Contacts of the helix formed by residues 253 - 263 (chain A) in PDB entry 5JG8
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 253 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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209A TRP* 3.9 2.9 - - + +
211A HIS* 5.1 1.8 - - - +
213A TYR* 3.6 51.1 - - + +
243A TYR 4.3 1.8 - - - +
244A TRP 4.2 7.9 - - - +
245A GLY* 4.4 0.9 - - - -
251A ASP 3.9 2.0 - - - +
252A LEU* 1.3 90.2 - - + +
254A LEU* 1.3 68.3 + - - +
255A ARG* 2.9 29.8 + - + +
256A THR* 2.9 32.1 + - - +
257A LEU* 3.7 3.3 + - - +
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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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209A TRP* 3.1 48.5 - - + +
253A PRO* 1.3 72.6 - - - +
255A ARG* 1.3 63.3 + - - +
257A LEU* 3.1 18.4 + - + +
258A GLU* 3.0 20.3 + - + +
298A THR* 5.2 7.2 - - - +
299A VAL* 4.7 7.6 - - + -
302A LEU* 3.5 33.2 - - + -
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Residues in contact with ARG 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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213A TYR* 4.5 6.7 + - - -
215A GLU* 3.1 30.7 + - - -
243A TYR* 2.1 82.6 + - - +
244A TRP* 3.8 17.3 - - + -
253A PRO* 2.9 22.8 + - + +
254A LEU* 1.3 79.0 - - - +
256A THR* 1.3 63.3 + - - +
258A GLU* 3.1 17.7 + - - +
259A SER* 2.8 27.5 + - - -
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Residues in contact with THR 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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244A TRP* 2.9 46.4 + - + +
252A LEU* 3.9 28.0 - - + -
253A PRO* 2.9 15.5 + - - +
255A ARG* 1.3 74.5 - - - +
257A LEU* 1.3 61.5 + - - +
259A SER* 3.3 1.4 + - - -
260A LEU* 2.9 27.4 + - + +
493A PRO* 4.7 1.8 - - + -
519A LEU* 4.3 11.2 - - + -
533A TRP* 3.6 21.2 - - + -
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Residues in contact with LEU 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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207A LEU* 3.9 36.6 - - + +
209A TRP* 3.8 32.1 - - + -
252A LEU* 3.6 28.5 - - + -
253A PRO 4.3 5.6 - - - +
254A LEU* 3.1 21.0 + - + +
256A THR* 1.3 75.6 - - - +
258A GLU* 1.3 65.0 + - - +
260A LEU* 3.2 10.4 + - + +
261A LEU* 2.9 33.4 + - + +
299A VAL* 4.5 14.1 - - + -
302A LEU* 4.3 9.0 - - + -
485A ALA* 4.9 4.3 - - + -
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Residues in contact with GLU 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 LEU* 3.0 13.6 + - + +
255A ARG* 3.3 18.0 - - - +
257A LEU* 1.3 76.1 - - - +
259A SER* 1.3 56.1 + - - +
261A LEU* 3.2 2.4 + - - +
262A SER* 2.9 36.5 + - - +
302A LEU* 4.1 15.6 - - + +
305A LYS* 4.7 8.2 + - - -
306A PHE* 3.7 27.9 - - + -
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Residues in contact with SER 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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244A TRP* 3.8 20.6 - - - -
255A ARG 2.8 12.7 + - - -
256A THR* 3.5 8.7 - - - -
257A LEU 3.2 0.2 - - - -
258A GLU* 1.3 76.7 - - - +
260A LEU* 1.3 63.1 + - - +
262A SER* 3.2 6.3 + - - -
263A GLY* 2.9 21.5 + - - -
519A LEU* 5.3 1.1 - - - +
531A PRO* 3.9 20.0 - - - +
533A TRP* 3.0 25.3 + - - -
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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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204A LEU* 4.2 15.3 - - + -
207A LEU* 5.9 2.5 - - + -
256A THR 2.9 10.8 + - - +
257A LEU* 3.2 16.8 + - + +
259A SER* 1.3 77.4 - - - +
261A LEU* 1.3 72.0 + - + +
263A GLY* 3.5 5.9 + - - -
264A LEU* 3.3 23.2 + - + +
485A ALA* 4.0 27.6 - - + +
494A GLY 4.7 0.9 - - - +
495A TYR* 3.3 45.4 - - + -
533A TRP* 3.4 30.6 + - + -
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Residues in contact with LEU 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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204A LEU* 4.4 19.1 - - + -
207A LEU* 6.2 2.7 - - + -
257A LEU* 2.9 22.9 + - + +
258A GLU 3.9 1.1 - - - +
260A LEU* 1.3 84.2 - - + +
262A SER* 1.3 61.2 + - - +
264A LEU* 3.4 27.5 - - + +
299A VAL* 6.4 0.7 - - + -
302A LEU* 3.8 30.1 - - + -
303A VAL* 4.1 18.8 - - + +
306A PHE* 3.6 33.3 - - + +
307A LEU* 3.7 27.8 - - + -
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Residues in contact with SER 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 GLU* 2.9 20.0 + - - +
259A SER* 3.2 5.8 + - - -
261A LEU* 1.3 74.6 - - - +
263A GLY* 1.3 56.8 + - - +
264A LEU* 3.0 10.2 + - - +
265A GLY* 4.1 4.5 + - - -
306A PHE* 2.9 31.1 - - - -
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Residues in contact with GLY 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 SER 2.9 15.2 + - - -
260A LEU 3.5 4.2 + - - -
261A LEU 3.4 0.2 - - - -
262A SER* 1.3 73.2 - - - +
264A LEU* 1.3 58.5 + - - +
265A GLY 3.1 7.8 + - - -
266A PRO* 3.4 14.9 - - - +
495A TYR* 4.1 10.2 + - - -
533A TRP* 4.5 14.1 - - - +
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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