Contacts of the helix formed by residues 324 - 334 (chain D) in PDB entry 4UQJ
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 324 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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93D HIS* 6.0 0.7 - - - -
322D PRO 3.4 5.9 + - - -
323D TRP* 1.3 69.8 - - - +
325D GLN* 1.3 61.4 + - - +
326D GLY 3.0 2.7 + - - -
327D VAL* 3.2 28.7 + - - +
328D GLU* 4.1 5.0 + - - +
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Residues in contact with GLN 325 (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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305D GLU 5.1 1.1 - - - +
306D ILE* 3.7 30.1 - - + +
323D TRP* 2.9 30.1 + - + -
324D GLY* 1.3 76.6 - - - +
326D GLY* 1.3 58.3 + - - +
328D GLU* 3.6 10.4 + - - +
329D ILE* 3.2 26.0 + - - +
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Residues in contact with GLY 326 (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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93D HIS* 3.7 15.9 - - - +
95D SER* 4.4 1.0 + - - -
109D PHE* 3.6 14.6 - - - -
323D TRP* 2.9 21.9 + - - -
325D GLN* 1.3 77.0 - - - +
327D VAL* 1.3 62.4 + - - +
328D GLU 3.1 0.7 - - - -
329D ILE* 3.2 14.9 + - - +
330D GLU 3.2 18.0 + - - -
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Residues in contact with VAL 327 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93D HIS* 3.6 28.0 - - + +
109D PHE* 4.3 8.5 - - + -
324D GLY* 3.2 19.2 + - - +
326D GLY* 1.3 76.8 - - - +
328D GLU* 1.3 66.1 + - + +
330D GLU* 3.6 9.3 + - - +
331D ARG* 3.3 20.8 + - + +
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Residues in contact with GLU 328 (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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299D LEU* 4.3 7.6 - - + +
304D ILE* 3.8 42.4 - - + +
306D ILE* 4.4 6.1 - - + -
324D GLY 4.8 6.3 - - - +
325D GLN* 3.6 10.9 + - - +
326D GLY 3.1 0.6 - - - -
327D VAL* 1.3 80.8 - - + +
329D ILE* 1.3 63.2 + - - +
330D GLU 3.1 2.0 - - - -
331D ARG* 3.3 11.8 + - - +
332D ALA* 3.1 23.4 + - - +
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Residues in contact with ILE 329 (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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71D TYR* 3.3 38.4 - - + +
72D ALA* 4.7 4.5 - - + -
95D SER* 3.9 11.4 - - - +
295D ALA* 6.4 0.4 - - + -
299D LEU* 4.2 11.4 - - + -
306D ILE* 4.0 24.2 - - + -
323D TRP* 3.7 24.5 - - + -
325D GLN 3.2 18.4 - - - +
326D GLY* 3.2 8.0 + - - +
328D GLU* 1.3 77.1 - - - +
330D GLU* 1.3 60.4 + - - +
332D ALA* 3.4 2.8 + - + +
333D LEU* 3.2 33.2 + - + +
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Residues in contact with GLU 330 (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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95D SER* 3.9 7.5 + - - +
108D PRO* 4.2 8.5 - - - +
109D PHE* 3.4 60.1 + - + +
111D ILE* 5.2 7.0 - - + +
326D GLY 3.2 10.7 + - - +
327D VAL* 3.7 12.5 - - - +
328D GLU 3.1 0.4 - - - -
329D ILE* 1.3 73.2 - - - +
331D ARG* 1.3 58.8 + - - +
332D ALA 2.9 9.1 + - - -
333D LEU* 3.3 4.4 + - - +
334D LYS* 3.0 29.1 + - + +
349D GLN 4.3 13.5 - - - +
350D ASN 5.1 1.7 - - - +
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Residues in contact with ARG 331 (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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327D VAL* 3.3 11.0 + - + +
328D GLU* 3.3 18.3 + - - +
330D GLU* 1.3 79.6 - - - +
332D ALA* 1.3 55.7 + - - +
334D LYS* 4.8 4.0 - - - +
335D GLN* 3.1 26.9 + - - +
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Residues in contact with ALA 332 (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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295D ALA* 3.7 18.4 - - + +
298D ASN* 5.1 5.1 + - + -
299D LEU* 3.3 39.5 - - + -
328D GLU 3.1 6.3 + - - +
329D ILE* 3.5 10.1 - - + +
330D GLU 2.9 0.6 - - - -
331D ARG* 1.3 78.4 - - - +
333D LEU* 1.3 66.5 + - - +
334D LYS 3.2 0.2 - - - -
335D GLN* 3.1 13.8 + - - +
336D VAL* 3.1 15.4 + - - +
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Residues in contact with LEU 333 (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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72D ALA* 4.9 2.9 - - + -
95D SER* 3.7 28.3 - - - +
97D ILE* 3.7 18.8 - - + -
111D ILE* 4.1 20.4 - - + -
291D VAL* 3.9 13.6 - - + +
292D MET* 3.8 28.3 - - + +
295D ALA* 3.4 24.0 - - + -
329D ILE* 3.2 24.5 + - + +
330D GLU* 4.0 2.9 - - - +
332D ALA* 1.3 78.1 - - - +
334D LYS* 1.3 62.8 + - - +
336D VAL* 3.2 18.8 + - - +
347D PHE* 3.8 11.3 - - - -
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Residues in contact with LYS 334 (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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111D ILE* 4.5 12.3 - - + +
330D GLU* 3.0 22.7 + - + +
331D ARG* 4.8 4.5 - - - -
333D LEU* 1.3 77.7 - - - +
335D GLN* 1.3 59.2 + - - +
336D VAL 3.7 1.0 + - - +
347D PHE* 3.6 33.8 + - + +
348D ASP 3.9 19.3 - - - +
349D GLN* 5.3 6.5 - - - +
350D ASN 6.1 0.2 - - - -
351D GLY* 5.7 0.9 - - - -
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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