Contacts of the helix formed by residues 308 - 317 (chain D) in PDB entry 1Z6T
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 GLU 308 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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307D PRO* 1.3 71.1 - - - +
309D GLN* 1.3 70.4 + - - +
311D HIS* 2.8 31.3 + - + +
312D SER* 4.1 6.2 + - - -
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Residues in contact with GLN 309 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
307D PRO* 3.2 14.1 - - - +
308D GLU* 1.3 84.2 + - + +
310D ALA* 1.3 60.4 + - - +
312D SER* 3.2 6.0 + - - -
313D ILE* 2.9 33.3 + - + +
338D TRP* 3.5 44.0 - - + +
339D GLU* 3.9 26.0 + - + +
342D LEU* 3.6 26.5 - - + -
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Residues in contact with ALA 310 (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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292D LEU* 3.9 15.3 - - + -
295D LEU* 4.0 3.6 - - + +
306D LEU* 3.9 19.5 - - + -
307D PRO 3.2 17.1 + - - +
308D GLU 3.1 0.8 - - - -
309D GLN* 1.3 77.9 - - - +
311D HIS* 1.3 58.2 + - - +
313D ILE* 3.4 5.2 + - - +
314D ILE* 3.1 32.6 + - - +
338D TRP* 3.5 27.9 - - + -
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Residues in contact with HIS 311 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
292D LEU* 3.6 34.7 - - + +
303D LYS 5.4 2.8 + - - -
306D LEU* 4.6 9.1 + - - +
307D PRO 3.3 24.4 + - - -
308D GLU* 2.8 27.7 + - + +
310D ALA* 1.3 72.4 - - - +
312D SER* 1.3 64.4 + - - +
314D ILE* 3.6 6.3 + - - +
315D LYS* 3.2 21.8 + - - +
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Residues in contact with SER 312 (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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308D GLU 4.1 5.2 + - - -
309D GLN* 3.2 11.2 + - - -
311D HIS* 1.3 76.5 - - - +
313D ILE* 1.3 58.3 + - - -
315D LYS* 3.4 11.3 + - - +
316D GLU* 3.0 32.2 + - - +
342D LEU* 3.4 27.0 - - - +
346D GLN* 5.0 4.7 + - - -
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Residues in contact with ILE 313 (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 LEU* 4.4 12.6 - - + -
309D GLN 2.9 22.9 + - - +
310D ALA* 3.4 5.6 + - - +
312D SER* 1.3 71.7 - - - +
314D ILE* 1.3 65.6 + - + +
316D GLU* 3.2 7.3 + - - +
317D CYS* 3.0 32.4 + - - -
327D ILE* 3.5 28.5 - - + -
331D LEU* 4.3 10.1 - - + -
338D TRP* 3.6 47.3 - - + +
341D TYR* 5.2 1.1 - - + -
342D LEU* 3.9 25.1 - - + +
345D LEU* 3.9 9.2 - - + -
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Residues in contact with ILE 314 (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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287D GLY 5.3 0.7 - - - +
288D LYS* 3.9 35.4 - - + +
291D GLY* 3.5 29.6 - - - +
292D LEU* 3.9 20.9 - - + +
295D LEU* 3.7 15.9 - - + -
310D ALA 3.1 21.2 + - - +
311D HIS* 3.7 7.4 - - - +
312D SER 3.3 0.2 - - - -
313D ILE* 1.3 75.9 - - - +
315D LYS* 1.3 62.9 + - - +
317D CYS* 3.0 19.8 + - - +
318D LYS* 3.4 5.2 + - - -
319D GLY* 4.4 5.8 + - - +
324D VAL* 3.9 20.1 - - + +
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Residues in contact with LYS 315 (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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311D HIS 3.2 11.1 + - - +
312D SER* 3.5 13.9 - - - +
314D ILE* 1.3 81.0 - - - +
316D GLU* 1.3 90.2 + - - +
318D LYS* 3.3 32.3 + - - +
346D GLN* 5.1 4.6 - - - +
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Residues in contact with GLU 316 (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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312D SER* 3.0 18.2 + - - +
313D ILE 3.2 8.3 + - - +
315D LYS* 1.3 102.4 + - - +
317D CYS* 1.3 60.2 + - - +
318D LYS* 3.2 15.3 + - - +
342D LEU* 4.2 8.5 - - + -
345D LEU* 3.9 27.2 - - + +
346D GLN* 3.4 36.5 + - + +
348D LYS* 3.6 23.4 + - - -
363D ALA* 3.4 17.8 - - - +
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Residues in contact with CYS 317 (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 LEU* 6.3 0.2 - - - -
313D ILE* 3.0 28.9 + - - -
314D ILE* 3.0 12.0 + - - +
316D GLU* 1.3 76.4 - - - +
318D LYS* 1.3 70.1 + - - +
319D GLY 3.2 1.9 + - - +
320D SER* 3.2 18.2 + - - -
323D VAL* 3.7 29.2 - - + +
324D VAL* 3.8 36.8 - - + +
327D ILE* 4.1 14.8 - - - -
345D LEU* 4.6 3.1 - - - -
363D ALA* 4.3 4.0 - - - +
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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