Contacts of the helix formed by residues 250 - 263 (chain A) in PDB entry 1X6N
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 LYS 250 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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45A GLN* 4.0 13.3 + - - +
234A ALA 3.3 7.8 - - - +
235A LEU* 2.9 21.7 + - - +
236A GLN 3.6 17.1 + - - +
237A LYS 3.5 6.5 - - - +
238A ALA* 4.4 10.6 - - + +
242A VAL* 3.6 26.0 - - - +
243A THR 4.7 2.0 + - - -
244A ALA 3.0 27.6 + - - +
245A TRP* 3.3 21.8 + - - +
247A ASP* 3.5 23.8 - - + +
249A TYR* 1.3 77.4 - - - +
251A GLY* 1.3 66.1 + - - +
253A PHE* 4.4 0.2 - - - +
254A GLY* 2.9 22.6 + - - -
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Residues in contact with GLY 251 (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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233A ALA 3.4 12.8 - - - -
234A ALA 3.8 4.5 - - - -
235A LEU 3.9 0.4 - - - -
237A LYS* 2.7 32.4 + - - -
239A GLN* 4.0 11.4 - - - +
242A VAL* 4.2 2.4 - - - +
250A LYS* 1.3 78.5 - - - +
252A ASN* 1.3 63.1 + - - -
255A GLN* 3.2 22.3 + - - +
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Residues in contact with ASN 252 (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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164A PHE* 3.9 12.2 - - - -
166A GLU* 3.5 28.9 + - - +
169A VAL* 3.2 23.1 - - - +
176A VAL* 3.8 14.0 + - + +
189A TYR* 2.9 39.1 + - + +
233A ALA 2.9 18.3 + - - +
234A ALA 3.2 1.7 + - - +
239A GLN* 5.0 2.8 + - - -
251A GLY* 1.3 72.1 - - - -
253A PHE* 1.3 58.6 + - - +
255A GLN* 3.3 5.5 + - - +
256A LEU* 2.8 34.3 + - - +
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Residues in contact with PHE 253 (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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189A TYR* 3.6 35.4 - + - -
192A ILE* 4.6 1.8 - - + -
228A ILE* 3.8 28.7 - - + -
234A ALA* 2.8 30.2 + - + +
235A LEU* 3.8 19.7 - - + -
252A ASN* 1.3 71.2 - - - +
254A GLY* 1.3 65.2 + - - +
256A LEU* 3.2 4.1 + - + +
257A MET* 2.9 33.0 + - + +
300A PHE* 4.2 7.0 - + - -
304A TRP* 3.9 32.8 - + - -
306A PHE* 3.6 27.4 - + + -
307A PHE* 3.8 23.3 - + - -
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Residues in contact with GLY 254 (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 LEU* 3.6 9.7 - - - +
242A VAL* 4.1 8.1 - - - +
249A TYR* 3.6 27.8 - - - -
250A LYS 2.9 20.3 + - - -
251A GLY 3.9 0.4 - - - -
253A PHE* 1.3 77.7 - - - +
255A GLN* 1.3 60.5 + - - +
257A MET* 3.3 8.4 + - - +
258A ALA* 3.2 16.1 + - - +
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Residues in contact with GLN 255 (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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141A LEU* 3.6 10.7 - - + +
175A THR* 3.8 1.7 - - - -
176A VAL* 3.4 41.2 + - + +
177A ASP* 3.0 32.8 + - - +
239A GLN* 3.3 26.0 - - + +
240A LYS 2.8 35.5 + - - +
242A VAL* 4.1 6.0 - - + +
251A GLY 3.2 13.1 + - - +
252A ASN* 3.8 4.6 - - - +
254A GLY* 1.3 74.4 - - - +
256A LEU* 1.3 59.6 + - - +
258A ALA* 3.1 6.4 + - - +
259A LEU* 2.7 28.2 + - - +
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Residues in contact with LEU 256 (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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164A PHE* 5.9 1.8 - - + -
176A VAL* 4.0 20.4 - - + -
179A ILE* 5.1 0.9 - - + -
187A LEU* 3.6 30.7 - - + -
189A TYR* 3.8 34.1 - - + -
252A ASN* 2.8 27.4 + - + +
253A PHE* 3.2 2.9 + - + +
255A GLN* 1.3 72.1 - - - +
257A MET* 1.3 58.1 + - - +
259A LEU* 3.2 8.4 + - + +
260A LYS* 3.0 27.9 + - - +
268A ILE* 3.8 19.0 - - + +
306A PHE* 3.7 34.8 - - + -
307A PHE* 4.7 0.2 - - + -
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Residues in contact with MET 257 (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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132A ASP 4.2 2.0 - - - +
133A THR* 3.4 41.1 - - + +
134A ASP 4.1 0.7 - - - +
135A GLY* 3.7 17.5 - - - -
137A HIS* 4.6 2.0 - - - -
138A LEU* 3.9 3.6 - - + -
249A TYR* 3.4 47.6 - - + -
253A PHE* 2.9 26.0 + - + +
254A GLY* 3.4 8.1 - - - +
256A LEU* 1.3 76.4 - - - +
258A ALA* 1.3 61.5 + - - +
260A LYS* 3.3 5.8 + - - +
261A GLN* 3.2 23.4 + - - +
304A TRP* 4.2 7.9 - - + -
306A PHE* 3.4 30.1 - - + -
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Residues in contact with ALA 258 (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 LEU* 3.9 15.0 - - + +
139A PRO 3.8 16.4 - - - +
141A LEU* 3.0 39.1 + - + -
241A GLY* 6.1 4.0 - - - +
242A VAL* 5.8 2.2 - - + -
254A GLY 3.2 9.0 + - - +
255A GLN* 3.1 9.9 + - - +
257A MET* 1.3 76.4 - - - +
259A LEU* 1.3 64.3 + - - +
261A GLN* 3.2 8.6 + - - +
262A ALA 3.2 9.9 + - - -
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Residues in contact with LEU 259 (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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141A LEU* 3.8 29.6 - - + +
176A VAL* 4.2 18.2 - - + +
179A ILE* 4.9 4.0 - - + +
181A ALA* 3.6 26.9 - - + -
187A LEU* 3.7 31.0 - - + -
255A GLN 2.7 14.4 + - - +
256A LEU* 3.4 13.2 - - + +
257A MET 3.2 0.2 - - - -
258A ALA* 1.3 78.3 - - - +
260A LYS* 1.3 50.7 + - - +
262A ALA* 2.9 5.9 + - - +
263A HIS* 2.8 40.9 + - + +
266A LEU* 3.9 15.5 - - + -
268A ILE* 4.6 2.0 - - + -
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Residues in contact with LYS 260 (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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134A ASP 4.8 6.3 - - - +
256A LEU 3.0 10.2 + - - +
257A MET* 3.3 10.5 + - - +
259A LEU* 1.3 76.3 - - - +
261A GLN* 1.3 65.2 + - - +
263A HIS 3.1 7.4 - - - +
264A PRO* 3.1 50.6 - - - +
266A LEU* 3.4 18.8 - - + +
268A ILE* 3.3 27.6 - - + +
305A LYS 5.1 0.2 + - - -
306A PHE* 3.2 27.4 + - + +
308A ASP* 2.9 34.2 + - - -
355A ARG* 4.8 2.6 - - - +
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Residues in contact with GLN 261 (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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134A ASP* 2.9 27.7 + - - -
135A GLY 3.2 27.2 - - - +
136A SER* 3.6 11.0 - - - +
138A LEU 3.6 17.7 - - - +
140A PRO* 4.0 18.3 - - + +
257A MET 3.2 9.2 + - - +
258A ALA* 3.2 11.4 + - - +
259A LEU 3.1 0.4 - - - -
260A LYS* 1.3 80.0 - - - +
262A ALA* 1.3 61.6 + - - +
264A PRO* 4.1 10.3 - - - +
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Residues in contact with ALA 262 (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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140A PRO* 3.7 12.1 - - + +
141A LEU 3.4 40.2 - - - +
142A LYS* 3.4 26.3 + - + +
258A ALA 3.2 3.0 + - - -
259A LEU 2.9 7.1 + - - +
261A GLN* 1.3 80.2 - - - +
263A HIS* 1.3 70.0 + - + +
264A PRO* 3.6 6.1 - - - +
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Residues in contact with HIS 263 (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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141A LEU 4.8 1.8 + - - -
142A LYS* 4.0 23.4 + - + +
181A ALA* 3.7 30.7 + - + +
182A GLN* 3.9 29.9 + - + +
259A LEU* 2.8 21.9 + - + +
260A LYS* 3.1 13.8 - - - +
262A ALA* 1.3 88.6 + - + +
264A PRO* 1.3 66.5 - - - +
265A ASP 3.2 2.7 - - - -
266A LEU* 3.1 31.3 + - + +
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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