Contacts of the helix formed by residues 249 - 262 (chain A) in PDB entry 4KM9
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 PRO 249 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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245A PHE* 3.6 13.2 - - + +
246A GLU* 5.0 3.4 - - - +
247A ILE 4.4 3.4 - - - +
248A ASP* 1.3 84.7 - - - +
250A HIS* 1.3 65.8 - - + +
251A LEU 3.0 5.6 - - - -
252A GLN* 3.0 26.0 + - + +
253A GLU* 3.9 1.7 + - - +
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Residues in contact with HIS 250 (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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248A ASP* 2.7 25.8 + - - +
249A PRO* 1.3 77.2 - - + +
251A LEU* 1.3 58.9 + - + -
252A GLN 3.4 0.2 - - - -
253A GLU* 3.3 23.4 + - + +
254A ARG* 3.5 7.8 + - - +
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Residues in contact with LEU 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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222A LEU* 4.3 24.3 - - + +
225A THR* 4.2 17.5 - - + +
226A VAL* 3.7 22.4 - - + -
244A ILE* 3.3 40.4 - - + +
245A PHE* 4.1 11.4 - - + -
248A ASP* 3.6 21.1 - - + +
249A PRO 3.0 0.8 - - - -
250A HIS* 1.3 75.8 - - + +
252A GLN* 1.3 65.8 + - - +
253A GLU 3.0 1.8 - - - -
254A ARG* 2.9 24.4 + - + +
255A VAL* 3.2 15.3 + - - +
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Residues in contact with GLN 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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210A SER* 5.9 0.8 + - - -
245A PHE* 3.9 37.0 - - + +
249A PRO* 3.0 16.4 + - + +
251A LEU* 1.3 77.5 - - - +
253A GLU* 1.3 54.9 + - - +
255A VAL* 3.5 15.5 + - - +
256A ASP* 2.7 38.1 + - - +
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Residues in contact with GLU 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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249A PRO 3.9 1.0 + - - +
250A HIS* 3.3 19.3 + - + +
251A LEU 3.0 0.6 - - - -
252A GLN* 1.3 78.7 - - - +
254A ARG* 1.3 61.0 + - - +
255A VAL 3.4 0.5 + - - -
256A ASP* 3.7 7.5 + - - +
257A LYS* 3.6 19.6 + - - +
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Residues in contact with ARG 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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214A TRP* 4.2 11.5 - - + -
221A GLU* 4.3 12.1 + - - +
222A LEU* 3.4 33.1 - - + +
225A THR* 4.1 22.0 + - - +
250A HIS 3.5 7.9 + - - +
251A LEU* 2.9 18.9 + - - +
253A GLU* 1.3 76.5 - - - +
255A VAL* 1.3 65.1 + - - +
257A LYS* 4.0 8.1 + - + +
258A GLY 3.5 11.1 + - - -
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Residues in contact with VAL 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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210A SER* 5.1 8.5 - - - +
213A GLN* 6.0 1.3 - - - +
214A TRP* 3.9 22.2 - - + -
219A ILE* 4.2 10.3 - - + -
222A LEU* 3.7 21.3 - - + -
245A PHE* 4.1 16.4 - - + -
251A LEU 3.4 14.4 - - - +
252A GLN* 3.6 15.9 - - - +
253A GLU 3.2 0.4 - - - -
254A ARG* 1.3 76.2 - - - +
256A ASP* 1.3 68.9 + - - +
258A GLY* 2.9 4.9 + - - -
259A ILE* 2.9 39.7 + - + +
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Residues in contact with ASP 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 GLN* 2.7 30.3 + - - +
253A GLU* 3.7 7.6 + - - +
254A ARG 3.6 0.4 - - - -
255A VAL* 1.3 76.2 - - - +
257A LYS* 1.3 59.2 + - - +
259A ILE* 3.0 15.4 + - - +
260A GLU* 2.7 30.6 + - - +
386A ARG* 4.5 20.9 + - - +
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Residues in contact with LYS 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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253A GLU 3.6 14.6 + - - +
254A ARG* 4.1 9.0 - - + +
255A VAL 3.2 0.4 - - - -
256A ASP* 1.3 78.9 - - - +
258A GLY* 1.3 52.7 + - - +
260A GLU* 3.1 39.4 + - - +
261A THR* 2.6 47.3 + - - +
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Residues in contact with GLY 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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214A TRP* 3.5 27.1 - - - -
254A ARG 3.5 5.2 + - - -
255A VAL 2.9 7.4 + - - -
257A LYS* 1.3 76.4 - - - +
259A ILE* 1.3 58.1 + - - +
260A GLU 3.1 1.6 - - - -
261A THR* 2.9 7.1 + - - -
262A ASP* 2.5 38.8 + - - +
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Residues in contact with ILE 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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213A GLN* 3.9 27.1 - - + +
214A TRP* 3.6 19.5 - - + -
255A VAL* 2.9 33.4 + - + +
256A ASP* 3.5 14.6 - - - +
258A GLY* 1.3 75.0 - - - +
260A GLU* 1.3 57.7 + - - +
263A GLY* 3.1 31.1 - - - +
264A SER* 4.3 7.4 - - - -
383A LEU* 4.4 19.7 - - + -
386A ARG* 5.1 2.7 - - + -
387A GLY* 3.7 26.2 - - - +
391A HIS* 3.6 3.1 + - - -
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Residues in contact with GLU 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 ASP 2.7 11.3 + - - +
257A LYS* 3.1 43.6 + - - +
259A ILE* 1.3 78.0 - - - +
261A THR* 1.3 58.0 + - - +
386A ARG* 4.7 30.1 - - + +
391A HIS* 2.8 22.0 + - - -
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Residues in contact with THR 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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257A LYS* 2.6 41.9 + - - +
258A GLY* 2.9 6.3 + - - -
260A GLU* 1.3 76.8 - - - +
262A ASP* 1.3 71.3 + - - +
391A HIS* 3.1 15.2 - - - -
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Residues in contact with ASP 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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214A TRP* 2.7 32.0 + - - +
215A ASN* 2.9 23.6 + - - +
258A GLY* 2.5 16.2 + - - +
261A THR* 1.3 90.9 - - - +
263A GLY* 1.3 59.1 + - - +
391A HIS* 3.7 5.3 + - - -
393A ARG* 3.2 19.6 + - - -
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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