Contacts of the helix formed by residues 250 - 262 (chain A) in PDB entry 3KXG
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 GLY 250 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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246A ALA 2.8 24.2 + - - -
248A VAL 3.2 3.4 + - - -
249A LEU* 1.3 75.8 - - - +
251A THR* 1.3 62.0 + - - -
252A ASP 3.5 3.1 + - - -
253A GLY 3.9 1.4 + - - -
254A LEU 3.8 0.5 + - - -
276A HIS 3.3 13.2 - - - -
277A SER 3.8 13.2 + - - -
278A ARG* 3.8 1.8 - - - +
307A TYR* 2.7 28.7 + - - -
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Residues in contact with THR 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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246A ALA* 4.2 4.7 - - + -
250A GLY* 1.3 72.4 - - - -
252A ASP* 1.3 63.7 + - - +
253A GLY 3.3 0.2 - - - -
254A LEU* 3.1 8.6 + - + +
255A ASN* 2.8 42.3 + - - +
273A VAL* 3.7 21.8 - - + -
274A GLY 3.5 23.8 - - - +
275A ARG* 3.6 10.8 - - - +
276A HIS* 2.9 42.3 + - + +
307A TYR* 4.7 0.2 - - - -
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Residues in contact with ASP 252 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
250A GLY 3.5 0.6 - - - -
251A THR* 1.3 81.8 + - - +
253A GLY* 1.3 52.5 + - - +
255A ASN* 3.2 9.9 + - - +
256A VAL* 2.7 39.6 + - + +
275A ARG* 5.3 7.3 + - - +
276A HIS 4.5 2.2 + - - -
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Residues in contact with GLY 253 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
249A LEU 5.1 3.0 + - - -
250A GLY 3.9 3.4 + - - -
251A THR 3.3 0.4 - - - -
252A ASP* 1.3 76.5 - - - +
254A LEU* 1.3 60.6 + - - +
256A VAL* 3.6 11.9 + - - +
257A TYR* 3.1 23.6 + - - +
307A TYR* 3.5 19.1 - - - +
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Residues in contact with LEU 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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200A PRO* 5.7 0.2 - - + -
204A VAL* 4.7 5.8 - - + -
242A LEU* 4.6 17.3 - - + -
246A ALA* 4.5 10.1 - - + -
251A THR* 3.1 13.1 + - + +
253A GLY* 1.3 76.2 - - - +
255A ASN* 1.3 62.8 + - - +
257A TYR* 3.3 12.1 + - + +
258A LEU* 2.9 54.7 + - + +
265A LEU* 4.8 7.6 - - + -
273A VAL* 3.8 34.3 - - + -
307A TYR* 3.4 41.6 - - + +
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Residues in contact with ASN 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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251A THR* 2.8 29.7 + - - +
252A ASP* 3.6 9.6 - - - +
254A LEU* 1.3 79.4 - - - +
256A VAL* 1.3 63.3 + - - +
258A LEU* 3.4 17.6 + - - +
259A ASN* 2.8 38.3 + - - +
265A LEU* 6.0 1.2 - - - +
275A ARG* 5.3 7.4 + - - -
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Residues in contact with VAL 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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252A ASP* 2.7 29.1 + - + +
253A GLY* 3.6 15.5 - - - +
255A ASN* 1.3 74.5 - - - +
257A TYR* 1.3 63.2 + - - +
259A ASN* 3.4 4.9 + - - +
260A LYS* 3.0 27.9 + - + +
311A GLU* 6.1 0.7 - - - +
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Residues in contact with TYR 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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200A PRO* 4.1 11.4 - - + -
201A GLU* 3.5 25.6 + - - +
204A VAL* 4.0 21.9 - - + +
206A LEU* 4.2 5.8 - - + +
253A GLY 3.1 15.3 + - - +
254A LEU* 3.4 21.5 - - + +
256A VAL* 1.3 77.5 - - - +
258A LEU* 1.3 67.5 + - + +
260A LYS* 3.2 16.8 + - - +
261A TYR* 3.2 49.5 + + - +
263A ILE* 5.1 1.6 - - + -
307A TYR* 3.4 36.7 + + + -
308A ASP* 3.6 22.7 - - + +
309A HIS* 3.5 17.4 + - - -
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Residues in contact with LEU 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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204A VAL* 4.3 16.2 - - + -
254A LEU* 2.9 35.0 + - + +
255A ASN* 3.4 19.0 + - - +
257A TYR* 1.3 80.4 - - + +
259A ASN* 1.3 62.0 + - - +
261A TYR 3.4 0.5 + - - -
262A ARG 2.9 8.3 + - - -
263A ILE* 2.9 68.4 + - + +
265A LEU* 3.9 39.9 - - + +
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Residues in contact with ASN 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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255A ASN* 2.8 32.5 + - - +
256A VAL* 4.1 4.9 - - - +
258A LEU* 1.3 75.5 - - - +
260A LYS* 1.3 66.0 + - - +
262A ARG* 3.2 20.8 + - - +
263A ILE 5.1 2.9 - - - +
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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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256A VAL* 3.0 18.6 + - + +
257A TYR* 3.2 11.4 + - - +
259A ASN* 1.3 79.1 - - - +
261A TYR* 1.3 84.4 + - + +
262A ARG* 3.5 17.0 + - - -
308A ASP* 2.8 30.2 + - - +
310A GLN* 4.1 14.6 - - - +
311A GLU* 5.3 4.4 + - - +
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Residues in contact with TYR 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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7A SER* 4.1 13.0 - - - -
206A LEU* 3.7 16.6 - - + -
257A TYR* 3.2 44.3 + + - +
260A LYS* 1.3 97.3 - - + +
262A ARG* 1.3 81.9 + - - +
263A ILE* 3.3 27.7 + - + +
308A ASP* 2.8 33.8 + - - -
309A HIS* 3.6 11.8 - + - -
310A GLN* 3.0 34.8 - - - +
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Residues in contact with ARG 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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258A LEU 2.9 5.9 + - - -
259A ASN* 3.2 15.7 + - - +
260A LYS 3.5 19.8 + - - -
261A TYR* 1.3 87.4 + - - +
263A ILE* 1.3 60.0 + - - +
264A GLU 4.3 0.5 + - - -
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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