Contacts of the helix formed by residues 141 - 150 (chain D) in PDB entry 3KDO
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 PHE 141 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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140D ALA* 1.3 93.8 - - + +
142D GLY* 1.3 63.3 + - - +
144D GLU* 4.1 2.9 + - - +
145D GLY* 2.9 41.6 + - - -
146D VAL* 4.2 6.3 - - + -
149D MET* 3.9 25.6 - - + -
272D ALA* 5.7 1.6 - - - -
275D GLY* 3.5 28.0 - - - -
276D LEU 3.7 8.1 - - - -
277D ALA* 3.7 30.3 - - + -
311D ASP* 2.9 11.9 + - - +
360D LYS* 4.1 12.6 + - - +
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Residues in contact with GLY 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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139D PRO* 3.8 12.8 - - - +
141D PHE* 1.3 78.0 - - - +
143D ILE* 1.3 66.6 + - - -
144D GLU 3.2 0.4 - - - -
146D VAL* 3.0 27.2 + - - +
311D ASP* 3.1 18.3 + - - +
360D LYS* 4.7 5.4 - - - -
361D ALA 3.1 16.2 - - - -
363D PHE* 4.9 0.2 - - - -
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Residues in contact with ILE 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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142D GLY* 1.3 71.6 - - - +
144D GLU* 1.3 58.8 + - - +
147D ARG* 2.9 46.5 + - - +
338D ARG* 3.6 39.3 - - + -
361D ALA* 3.1 21.4 + - + +
362D ALA 3.7 9.2 - - - +
363D PHE* 3.7 48.2 - - + +
364D PRO* 4.4 1.8 - - + -
385D ASP* 4.1 16.6 - - + +
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Residues in contact with GLU 144 (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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141D PHE 4.6 2.6 - - - +
142D GLY 3.2 0.6 - - - -
143D ILE* 1.3 81.9 - - - +
145D GLY* 1.3 56.7 + - - +
147D ARG* 4.0 4.5 - - - +
148D LYS* 3.0 33.5 + - + +
360D LYS* 5.4 11.3 + - + +
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Residues in contact with GLY 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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141D PHE* 2.9 41.5 + - - -
142D GLY 3.7 0.2 - - - -
144D GLU* 1.3 78.7 + - - +
146D VAL* 1.3 56.8 + - - +
148D LYS* 3.4 9.4 + - - +
149D MET* 2.8 28.2 + - - +
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Residues in contact with VAL 146 (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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141D PHE* 4.2 12.1 - - + -
142D GLY 3.0 21.7 + - - +
145D GLY* 1.3 74.7 - - - +
147D ARG* 1.3 66.3 + - - +
149D MET* 3.1 7.7 + - + +
150D LEU* 2.9 44.4 + - + +
157D ILE* 5.2 4.0 - - + -
251D HIS* 4.4 10.3 - - + +
277D ALA* 4.5 5.4 - - + -
311D ASP* 4.7 2.9 - - + -
312D GLN* 3.4 35.9 - - + +
363D PHE* 4.0 19.7 - - + -
387D VAL* 5.9 0.7 - - + -
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Residues in contact with ARG 147 (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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143D ILE* 2.9 27.1 + - - +
144D GLU* 4.0 4.5 - - - +
146D VAL* 1.3 77.2 - - - +
148D LYS* 1.3 57.1 + - - +
150D LEU* 5.2 0.7 - - - -
151D GLU* 2.8 23.4 + - - -
152D ILE* 2.8 50.1 + - - +
153D LYS* 3.4 24.4 + - - +
154D ASP 3.2 9.7 + - - -
155D ARG 2.9 29.3 + - - -
156D PRO* 4.2 0.6 - - - +
157D ILE* 4.0 6.1 - - + +
363D PHE* 3.8 23.3 - - + -
384D THR 3.3 11.9 + - - -
385D ASP* 2.9 33.6 + - - +
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Residues in contact with LYS 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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144D GLU* 3.0 22.6 + - + +
145D GLY* 3.5 7.6 - - - +
147D ARG* 1.3 74.9 - - - +
149D MET* 1.3 66.2 + - - +
151D GLU* 3.2 20.8 + - - +
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Residues in contact with MET 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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141D PHE* 3.9 28.7 - - + -
145D GLY 2.8 18.5 + - - +
146D VAL* 3.5 7.9 - - - +
148D LYS* 1.3 76.1 - - - +
150D LEU* 1.3 68.4 + - + +
151D GLU* 3.3 0.4 - - - +
223D LYS* 3.6 21.3 + - - +
250D LYS* 3.7 43.0 + - + +
251D HIS* 3.4 35.9 - - + -
277D ALA* 4.0 12.8 - - + -
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Residues in contact with LEU 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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146D VAL* 2.9 35.0 + - + +
147D ARG* 4.6 0.9 - - - +
149D MET* 1.3 89.9 - - + +
151D GLU* 1.3 72.5 + - - +
152D ILE* 3.3 22.7 + - + +
157D ILE* 4.0 27.8 - - + -
186D ASP* 4.8 5.4 - - + +
187D TYR* 5.8 0.4 - - + -
223D LYS* 3.5 28.3 + - + +
224D LYS* 4.1 14.1 - - - +
225D THR* 3.8 37.0 - - + -
227D PHE* 6.1 1.3 - - + -
250D LYS* 5.0 0.4 - - - +
251D HIS* 5.1 0.7 - - + -
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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