
144A ARG 3.5 5.6 - - - +
146A ARG* 1.3 73.5 - - - +
148A GLY* 1.3 59.6 + - - +
150A ALA* 2.9 18.7 + - - +
151A GLY* 3.1 11.1 + - - -
152A VAL* 3.2 39.2 + - + +
155A PHE* 3.9 23.6 - - + -
202A ALA* 4.1 4.7 - - + +
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Residues in contact with GLY 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 14.5 + - - -
145A ILE 3.1 0.6 + - - -
147A ALA* 1.3 73.4 - - - +
149A GLY* 1.3 60.3 + - - +
151A GLY* 3.8 6.1 + - - -
202A ALA* 3.5 10.2 - - - +
203A ILE 3.4 22.0 - - - -
204A THR* 3.5 24.3 - - - +
237A ALA* 4.1 2.5 - - - -
391B GLY* 5.4 1.9 - - - +
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Residues in contact with GLY 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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145A ILE 3.0 12.2 + - - -
146A ARG 3.0 4.7 + - - -
148A GLY* 1.3 74.9 - - - +
150A ALA* 1.3 58.4 + - - +
151A GLY 3.4 0.4 - - - -
236A LYS* 3.0 39.1 - - - +
237A ALA* 3.6 1.6 - - - +
265A TYR* 5.2 0.5 + - - -
387B ALA* 3.3 10.1 - - - +
391B GLY* 3.6 3.7 - - - -
393B HIS* 3.1 22.1 + - - -
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Residues in contact with ALA 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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146A ARG* 2.8 38.7 + - + +
147A ALA* 2.9 6.5 + - - +
149A GLY* 1.3 73.3 - - - +
151A GLY* 1.3 58.9 + - - +
152A VAL* 3.3 4.9 + - + -
387B ALA* 3.6 26.9 - - + +
390B ARG* 3.1 36.3 + - - +
391B GLY 3.5 5.1 + - - -
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Residues in contact with GLY 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 ALA 3.1 3.0 + - - -
148A GLY 3.8 4.5 + - - -
149A GLY 3.4 3.4 - - - -
150A ALA* 1.3 78.8 - - - +
152A VAL* 1.3 57.7 + - - +
153A PRO* 3.7 4.6 - - - +
158B PRO* 3.6 26.2 - - - +
197B PHE* 4.3 3.8 - - - -
390B ARG* 3.6 21.1 - - - +
391B GLY* 3.6 5.6 - - - -
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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