Contacts of the helix formed by residues 254 - 264 (chain A) in PDB entry 4E52
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 PHE 254 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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253A PRO* 1.3 69.9 - - - +
255A THR* 1.3 66.1 + - - +
257A ALA* 3.1 3.0 + - - +
258A GLN* 2.8 66.0 + - - +
268A LEU* 3.4 24.2 - - + -
292A PHE* 3.3 25.6 - + + -
293A LEU 3.6 15.3 - - - -
294A SER 3.8 7.0 - - - -
295A MET 5.0 0.2 - - - -
296A THR* 3.5 26.9 - - + -
331A CYS* 3.3 30.1 - - + -
345A CYS* 3.1 26.7 + - + +
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Residues in contact with THR 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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253A PRO* 3.5 3.2 - - - +
254A PHE* 1.3 88.7 - - - +
256A GLU* 1.3 62.6 + - + +
258A GLN* 3.5 10.6 + - - +
259A LEU* 3.0 29.8 + - + +
345A CYS* 4.8 2.0 + - - +
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Residues in contact with GLU 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 LYS* 3.8 24.6 + - + +
253A PRO* 3.2 39.4 + - + +
254A PHE 3.2 0.6 - - - -
255A THR* 1.3 77.4 - - + +
257A ALA* 1.3 64.7 + - - +
259A LEU* 3.4 9.4 + - + +
260A LEU* 3.0 29.7 + - + +
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Residues in contact with ALA 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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252A LYS* 4.2 5.5 - - + +
253A PRO 2.9 17.3 + - - +
254A PHE* 3.5 7.9 - - - +
256A GLU* 1.3 76.0 - - - +
258A GLN* 1.3 62.6 + - - +
260A LEU* 3.2 7.0 + - - +
261A CYS* 3.1 25.8 + - - -
268A LEU* 4.0 18.2 - - + -
292A PHE* 4.7 7.0 - - + -
351A VAL* 3.9 31.0 - - + +
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Residues in contact with GLN 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 PHE* 2.8 49.5 + - + +
255A THR* 3.7 10.8 + - - +
257A ALA* 1.3 75.0 - - - +
259A LEU* 1.3 55.0 + - - +
261A CYS* 3.3 2.8 + - - +
262A THR* 3.0 45.3 + - + +
268A LEU* 3.7 23.2 - - + +
294A SER* 4.8 5.3 + - - +
296A THR* 5.6 0.6 - - - +
307A PRO* 5.0 13.1 - - - +
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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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255A THR* 3.0 20.1 + - + +
256A GLU* 3.7 8.3 - - + +
257A ALA 3.2 0.2 - - - -
258A GLN* 1.3 74.0 - - - +
260A LEU* 1.3 61.2 + - + +
262A THR* 3.5 9.6 - - - +
263A GLN* 2.9 67.9 + - + +
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Residues in contact with LEU 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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250A PHE* 3.7 35.7 - - + -
252A LYS* 4.3 15.5 - - + -
256A GLU* 3.0 19.5 + - + +
257A ALA 3.2 6.5 + - - +
259A LEU* 1.3 77.2 - - - +
261A CYS* 1.3 62.5 + - - +
263A GLN* 4.0 14.4 - - - +
264A ALA* 3.2 23.4 + - - +
351A VAL* 4.4 11.7 - - + -
234C PHE* 4.2 18.1 - - + -
235C PRO* 6.1 2.7 - - + -
286C ALA* 6.0 6.1 - - + -
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Residues in contact with CYS 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 ALA 3.1 7.5 + - - -
258A GLN 3.8 5.4 - - - +
260A LEU* 1.3 78.1 - - - +
262A THR* 1.3 64.1 + - - +
264A ALA* 3.1 9.9 + - - +
265A GLY 3.2 0.2 + - - -
266A GLY* 2.9 25.0 + - - -
267A GLN* 3.5 21.3 - - - -
268A LEU* 3.6 29.2 - - - +
351A VAL* 4.3 2.5 - - - -
352A VAL 4.2 0.4 - - - -
353A CYS* 2.0 56.8 - - + -
355A PHE* 4.8 0.2 - - - -
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Residues in contact with THR 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 GLN* 3.0 27.3 + - + +
259A LEU* 3.0 23.2 + - - +
261A CYS* 1.3 75.8 - - - +
263A GLN* 1.3 60.8 + - - +
265A GLY* 3.0 19.6 + - - -
266A GLY 3.5 13.4 - - - +
267A GLN* 5.1 7.4 - - + -
268A LEU 6.0 0.2 - - - +
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Residues in contact with GLN 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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259A LEU* 2.9 59.0 + - + +
260A LEU* 4.0 15.2 - - - +
262A THR* 1.3 77.9 + - - +
264A ALA* 1.3 59.0 + - - +
265A GLY 3.2 0.7 + - - -
282C GLN* 5.5 6.9 + - - +
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Residues in contact with ALA 264 (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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260A LEU 3.2 17.6 + - - +
261A CYS* 3.1 6.4 + - - +
262A THR 3.1 1.0 - - - -
263A GLN* 1.3 76.7 - - - +
265A GLY* 1.3 59.1 + - - +
266A GLY 3.4 0.2 - - - -
355A PHE* 3.5 19.7 - - + -
230C LYS* 3.8 17.0 - - - +
234C PHE* 3.7 29.2 - - + -
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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