Contacts of the helix formed by residues 289 - 297 (chain D) in PDB entry 4HYY
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 289 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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226D MET* 3.5 23.1 - - - +
242D ARG* 4.6 14.1 - - - +
243D GLN* 5.4 2.4 + - - -
246D LEU* 4.4 4.1 - - - +
288D ILE* 1.3 78.4 - - - +
290D GLY* 1.3 66.4 + - - +
292D ILE* 3.3 13.3 + - - +
293D LEU* 3.0 21.2 + - - -
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Residues in contact with GLY 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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243D GLN* 6.1 2.0 - - - -
287D PRO 4.8 3.4 + - - -
288D ILE 3.6 3.1 + - - +
289D GLY* 1.3 79.2 - - - +
291D HIS* 1.3 62.6 + - - -
292D ILE* 5.6 0.7 - - - -
293D LEU* 4.4 0.2 - - - +
294D ALA* 3.2 20.5 + - - +
300D ARG* 4.7 3.1 + - - -
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Residues in contact with HIS 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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230C ARG* 3.1 70.4 + - + +
231C VAL* 3.9 4.7 - - + +
234C SER* 4.4 16.4 + - - -
271C THR* 5.3 3.2 - - + +
290D GLY* 1.3 71.1 - - - -
292D ILE* 1.3 61.9 + - + +
293D LEU 3.4 0.2 - - - -
294D ALA* 3.6 7.7 - - + +
295D HIS* 2.8 34.2 + - + +
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Residues in contact with ILE 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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231C VAL* 3.8 32.8 - - + +
234C SER* 3.6 16.8 - - - +
243D GLN* 3.4 54.5 - - + +
246D LEU* 3.9 13.9 - - + -
247D ALA* 3.8 31.0 - - + -
250D LEU* 4.1 5.7 - - + +
289D GLY 3.5 8.5 - - - +
290D GLY* 3.1 0.8 - - - -
291D HIS* 1.3 79.7 - - - +
293D LEU* 1.3 64.6 + - - +
295D HIS* 3.3 8.7 + - - +
296D ALA* 3.4 14.2 + - - +
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Residues in contact with LEU 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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121D ILE* 6.3 0.4 - - + -
123D GLU* 3.5 22.3 - - + +
225D ILE* 4.1 14.4 - - + -
226D MET* 4.2 15.0 - - + -
246D LEU* 5.1 0.4 - - + -
250D LEU* 3.8 33.1 - - + +
266D VAL* 5.6 2.2 - - + -
268D ASN* 3.5 30.5 - - - +
288D ILE 3.6 8.1 - - - +
289D GLY* 3.0 23.1 + - - +
290D GLY 4.4 0.4 - - - +
292D ILE* 1.3 74.8 - - - +
294D ALA* 1.3 67.3 + - - +
295D HIS 3.3 0.3 + - - -
296D ALA* 3.5 1.9 + - + +
297D SER* 3.3 29.8 + - - +
300D ARG* 4.2 3.1 - - - +
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Residues in contact with ALA 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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290D GLY 3.2 17.8 + - - +
291D HIS* 3.6 10.1 - - + +
292D ILE 3.2 0.2 - - - -
293D LEU* 1.3 79.9 - - - +
295D HIS* 1.3 61.4 + - - +
297D SER* 3.3 16.1 - - - +
300D ARG* 3.4 35.1 + - - +
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Residues in contact with HIS 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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161C THR 2.6 28.5 + - - -
162C GLU* 3.9 19.6 + - - +
193C ALA 5.4 0.9 - - - -
194C TYR 5.4 0.7 - - - -
227C ALA* 4.0 13.9 - - + +
228C LEU* 3.4 30.0 - - + +
231C VAL* 3.6 23.5 - - + +
254D GLN* 4.0 20.8 - - - +
291D HIS 2.8 17.9 + - - +
292D ILE 3.8 1.7 + - - +
293D LEU 3.2 0.2 - - - -
294D ALA* 1.3 78.9 - - - +
296D ALA* 1.3 66.3 + - - +
297D SER 3.3 6.9 - - - +
298D THR* 5.3 0.9 - - - -
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Residues in contact with ALA 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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121D ILE* 3.9 10.5 - - + +
250D LEU* 3.8 38.4 - - + +
254D GLN* 3.0 34.9 - - + +
292D ILE 3.4 11.0 + - - +
293D LEU* 4.1 3.8 - - + +
294D ALA 3.5 0.2 - - - -
295D HIS* 1.3 78.5 + - - +
297D SER* 1.3 67.6 + - - +
298D THR* 3.4 11.3 + - - +
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Residues in contact with SER 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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121D ILE* 3.7 15.5 - - - +
123D GLU* 2.8 41.9 + - - +
293D LEU* 3.3 18.8 + - - +
294D ALA 3.3 8.1 - - - +
295D HIS 3.3 9.4 - - - +
296D ALA* 1.3 79.3 - - - +
298D THR* 1.3 62.2 + - - +
299D THR 4.0 4.7 - - - -
300D ARG* 3.7 15.7 - - - +
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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