Contacts of the helix formed by residues 205 - 222 (chain A) in PDB entry 2KSB
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 TYR 205 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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116A VAL* 5.7 1.1 - - + -
120A ILE* 4.4 14.3 - - + +
201A THR* 2.9 14.2 + - - +
204A ILE* 1.4 86.9 - - + +
206A PHE* 1.4 82.2 + + - +
208A PRO* 3.6 1.9 - - - +
209A LEU* 3.1 53.6 + - + +
257A PHE* 3.9 23.4 - + - -
258A ALA* 4.3 10.2 - - - +
261A TRP* 4.3 1.3 - - + -
262A LEU* 3.6 32.9 + - + +
265A HIS* 2.9 61.9 - + + +
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Residues in contact with PHE 206 (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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201A THR* 2.9 50.8 + - + -
202A VAL* 3.4 22.2 - - + +
205A TYR* 1.4 91.1 - + - +
207A LEU* 1.3 66.5 + - - +
209A LEU* 3.0 19.4 + - + +
210A LEU* 3.0 28.1 + - + +
262A LEU* 5.0 10.5 - - + -
265A HIS* 4.4 9.4 - - + -
266A ILE* 5.4 7.6 - - + -
269A LEU* 3.8 19.7 - - + -
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Residues in contact with LEU 207 (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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121A TYR* 5.7 1.6 - - + +
202A VAL* 2.7 18.6 + - + +
203A LEU* 3.6 12.6 - - - +
206A PHE* 1.3 71.7 - - - +
208A PRO* 1.3 82.2 - - + +
210A LEU* 3.0 30.9 + - + +
211A VAL* 3.0 20.9 + - + +
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Residues in contact with PRO 208 (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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120A ILE* 3.4 23.3 - - + -
121A TYR* 3.2 30.1 - - + +
124A THR* 3.6 10.1 - - + -
203A LEU 2.9 16.4 - - - +
204A ILE 2.8 22.2 - - - +
205A TYR 3.7 1.3 - - - +
207A LEU* 1.3 100.9 - - + +
209A LEU* 1.3 56.5 + - - +
211A VAL* 2.8 28.3 - - + +
212A ILE* 2.9 15.2 - - - +
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Residues in contact with LEU 209 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
120A ILE* 3.9 9.4 - - + +
205A TYR* 3.1 51.3 + - + +
206A PHE* 3.0 17.5 + - + +
208A PRO* 1.3 77.2 - - - +
210A LEU* 1.3 64.7 + - + +
212A ILE* 3.3 7.1 + - + +
213A GLY* 2.9 27.1 + - - +
254A VAL* 6.2 3.6 - - + -
257A PHE* 6.5 0.4 - - + -
258A ALA* 5.3 10.8 - - + -
262A LEU* 4.6 8.5 - - + -
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Residues in contact with LEU 210 (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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206A PHE* 3.0 28.8 + - + +
207A LEU* 3.0 22.4 + - + +
209A LEU* 1.3 83.2 - - + +
211A VAL* 1.3 51.4 + - - +
213A GLY* 3.0 3.7 + - - -
214A TYR* 2.6 36.4 + - - +
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Residues in contact with VAL 211 (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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124A THR* 3.6 20.0 - - + +
128A PHE* 6.3 3.1 - - + -
207A LEU* 3.0 17.3 + - + +
208A PRO* 2.8 38.1 - - + +
210A LEU* 1.3 74.1 - - - +
212A ILE* 1.3 58.4 + - - +
214A TYR* 3.0 12.1 + - + +
215A ALA* 2.7 39.7 + - + +
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Residues in contact with ILE 212 (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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120A ILE* 3.0 41.5 - - + +
123A MET* 3.8 10.5 - - + +
124A THR* 3.0 28.9 - - + +
127A ALA* 4.2 20.2 - - + +
208A PRO 2.9 13.8 + - - +
209A LEU* 3.6 8.7 - - + +
210A LEU 3.2 0.2 - - - -
211A VAL* 1.3 80.5 - - - +
213A GLY* 1.3 60.7 + - - +
215A ALA* 3.4 1.7 + - - +
216A TYR* 2.9 29.6 + - + +
254A VAL* 4.1 35.0 - - + -
257A PHE* 6.2 1.3 - - + -
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Residues in contact with GLY 213 (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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209A LEU* 2.9 19.0 + - - +
210A LEU* 3.4 4.5 - - - -
212A ILE* 1.3 80.0 - - - +
214A TYR* 1.3 60.4 + - - +
216A TYR* 3.2 11.6 - - - +
217A THR* 3.0 19.2 + - - -
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Residues in contact with TYR 214 (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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210A LEU 2.6 16.9 + - - +
211A VAL* 3.5 14.8 - - + +
213A GLY* 1.3 70.3 - - - +
215A ALA* 1.3 66.1 + - + +
217A THR* 2.7 51.5 + - + +
218A VAL* 3.1 14.1 + - + +
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Residues in contact with ALA 215 (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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127A ALA* 3.8 34.3 - - + +
128A PHE* 4.6 8.1 - - + +
131A TYR* 5.0 2.9 - - + -
211A VAL* 2.7 24.5 + - + +
214A TYR* 1.3 79.6 - - + +
216A TYR* 1.3 61.6 + - - +
218A VAL* 2.7 34.1 - - + +
219A VAL* 3.2 9.8 - - - +
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Residues in contact with TYR 216 (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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127A ALA* 5.2 1.5 - - - +
212A ILE* 2.9 18.0 + - + +
213A GLY* 3.2 14.4 - - - +
215A ALA* 1.3 78.0 - - - +
217A THR* 1.3 68.3 + - - +
219A VAL* 3.1 23.9 + - + +
220A GLY* 3.2 14.8 + - - -
224A TRP* 4.8 15.8 + + - -
247A VAL* 6.0 0.9 - - + -
251A ILE* 3.5 48.8 - - + +
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Residues in contact with THR 217 (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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213A GLY 3.0 10.3 + - - -
214A TYR* 2.7 48.2 + - + +
216A TYR* 1.3 84.7 - - - +
218A VAL* 1.3 59.2 + - - +
220A GLY* 2.8 20.7 + - - -
221A ILE* 3.8 5.9 + - - +
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Residues in contact with VAL 218 (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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131A TYR* 2.9 52.5 - - + +
135A ILE* 5.5 0.4 - - + -
214A TYR* 3.1 17.0 + - + +
215A ALA* 2.7 31.4 - - - +
217A THR* 1.3 86.2 - - + +
219A VAL* 1.3 62.1 + - + +
220A GLY 3.1 1.0 + - - -
221A ILE* 3.2 22.1 + - + +
222A THR* 3.8 7.0 + - + +
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Residues in contact with VAL 219 (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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127A ALA 5.0 1.6 - - - +
130A ARG* 4.7 6.7 - - + -
131A TYR* 4.2 17.3 - - + +
134A ILE* 3.0 32.1 - - + -
215A ALA 3.2 17.5 - - - +
216A TYR* 3.1 18.3 + - + +
218A VAL* 1.3 87.0 - - + +
220A GLY* 1.3 57.6 + - - +
221A ILE 3.3 0.2 - - - -
222A THR* 2.8 15.3 + - - -
223A LEU 2.7 36.1 - - - +
247A VAL* 4.2 19.3 - - + -
251A ILE* 6.3 0.2 - - + -
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Residues in contact with GLY 220 (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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216A TYR* 3.2 14.8 + - - -
217A THR* 2.8 14.0 + - - -
219A VAL* 1.3 74.4 - - - +
221A ILE* 1.3 67.9 + - - +
222A THR 3.4 6.4 - - - +
223A LEU 4.6 1.6 - - - -
224A TRP* 4.2 24.0 - - - +
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Residues in contact with ILE 221 (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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217A THR 3.8 5.5 + - - +
218A VAL* 3.2 14.1 + - + +
220A GLY* 1.3 76.5 - - - +
222A THR* 1.3 71.3 + - + +
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Residues in contact with THR 222 (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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131A TYR* 5.8 1.1 - - + -
134A ILE* 2.9 39.0 - - + +
135A ILE* 4.6 15.3 - - + -
218A VAL* 4.3 8.3 - - + +
219A VAL* 2.8 21.8 + - - -
220A GLY 3.4 4.0 - - - +
221A ILE* 1.3 93.1 - - + +
223A LEU* 1.3 71.4 + - - -
224A TRP* 3.1 5.2 + - - +
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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