Contacts of the helix formed by residues 251 - 260 (chain A) in PDB entry 5PAH
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 SER 251 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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249A LEU 3.7 1.0 + - - -
250A SER* 1.3 72.7 - - - +
252A ARG* 1.3 57.7 + - - +
254A PHE* 4.4 5.8 - - - -
255A LEU* 2.9 38.9 + - - +
318A ILE* 3.6 20.2 - - - -
319A GLU* 5.9 0.4 - - - -
322A ALA* 3.8 23.7 - - - +
600A LDP 4.6 14.1 + - - -
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Residues in contact with ARG 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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119A PRO* 3.5 26.9 - - - +
120A TRP 4.4 15.2 + - - +
121A PHE* 6.4 1.3 - - + -
250A SER* 3.1 8.9 - - - +
251A SER* 1.3 80.2 - - - +
253A ASP* 1.3 64.0 + - - +
255A LEU* 4.2 0.9 - - - +
256A GLY* 2.9 25.5 + - - -
310A SER* 4.1 6.1 + - - +
312A GLY* 4.3 4.0 - - - +
313A ALA 2.8 35.9 + - - +
315A ASP* 2.6 38.8 + - - +
318A ILE* 3.6 37.2 - - + +
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Residues in contact with ASP 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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120A TRP* 5.4 2.6 - - - -
131A PHE* 3.0 64.0 - - + +
134A GLN* 2.8 33.7 - - - +
249A LEU* 4.3 11.2 - - + +
250A SER* 3.1 22.4 + - - +
252A ARG* 1.3 81.9 - - - +
254A PHE* 1.3 68.3 + - - +
256A GLY 3.3 0.3 + - - -
257A GLY* 3.2 8.8 + - - -
264A HIS* 4.6 0.7 - - - -
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Residues in contact with PHE 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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249A LEU* 4.0 28.2 - - + +
250A SER 2.9 17.5 + - - +
251A SER* 3.8 6.5 - - - +
253A ASP* 1.3 79.8 - - - +
255A LEU* 1.3 74.8 + - + +
257A GLY* 3.3 8.1 + - - -
258A LEU* 3.8 14.1 + - + +
262A VAL 5.1 0.7 - - - +
263A PHE* 3.5 20.6 - + - -
264A HIS* 3.5 32.8 + - + -
325A TYR* 3.4 42.8 - + - -
600A LDP 4.0 28.7 - + - +
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Residues in contact with LEU 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 SER* 2.9 24.1 + - - +
252A ARG 4.3 0.7 - - - +
254A PHE* 1.3 83.4 - - + +
256A GLY* 1.4 66.3 + - - +
258A LEU* 3.0 21.6 + - + +
306A ILE* 4.2 9.0 - - + -
307A GLY* 3.2 20.5 - - - -
310A SER* 3.8 20.9 - - - +
318A ILE* 4.3 8.5 - - + +
321A LEU* 3.9 29.4 - - + +
322A ALA* 3.9 18.6 - - + +
325A TYR* 3.8 32.8 - - + -
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Residues in contact with GLY 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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122A PRO* 5.4 2.0 - - - -
128A LEU* 4.9 3.1 - - - -
131A PHE* 5.0 4.3 - - - -
252A ARG 2.9 19.5 + - - -
253A ASP* 3.3 2.4 + - - -
254A PHE 3.3 0.4 - - - -
255A LEU* 1.4 76.6 - - - +
257A GLY* 1.3 62.1 + - - +
259A ALA* 3.1 19.4 + - - +
260A PHE* 3.4 12.0 - - - -
307A GLY 4.5 0.4 - - - -
310A SER* 3.6 11.1 + - - -
311A LEU* 4.1 13.9 - - - -
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Residues in contact with GLY 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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128A LEU* 4.2 22.4 - - - -
131A PHE* 4.3 1.0 - - - -
253A ASP 3.2 12.5 + - - -
254A PHE 3.3 4.9 + - - -
255A LEU 3.2 1.4 - - - -
256A GLY* 1.3 75.9 - - - +
258A LEU* 1.3 62.6 + - - +
260A PHE* 3.0 13.7 + - - +
262A VAL* 3.1 29.8 + - - +
264A HIS* 4.5 7.4 - - - -
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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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240A PHE* 4.3 19.5 - - + -
254A PHE* 3.8 12.0 + - + +
255A LEU* 3.0 28.3 + - + +
257A GLY* 1.3 76.0 - - - +
259A ALA* 1.3 63.0 + - - +
261A ARG* 2.9 15.0 + - - +
262A VAL 3.5 14.7 + - - +
263A PHE* 4.3 18.8 - - + -
294A PHE* 4.5 7.4 - - + -
303A SER* 3.7 30.1 - - - +
304A GLN* 3.5 15.1 - - - -
306A ILE* 4.8 2.5 - - + -
307A GLY* 4.0 4.5 - - - +
325A TYR* 4.1 26.2 - - + -
329A VAL* 5.9 0.2 - - + -
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Residues in contact with ALA 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 LEU 3.7 2.4 + - - -
256A GLY 3.1 14.3 + - - +
258A LEU* 1.3 78.0 - - - +
260A PHE* 1.3 63.1 + - + +
261A ARG 3.4 0.2 - - - -
304A GLN* 2.9 36.1 + - - +
307A GLY* 3.7 21.2 - - - +
308A LEU* 3.9 8.6 - - + +
311A LEU* 3.9 21.8 - - + -
414A TYR* 3.9 11.0 - - - +
421A ILE* 4.5 1.3 - - + -
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Residues in contact with PHE 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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122A PRO* 3.5 39.0 - - + -
123A ARG 4.2 0.7 - - - -
124A THR* 3.4 30.3 - - - -
125A ILE* 3.6 29.0 - - + +
128A LEU* 4.2 9.6 - - + -
239A GLY 5.1 0.5 - - - +
241A ARG* 5.4 1.0 + - - -
256A GLY 3.4 20.0 - - - -
257A GLY 3.0 8.2 + - - +
259A ALA* 1.3 85.0 - - + +
261A ARG* 1.3 70.9 + - - +
262A VAL* 3.7 17.2 - - + +
311A LEU* 4.9 2.5 - - + -
414A TYR* 3.6 34.4 + + - +
419A GLN 4.3 0.7 - - - -
421A ILE* 3.5 22.0 - - + -
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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