Contacts of the helix formed by residues 153 - 162 (chain D) in PDB entry 1THF
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 LEU 153 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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129D ILE* 3.6 31.4 - - + -
131D ALA* 4.1 12.3 - - + -
138D PHE* 2.9 45.0 + - + +
139D MET 4.5 0.9 - - - +
140D VAL* 3.8 10.5 - - + +
151D ILE 3.5 2.4 + - - -
152D LEU* 1.3 71.1 - - - +
154D ARG* 1.3 64.0 + - - +
156D TRP 3.3 0.9 + - - -
157D VAL* 3.0 37.8 + - + +
170D LEU* 4.2 7.6 - - + -
186D MET* 4.0 13.5 - - + -
189D PHE* 4.0 9.6 - - + -
190D VAL* 3.6 26.2 - - + -
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Residues in contact with ARG 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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138D PHE 4.8 0.4 + - - -
152D LEU* 3.1 24.7 - - + +
153D LEU* 1.3 80.1 - - - +
155D ASP* 1.3 94.1 + - - +
157D VAL* 3.9 2.1 - - - +
158D VAL* 3.4 25.7 + - + +
189D PHE* 3.9 21.6 - - + -
193D LEU* 3.7 32.0 - - + +
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Residues in contact with ASP 155 (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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151D ILE* 4.7 7.9 - - + -
152D LEU* 3.0 24.0 + - + +
154D ARG* 1.3 113.5 + - - +
156D TRP* 1.3 59.2 + - - +
158D VAL* 3.5 6.6 + - - +
159D GLU* 3.0 27.9 + - - +
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Residues in contact with TRP 156 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103D ASN* 5.5 0.4 - - - +
106D ALA* 3.4 30.1 - - + -
107D VAL* 3.7 36.7 - - + +
110D PRO* 4.0 18.8 - - + -
113D ILE* 4.2 5.4 - - + -
127D VAL* 4.4 3.9 - - + +
128D ALA 5.3 1.0 + - - -
129D ILE* 3.7 33.4 - - + +
140D VAL* 3.8 36.1 - - + +
151D ILE* 3.9 18.8 - - + +
152D LEU 3.1 7.6 + - - +
153D LEU 4.0 1.3 - - - +
155D ASP* 1.3 74.2 - - - +
157D VAL* 1.3 58.3 + - - +
159D GLU* 3.2 25.1 + - + -
160D VAL* 2.8 54.9 + - + +
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Residues in contact with VAL 157 (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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129D ILE* 4.0 17.7 - - + -
153D LEU* 3.0 41.7 + - + +
154D ARG 3.9 3.8 - - - +
156D TRP* 1.3 77.2 - - - +
158D VAL* 1.3 63.1 + - - +
160D VAL* 3.3 3.1 + - - +
161D GLU* 3.2 21.7 + - - +
168D ILE* 4.0 7.4 - - + +
170D LEU* 5.5 0.4 - - + -
190D VAL* 3.9 19.7 - - + -
193D LEU* 3.9 21.1 - - + +
194D THR* 3.7 32.7 - - + -
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Residues in contact with VAL 158 (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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154D ARG* 3.4 16.2 + - + +
155D ASP* 3.8 8.7 - - - +
156D TRP 3.3 0.4 - - - -
157D VAL* 1.3 77.2 - - - +
159D GLU* 1.3 63.3 + - - +
161D GLU* 3.4 4.7 + - - +
162D LYS* 3.0 42.3 + - - +
193D LEU* 3.9 32.1 - - + +
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Residues in contact with GLU 159 (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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110D PRO* 4.9 2.5 - - + -
155D ASP 3.0 18.1 + - - +
156D TRP* 3.2 28.5 + - + +
158D VAL* 1.3 77.3 - - - +
160D VAL* 1.3 57.7 + - - +
162D LYS* 3.1 24.9 + - - +
163D ARG* 2.8 75.9 + - + +
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Residues in contact with VAL 160 (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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113D ILE* 4.2 8.5 - - + +
127D VAL* 3.8 24.2 - - + -
129D ILE* 4.4 2.2 - - + -
156D TRP* 2.8 63.2 + - + +
157D VAL* 3.3 5.8 + - - +
159D GLU* 1.3 72.5 - - - +
161D GLU* 1.3 64.5 + - - +
163D ARG* 3.3 9.0 + - - +
164D GLY 3.4 0.3 + - - -
165D ALA* 3.3 39.2 + - + +
168D ILE* 3.9 19.7 - - + -
196D LEU* 4.7 0.2 - - + -
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Residues in contact with GLU 161 (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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157D VAL 3.2 12.8 + - - +
158D VAL* 3.9 7.6 - - - +
160D VAL* 1.3 77.6 - - - +
162D LYS* 1.3 62.1 + - - +
164D GLY* 3.0 15.6 + - - +
165D ALA 4.3 1.1 + - - +
193D LEU 4.3 2.0 - - - +
194D THR* 2.7 32.0 + - - +
195D THR* 2.9 37.6 + - - +
196D LEU* 3.8 27.4 - - + -
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Residues in contact with LYS 162 (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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158D VAL* 3.0 32.1 + - - +
159D GLU* 3.1 30.0 + - - +
161D GLU* 1.3 76.5 - - - +
163D ARG* 1.3 61.2 + - + +
164D GLY* 3.3 1.4 + - - -
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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