Contacts of the helix formed by residues 289 - 297 (chain D) in PDB entry 3GXM
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 289 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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288D LEU* 1.4 82.4 - - + +
290D HIS* 1.3 65.7 + - + +
291D TRP 3.4 2.2 - - - -
292D ALA* 3.0 16.5 + - + +
293D LYS* 3.1 26.0 + - - +
322D ALA 3.7 14.8 - - - +
326D GLU* 3.6 26.0 - - + -
327D THR* 3.4 22.9 - - + +
330D LEU* 4.0 18.4 - - + -
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Residues in contact with HIS 290 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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253D PRO* 4.2 16.6 - - + +
254D GLU* 4.5 6.6 + - - -
287D LEU 4.3 5.8 - - - +
288D LEU* 3.5 3.6 - - - +
289D PRO* 1.3 76.4 - - - +
291D TRP* 1.3 69.5 + + - +
292D ALA 3.1 0.7 + - - -
293D LYS* 3.2 19.2 + - + +
294D VAL* 3.0 49.8 + - + +
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Residues in contact with TRP 291 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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236D PRO* 3.5 26.5 - - + -
237D SER* 4.8 8.7 - - - -
240D LEU* 5.5 1.8 - - + -
251D PHE 3.3 27.8 - - - -
252D THR 3.8 2.5 - - - -
253D PRO* 3.4 44.8 - - + +
256D GLN* 3.4 41.5 - - + -
280D MET* 3.8 11.4 - - + -
281D LEU* 3.6 26.5 - - + -
287D LEU* 3.1 53.6 + - + +
288D LEU* 4.5 2.7 - - + -
290D HIS* 1.3 82.7 - + + +
292D ALA* 1.3 61.1 + - - +
294D VAL* 3.5 1.7 + - - +
295D VAL* 3.2 30.5 + - + +
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Residues in contact with ALA 292 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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280D MET* 4.0 11.4 - - - +
288D LEU* 3.8 17.9 - - + +
289D PRO* 3.0 10.9 + - + +
291D TRP* 1.3 75.8 - - - +
293D LYS* 1.3 57.1 + - - +
296D LEU* 2.7 41.4 + - + +
308D ILE* 4.0 14.1 - - + -
327D THR* 3.9 13.7 - - + -
331D PHE* 3.8 16.8 - - + -
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Residues in contact with LYS 293 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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289D PRO* 3.1 33.5 + - - +
290D HIS* 3.4 21.3 - - + +
292D ALA* 1.3 72.6 - - - +
294D VAL* 1.3 63.1 + - + +
297D THR* 2.7 42.3 + - + +
326D GLU* 5.3 2.3 + - - -
330D LEU* 3.7 38.4 - - + +
331D PHE* 3.8 15.0 - - + -
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Residues in contact with VAL 294 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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253D PRO* 3.7 39.7 - - + +
254D GLU* 3.7 17.9 - - + +
257D ARG* 3.4 34.4 + - + +
290D HIS* 3.0 49.6 + - + +
291D TRP 3.8 0.4 - - - +
293D LYS* 1.3 77.3 - - + +
295D VAL* 1.3 60.2 + - - +
297D THR* 4.2 3.8 + - - -
298D ASP* 4.1 4.7 - - - +
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Residues in contact with VAL 295 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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253D PRO 3.7 21.3 - - - +
256D GLN* 4.4 9.0 - - + -
257D ARG* 4.0 16.6 - - - +
260D ILE* 4.6 6.1 - - + -
280D MET* 3.6 31.9 - - + -
291D TRP* 3.2 21.5 + - + +
294D VAL* 1.3 78.3 - - - +
296D LEU* 1.3 69.8 + - + +
297D THR 3.4 0.2 - - - -
298D ASP* 3.4 19.9 + - - +
301D ALA* 3.5 21.8 - - + +
302D ALA 4.1 0.3 + - - -
305D VAL* 4.5 11.2 - - + -
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Residues in contact with LEU 296 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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280D MET* 4.1 9.0 - - - -
292D ALA 2.7 21.9 + - - +
295D VAL* 1.3 76.8 - - + +
297D THR* 1.3 57.1 + - - +
298D ASP 3.1 7.7 + - - -
299D PRO* 4.7 0.7 - - - +
302D ALA* 3.7 33.6 - - + +
305D VAL* 4.0 31.4 - - + +
308D ILE* 3.8 29.4 - - + -
331D PHE* 3.6 31.3 - - + -
334D THR* 3.9 23.3 - - + +
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Residues in contact with THR 297 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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293D LYS* 2.7 38.4 + - + +
294D VAL* 4.2 4.2 + - - -
296D LEU* 1.3 77.0 - - - +
298D ASP* 1.3 56.7 + - - +
299D PRO* 3.6 9.8 - - - +
331D PHE* 3.9 16.2 - - + -
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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