Contacts of the helix formed by residues 248 - 259 (chain A) in PDB entry 4UHW
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 THR 248 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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231A GLN* 3.5 49.8 - - + +
246A PRO* 4.2 1.4 - - - +
247A VAL* 1.3 79.7 - - - +
249A LEU* 1.3 64.6 + - - +
250A LYS* 3.5 24.9 - - - +
251A GLU* 3.1 31.0 + - + +
252A LEU* 3.1 19.6 + - - +
291A ILE* 3.4 12.7 - - - +
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Residues in contact with LEU 249 (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 THR* 1.3 72.4 - - - +
250A LYS* 1.3 70.1 + - + +
252A LEU* 3.2 10.9 + - + +
253A LEU* 3.2 30.0 + - + +
291A ILE* 3.8 25.2 - - + +
293A GLU* 3.8 37.4 + - + +
294A LEU* 4.6 6.3 - - + -
382A LEU* 3.8 31.9 - - + -
410A ILE* 4.5 15.3 - - + -
412A VAL* 5.5 1.1 - - + -
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Residues in contact with LYS 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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231A GLN* 4.0 18.6 + - - -
248A THR* 3.4 24.9 + - - +
249A LEU* 1.3 79.2 - - + +
251A GLU* 1.3 65.6 + - + +
253A LEU* 3.4 9.3 + - - +
254A GLU* 3.1 20.6 + - - +
384A LYS* 6.1 0.2 - - - +
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Residues in contact with GLU 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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231A GLN 4.6 2.7 - - - +
233A THR* 3.0 43.6 + - + +
246A PRO* 3.8 6.3 - - + -
248A THR* 3.1 25.5 + - + +
250A LYS* 1.3 80.7 - - + +
252A LEU* 1.3 60.2 + - - +
254A GLU* 3.0 14.6 + - - +
255A PHE* 2.8 42.0 + - + -
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Residues in contact with LEU 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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246A PRO* 3.6 16.3 - - + +
248A THR 3.1 12.1 + - - +
249A LEU* 3.2 13.9 + - + +
251A GLU* 1.3 78.0 - - - +
253A LEU* 1.3 56.5 + - - +
255A PHE* 3.3 2.3 + - - +
256A LYS* 2.9 27.1 + - + +
264A VAL* 4.5 11.9 - - + -
286A ILE* 3.8 24.7 - - + -
288A PRO* 4.2 17.3 - - + -
291A ILE* 4.6 4.7 - - + -
294A LEU* 4.0 30.1 - - + -
410A ILE* 4.3 31.9 - - + -
3006A FAD 6.2 0.7 - - - +
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Residues in contact with LEU 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 LEU* 3.2 21.0 + - + +
250A LYS* 3.8 9.2 - - - +
252A LEU* 1.3 75.3 - - - +
254A GLU* 1.3 64.0 + - - +
256A LYS* 3.9 5.3 - - + +
257A PHE* 3.1 24.1 + - - +
382A LEU* 3.3 46.7 - - + +
383A SER* 3.4 22.7 - - - +
384A LYS* 4.3 22.0 - - + +
408A GLN 4.9 4.3 - - - +
410A ILE* 3.6 25.6 - - + +
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Residues in contact with GLU 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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250A LYS 3.1 13.7 + - - +
251A GLU* 3.0 20.3 + - - +
253A LEU* 1.3 76.4 - - - +
255A PHE* 1.3 62.5 + - + +
257A PHE* 3.4 6.9 + - - +
258A LYS* 3.3 51.4 + - - +
384A LYS* 2.7 41.5 + - - +
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Residues in contact with PHE 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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233A THR* 3.6 29.8 - - + -
235A VAL* 5.5 2.0 - - + -
244A PHE* 3.3 51.4 - + + -
246A PRO* 4.1 11.4 - - + -
251A GLU* 2.8 44.8 + - - +
252A LEU 3.8 3.8 - - - +
254A GLU* 1.3 72.3 - - + +
256A LYS* 1.3 65.2 + - - +
258A LYS* 3.3 21.9 + - - +
259A TYR* 3.0 39.8 + + - -
286A ILE* 3.6 28.1 - - + +
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Residues in contact with LYS 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 LEU* 2.9 19.1 + - + +
253A LEU* 3.9 7.6 - - + +
254A GLU 3.4 0.2 - - - -
255A PHE* 1.3 75.8 - - - +
257A PHE* 1.3 61.4 + - - +
259A TYR 4.6 0.9 - - - +
260A PRO* 3.0 44.3 + - - +
262A ALA 3.4 16.1 + - - +
263A PRO* 5.5 0.2 - - - +
264A VAL* 4.0 17.6 - - + +
286A ILE* 4.0 7.3 - - + +
407A PRO 3.5 9.4 + - - -
408A GLN* 3.6 25.5 - - - +
409A GLU 3.4 19.5 - - - -
410A ILE* 3.6 26.0 - - + -
3006A FAD 5.0 7.4 + - - -
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Residues in contact with PHE 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 LEU 3.1 17.6 + - - +
254A GLU* 3.6 9.6 - - - +
255A PHE 3.2 0.6 - - - -
256A LYS* 1.3 75.4 - - - +
258A LYS* 1.3 72.4 + - + +
259A TYR 3.5 0.3 + - - -
260A PRO* 3.5 13.7 - - - +
383A SER* 5.8 0.2 - - - -
384A LYS* 4.5 24.5 - - + -
385A GLU* 4.0 21.1 - - - -
408A GLN* 4.0 33.7 + - + +
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Residues in contact with LYS 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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254A GLU* 3.3 43.3 + - - +
255A PHE* 3.3 23.1 + - + -
257A PHE* 1.3 84.0 - - + +
259A TYR* 1.3 93.7 + - + +
260A PRO* 3.2 7.8 - - - +
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Residues in contact with TYR 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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242A MET* 5.3 3.3 - - + +
244A PHE* 3.7 33.3 - + - -
255A PHE* 3.0 28.6 + + + +
256A LYS* 3.8 5.2 - - - +
258A LYS* 1.3 111.0 + - + +
260A PRO* 1.4 66.2 - - - +
261A GLN 3.2 2.5 - - - -
262A ALA* 3.0 32.1 + - + +
284A VAL* 3.7 31.2 - - + -
286A ILE* 4.2 4.6 - - + +
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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