Contacts of the helix formed by residues 137 - 150 (chain C) 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 C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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136C THR* 1.4 87.4 - - + +
138C GLN* 1.3 54.2 + - - +
139C GLY 3.2 0.7 - - - -
140C THR* 3.0 14.5 + - + +
141C LEU 2.8 30.7 + - - -
159C THR* 3.7 29.4 - - + +
165C VAL* 4.0 28.9 - - + -
200C GLU* 5.5 0.2 - - - +
423C MET* 3.6 9.8 - - + -
424C GLY 3.7 7.9 - - - +
427C MET* 3.9 27.1 - - + -
428C ASP* 3.9 4.9 - - - +
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Residues in contact with GLN 138 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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64C PHE* 3.5 14.3 - - - -
90C ASN* 3.3 27.6 - - - +
91C ASN* 5.7 0.2 - - - +
114C SER* 3.6 21.0 + - - +
115C TYR* 5.6 1.4 - - - +
136C THR 3.2 2.0 + - - -
137C PRO* 1.3 70.5 - - - +
139C GLY* 1.3 57.6 + - - +
141C LEU* 3.4 6.3 + - - +
142C ALA* 3.0 27.0 + - - +
230C PHE* 3.6 11.2 - - + -
344C GLU* 2.9 38.6 + - - +
345C ASN* 4.8 0.7 - - - -
382C SER* 4.9 0.7 + - - -
386C PHE* 3.3 26.9 - - + -
424C GLY* 2.9 21.5 + - - +
425C GLY* 3.9 5.2 - - - +
428C ASP* 4.1 0.6 + - - -
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Residues in contact with GLY 139 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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138C GLN* 1.3 75.4 - - - +
140C THR* 1.3 60.5 + - - +
142C ALA* 3.5 2.0 + - - +
143C GLU 2.9 22.3 + - - -
386C PHE* 3.4 29.5 - - - -
390C ARG* 3.0 19.6 + - - -
428C ASP* 3.0 19.8 + - - -
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Residues in contact with THR 140 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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136C THR* 4.1 9.4 - - + -
137C PRO* 3.0 18.0 + - + +
139C GLY* 1.3 72.7 - - - +
141C LEU* 1.3 57.7 + - - +
143C GLU* 4.6 4.0 - - - -
144C ARG* 2.7 53.0 + - + +
155C PHE* 5.0 2.5 - - + -
157C THR* 4.0 11.9 + - + +
159C THR* 3.9 25.8 + - - +
200C GLU* 3.5 37.0 + - + +
390C ARG* 4.8 0.9 - - - +
428C ASP* 4.0 2.1 + - - -
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Residues in contact with LEU 141 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88C VAL* 3.6 28.3 - - + -
89C SER 4.6 0.2 - - - -
90C ASN* 3.7 41.3 - - - +
112C VAL* 3.9 20.2 - - + +
113C SER* 4.2 5.4 - - - -
114C SER* 4.0 14.1 - - - +
136C THR* 3.9 10.3 - - + +
137C PRO 2.8 12.9 + - - +
138C GLN 3.5 8.5 - - - +
140C THR* 1.3 77.1 - - - +
142C ALA* 1.3 61.1 + - - +
144C ARG* 3.9 3.2 - - - +
145C ILE* 3.2 33.6 + - + +
203C ILE* 3.9 8.1 - - + -
230C PHE* 4.0 11.2 - - + -
234C MET* 6.0 0.4 - - + -
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Residues in contact with ALA 142 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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138C GLN 3.0 16.8 + - - +
139C GLY* 3.8 6.3 - - - +
141C LEU* 1.3 76.7 - - - +
143C GLU* 1.3 58.1 + - - +
145C ILE* 3.9 3.4 - - - +
146C ARG* 3.0 27.7 + - - +
230C PHE* 3.7 21.7 - - + -
233C PRO* 4.4 3.4 - - + +
382C SER* 3.7 8.3 - - - +
383C ASP* 3.6 34.5 - - + +
386C PHE* 4.7 0.9 - - + -
390C ARG* 5.9 0.2 - - - +
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Residues in contact with GLU 143 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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139C GLY 2.9 19.0 + - - +
140C THR 4.2 0.2 - - - +
142C ALA* 1.3 75.7 - - - +
144C ARG* 1.3 61.0 + - - +
146C ARG* 3.5 20.0 + - - -
147C ALA* 2.8 30.8 + - - +
155C PHE* 3.3 35.4 - - + -
383C ASP* 4.3 7.7 - - - +
390C ARG* 3.6 23.2 + - - +
143D GLU* 4.9 1.2 - - - +
146D ARG* 2.9 40.3 + - - -
152D VAL* 4.7 5.3 - - + +
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Residues in contact with ARG 144 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
112C VAL* 5.3 1.6 - - - +
134C GLU* 4.7 11.9 + - - -
136C THR* 3.8 23.6 + - - +
140C THR* 2.7 42.7 + - + +
141C LEU 3.9 2.0 - - - +
143C GLU* 1.3 71.3 - - - +
145C ILE* 1.3 59.2 + - - +
147C ALA* 3.5 1.0 + - - +
148C GLY 3.0 15.6 + - - -
155C PHE* 3.8 21.1 - - + -
187C ARG* 4.4 12.1 - - - +
200C GLU* 3.7 21.6 + - + -
201C GLU* 2.7 32.9 + - - +
202C ALA* 3.4 4.9 + - - -
203C ILE* 2.8 54.7 + - + +
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Residues in contact with ILE 145 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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60C LEU* 4.5 2.9 - - + -
88C VAL* 4.2 12.1 - - + -
141C LEU* 3.2 22.4 + - + +
142C ALA 3.9 3.4 - - - +
144C ARG* 1.3 72.3 - - - +
146C ARG* 1.3 67.4 + - - +
148C GLY 3.1 8.8 + - - -
149C GLY* 3.1 10.0 + - - -
203C ILE* 3.7 26.9 - - + -
230C PHE* 4.0 17.0 - - + -
233C PRO* 3.4 32.2 - - + +
234C MET* 3.8 36.1 - - + +
237C ALA* 3.3 17.6 - - + +
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Residues in contact with ARG 146 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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142C ALA 3.0 19.3 + - - +
143C GLU* 3.4 24.4 + - - +
145C ILE* 1.3 76.9 - - - +
147C ALA* 1.3 63.6 + - - +
149C GLY* 3.2 4.4 + - - -
150C ALA* 3.1 43.0 + - + +
152C VAL* 5.1 3.4 - - - +
233C PRO* 4.5 10.1 - - + +
236C LYS* 6.1 9.0 - - + +
383C ASP* 3.6 23.6 + - + +
143D GLU* 3.0 39.6 + - - -
146D ARG* 3.3 37.3 - - - +
383D ASP* 4.3 17.2 + - - +
384D GLU* 5.2 2.6 + - - +
387D ALA* 4.6 8.6 - - - +
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Residues in contact with ALA 147 (chain C).
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* 2.8 21.6 + - - +
144C ARG 3.6 5.2 - - - +
146C ARG* 1.3 79.9 - - - +
148C GLY* 1.3 60.4 + - - +
150C ALA* 3.1 13.7 + - - -
151C GLY* 3.2 1.0 + - - -
152C VAL* 3.1 52.0 + - + +
155C PHE* 4.1 20.0 - - + -
202C ALA* 4.3 4.0 - - + -
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Residues in contact with GLY 148 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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144C ARG 3.0 10.9 + - - -
145C ILE 3.1 5.3 + - - -
147C ALA* 1.3 76.4 - - - +
149C GLY* 1.3 57.2 + - - +
150C ALA 3.6 0.3 + - - -
151C GLY* 4.1 5.2 + - - -
202C ALA* 3.6 14.2 - - - +
203C ILE 3.5 16.4 - - - -
204C THR* 3.5 21.3 - - - +
236C LYS 4.5 0.7 - - - +
237C ALA* 4.2 3.7 - - - -
391D GLY* 5.4 2.1 - - - +
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Residues in contact with GLY 149 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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145C ILE 3.1 11.7 + - - -
146C ARG 3.2 4.2 + - - -
148C GLY* 1.3 75.8 - - - +
150C ALA* 1.3 57.3 + - - +
151C GLY 3.5 0.9 - - - -
236C LYS* 2.9 37.3 - - - +
237C ALA* 3.8 1.4 - - - +
265C TYR* 5.1 0.9 + - - -
387D ALA* 3.4 8.6 - - - +
391D GLY* 3.5 4.5 - - - -
393D HIS* 2.8 25.1 + - - -
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Residues in contact with ALA 150 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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146C ARG* 3.1 35.2 + - + +
147C ALA* 3.1 6.9 + - - +
149C GLY* 1.3 76.4 - - - +
151C GLY* 1.3 58.8 - - - +
152C VAL* 3.3 3.1 - - + -
387D ALA* 3.5 27.8 - - + +
390D ARG* 3.0 36.1 + - - +
391D GLY 3.7 5.8 - - - -
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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
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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