Contacts of the helix formed by residues 291 - 297 (chain A) in PDB entry 4M83
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 291 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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220A GLU 4.4 1.8 - - - +
221A GLU 3.6 11.0 - - - +
222A GLY* 3.5 46.0 - - - +
224A TRP* 4.4 14.8 - - + +
289A TRP* 3.6 19.5 - - + +
290A VAL* 1.3 83.4 - - + +
292A GLN* 1.3 57.5 + - - +
293A LEU 3.4 1.3 - - - -
294A ALA* 3.1 8.9 + - + -
295A ILE* 2.9 29.1 + - + +
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Residues in contact with GLN 292 (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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220A GLU 4.4 1.2 + - - -
235A LEU* 3.9 7.9 - - + -
237A SER* 2.7 38.7 + - - +
239A GLY 4.4 0.8 + - - +
290A VAL* 2.8 20.2 + - + -
291A PRO* 1.3 67.6 - - - +
293A LEU* 1.3 69.4 + - - +
295A ILE* 3.1 4.5 + - - +
296A LEU* 2.9 34.5 + - + +
302A PHE* 4.0 19.6 - - - -
310A GLY* 4.0 5.7 - - - -
313A GLU* 2.3 32.5 + - - -
1401A UDP 2.9 40.6 + - + +
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Residues in contact with LEU 293 (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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216A GLY* 4.0 3.4 - - - +
217A ASP* 3.8 36.3 - - + +
219A ALA* 3.0 19.4 - - + +
220A GLU* 3.3 39.9 + - + +
291A PRO 3.4 0.4 - - - -
292A GLN* 1.3 79.6 - - - +
294A ALA* 1.3 62.6 + - - +
296A LEU* 3.5 5.6 + - + +
297A ARG* 3.1 15.4 + - - +
312A GLN* 5.2 2.2 - - - +
313A GLU* 3.7 36.6 - - + -
316A ALA* 5.2 0.9 - - + -
317A THR* 4.2 17.8 - - + +
1401A UDP 4.6 3.1 + - - +
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Residues in contact with ALA 294 (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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219A ALA* 3.5 24.0 + - - +
220A GLU 4.0 0.4 + - - -
221A GLU 4.4 0.7 - - - +
222A GLY 3.5 27.4 - - - +
224A TRP* 4.9 4.0 - - + -
291A PRO* 3.1 19.5 + - + +
293A LEU* 1.3 79.3 - - - +
295A ILE* 1.3 58.9 + - - +
297A ARG* 3.0 15.1 + - - +
298A GLN* 2.8 22.5 - - - +
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Residues in contact with ILE 295 (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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224A TRP* 3.6 44.2 - - + +
233A VAL* 5.0 1.1 - - + -
235A LEU* 4.0 28.3 - - + -
265A VAL* 3.6 35.7 - - + -
287A HIS* 5.7 0.4 - - + -
290A VAL* 3.6 28.0 - - + -
291A PRO* 2.9 15.6 + - + +
292A GLN 3.7 5.6 - - - +
294A ALA* 1.3 72.4 - - - +
296A LEU* 1.3 65.5 + - - +
297A ARG 3.0 1.8 - - - -
298A GLN* 2.9 18.5 + - - +
299A ALA* 3.0 14.1 + - + +
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Residues in contact with LEU 296 (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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235A LEU* 3.9 14.6 - - + -
292A GLN* 2.9 34.2 + - + +
293A LEU* 3.8 5.2 - - - +
295A ILE* 1.3 73.2 - - - +
297A ARG* 1.3 61.3 + - - +
298A GLN 3.1 1.4 + - - -
299A ALA* 3.3 14.5 + - + +
302A PHE* 3.4 51.1 - - + -
313A GLU* 3.7 35.4 - - + -
317A THR* 3.7 19.1 - - + +
319A THR* 3.4 26.0 + - + +
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Residues in contact with ARG 297 (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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218A ARG* 3.3 50.0 + - + +
219A ALA* 3.4 28.8 + - + +
293A LEU 3.1 10.6 + - - +
294A ALA* 3.0 19.2 + - - +
295A ILE 3.0 0.6 - - - -
296A LEU* 1.3 76.7 - - - +
298A GLN* 1.3 68.3 + - - +
317A THR* 4.2 8.5 - - + +
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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