Contacts of the helix formed by residues 290 - 300 (chain A) in PDB entry 4EG8
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 GLY 290 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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289A HIS* 1.3 79.6 - - - +
291A GLN* 1.3 61.0 + - - -
292A LYS 3.3 2.7 - - - -
293A VAL 3.5 1.1 + - - -
294A ALA* 2.9 32.5 + - - +
368A GLU* 3.8 8.7 - - - -
456A LEU* 4.9 11.7 - - - -
459A TRP* 2.9 14.3 + - - -
460A ALA* 5.0 0.6 - - - +
473A VAL* 4.2 10.5 - - - -
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Residues in contact with GLN 291 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
290A GLY* 1.3 68.1 - - - -
292A LYS* 1.3 68.6 + - - +
294A ALA* 4.4 4.5 - - - -
295A GLU* 2.8 57.6 + - + +
363A TYR* 4.8 2.8 - - - -
365A ILE* 3.5 35.9 - - + +
368A GLU* 3.3 9.4 + - - +
451A ARG* 4.5 9.7 + - - -
455A THR* 3.4 43.1 + - - +
456A LEU* 4.5 19.7 - - + +
457A HIS* 4.6 2.0 + - + -
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Residues in contact with LYS 292 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
250A TYR* 3.8 34.8 - - + -
252A ASN* 3.5 40.0 - - + +
290A GLY* 5.7 0.2 - - - -
291A GLN* 1.3 79.5 - - - +
293A VAL* 1.3 59.2 + - + +
295A GLU* 3.8 3.4 - - - +
296A ALA* 2.9 26.9 + - - +
365A ILE* 3.7 20.1 - - + +
366A SER* 2.8 49.0 + - - +
368A GLU* 3.2 15.6 + - + +
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Residues in contact with VAL 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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250A TYR* 4.4 11.9 - - + -
251A VAL* 3.8 33.7 - - + +
252A ASN* 3.9 8.7 - - + +
287A ASP 4.0 10.5 - - - +
288A GLU 3.4 22.9 - - - +
289A HIS 3.9 11.7 - - - +
290A GLY 3.5 2.2 + - - +
291A GLN 3.3 0.2 - - - -
292A LYS* 1.3 77.3 - - + +
294A ALA* 1.3 65.9 + - - +
296A ALA* 3.1 8.4 + - - +
297A ALA* 3.0 22.0 + - + +
304A PRO* 6.1 0.4 - - + -
307A PHE* 4.3 7.7 - - + -
308A THR* 3.7 19.7 - - + -
459A TRP* 4.2 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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290A GLY 2.9 20.6 + - - +
291A GLN 3.9 2.7 - - - +
293A VAL* 1.3 77.7 - - - +
295A GLU* 1.3 58.0 + - - +
297A ALA* 3.4 8.4 + - - +
298A LYS* 3.1 26.0 + - - +
304A PRO* 5.2 7.9 - - + +
456A LEU 4.2 7.4 - - - +
457A HIS* 4.3 16.4 - - + -
459A TRP* 3.8 28.5 - - + -
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Residues in contact with GLU 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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291A GLN* 2.8 45.6 + - - +
292A LYS* 3.9 2.9 - - - +
294A ALA* 1.3 74.2 - - - +
296A ALA* 1.3 64.9 + - - +
298A LYS* 3.8 8.2 - - + +
299A GLN* 3.0 37.4 + - + +
365A ILE* 4.3 15.3 - - - +
457A HIS* 3.2 31.8 + - + +
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Residues in contact with ALA 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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252A ASN* 3.7 39.3 - - + +
292A LYS 2.9 15.5 + - - +
293A VAL 3.5 8.3 - - - +
295A GLU* 1.3 77.2 - - - +
297A ALA* 1.3 59.2 + - - +
299A GLN* 3.4 8.6 + - - +
300A LYS* 3.3 27.7 + - - +
307A PHE* 4.0 6.2 - - + -
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Residues in contact with ALA 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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293A VAL* 3.0 12.8 + - + +
294A ALA* 3.5 10.1 - - - +
296A ALA* 1.3 75.9 - - - +
298A LYS* 1.3 64.1 + - - +
300A LYS* 3.4 4.2 + - - +
301A GLN 3.2 13.0 + - - -
302A VAL* 3.1 25.1 + - - +
304A PRO* 4.1 15.5 - - + -
307A PHE* 3.6 37.1 - - + -
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Residues in contact with LYS 298 (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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294A ALA 3.1 16.2 + - - +
295A GLU* 3.8 11.9 - - + +
296A ALA 3.3 0.4 - - - -
297A ALA* 1.3 76.9 - - - +
299A GLN* 1.3 58.5 + - + +
301A GLN* 3.0 27.6 + - + +
302A VAL 4.8 2.7 - - - +
457A HIS* 5.5 12.9 + - + +
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Residues in contact with GLN 299 (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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295A GLU* 3.0 25.0 + - + +
296A ALA* 3.8 7.5 - - - +
297A ALA 3.3 0.2 - - - -
298A LYS* 1.3 77.0 - - + +
300A LYS* 1.3 64.4 + - + +
301A GLN* 3.2 8.6 + - - +
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Residues in contact with LYS 300 (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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296A ALA 3.3 13.9 + - - +
297A ALA 3.4 6.0 + - - +
298A LYS 3.3 0.4 - - - -
299A GLN* 1.3 80.3 - - - +
301A GLN* 1.3 70.1 + - - +
302A VAL* 3.3 9.4 + - + +
307A PHE* 3.9 25.6 - - + -
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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