Contacts of the helix formed by residues 308 - 322 (chain D) in PDB entry 1Z1G
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 HIS 308 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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177D ARG* 5.1 11.0 - - - +
212D ARG* 5.1 7.3 - - + -
213D VAL* 5.4 3.1 + - + -
306D THR* 4.5 0.9 - - - +
307D PHE* 1.3 76.5 - - - +
309D GLU* 1.3 51.3 + - - +
310D LEU 2.6 0.7 + - - -
311D ARG* 2.6 68.1 + - + +
312D SER* 3.5 6.9 + - - -
22I G 3.4 29.5 - - - +
23I T 2.4 30.9 + - - +
11L T 3.9 24.5 - - - -
12L G 2.9 31.7 + - - -
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Residues in contact with GLU 309 (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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177D ARG* 4.9 10.2 - - - +
178D SER 3.7 8.9 - - - +
179D ARG* 3.9 14.1 + - - -
180D LEU* 3.2 40.8 + - + +
289D PHE* 5.2 0.9 - - + -
305D PRO* 3.3 31.0 - - + -
306D THR* 2.3 34.2 + - - +
308D HIS* 1.3 72.9 - - - +
310D LEU* 1.3 55.6 + - - +
312D SER* 3.0 21.7 + - - -
313D LEU 2.9 18.2 + - - -
316D ARG* 3.9 4.2 + - - -
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Residues in contact with LEU 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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180D LEU* 3.9 15.9 - - + -
185D TYR* 3.6 33.2 - - + -
203D MSE 4.6 6.3 - - + +
206D ALA* 4.1 19.1 - - + -
207D VAL* 3.9 17.0 - - + +
289D PHE* 3.8 27.8 - - + -
307D PHE* 2.5 58.8 + - + +
308D HIS 2.6 0.6 + - - -
309D GLU* 1.3 70.4 - - - +
311D ARG* 1.3 59.1 + - - +
313D LEU* 3.6 2.6 - - + +
314D SER* 2.9 28.2 + - - -
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Residues in contact with ARG 311 (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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206D ALA* 4.4 3.4 - - + +
210D GLY* 2.8 34.0 + - - -
211D GLN* 2.7 50.5 + - - +
212D ARG* 2.8 55.3 - - - +
213D VAL 4.8 0.2 - - - +
233D GLN* 5.4 1.2 - - - +
307D PHE* 5.9 1.8 - - + -
308D HIS* 2.6 42.0 + - + +
310D LEU* 1.3 75.4 - - + +
312D SER* 1.3 55.2 + - - +
314D SER* 3.2 7.7 - - - -
315D ALA* 3.1 27.2 + - - +
331D LEU* 2.6 46.3 + - + +
12L G 4.6 8.3 + - - -
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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
----------------------------------------------------------
179D ARG* 3.8 29.4 + - - -
308D HIS* 3.5 7.7 + - - -
309D GLU* 3.0 28.7 + - - -
311D ARG* 1.3 76.9 - - - +
313D LEU* 1.3 64.9 + - - +
315D ALA* 3.4 6.8 + - - +
316D ARG* 3.1 29.8 + - - +
11L T 5.4 0.9 + - - -
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Residues in contact with LEU 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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180D LEU* 3.7 25.4 - - + +
181D THR 4.9 0.2 - - - +
182D ALA* 4.0 12.6 - - - +
185D TYR* 3.8 31.2 - - + -
207D VAL* 4.5 11.4 - - + -
251D LEU* 4.4 8.5 - - + -
309D GLU 2.9 11.2 + - - +
310D LEU* 3.6 7.0 - - + +
312D SER* 1.3 75.8 - - - +
314D SER* 1.3 65.0 + - - +
316D ARG* 2.8 49.3 + - - +
317D LEU* 3.0 54.5 + - + +
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Residues in contact with SER 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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207D VAL* 2.6 38.4 + - - -
210D GLY* 3.1 23.3 + - - -
248D ILE* 4.2 2.5 - - - +
310D LEU 2.9 15.4 + - - -
311D ARG 3.2 11.4 - - - -
313D LEU* 1.3 76.1 - - - +
315D ALA* 1.3 60.9 + - - +
317D LEU* 3.6 0.7 + - - -
318D TYR* 3.1 36.1 + - - -
330D LEU* 5.1 0.5 - - - +
331D LEU* 4.8 2.4 - - - +
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Residues in contact with ALA 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 ARG 3.1 10.1 + - - +
312D SER* 3.8 8.7 - - - +
313D LEU 3.2 0.2 - - - -
314D SER* 1.3 78.0 - - - +
316D ARG* 1.3 58.5 + - + +
318D TYR* 3.2 2.9 + - - +
319D GLU* 2.9 32.3 + - - +
327D ALA* 3.9 15.9 - - + +
331D LEU* 3.9 30.9 - - + +
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Residues in contact with ARG 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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179D ARG* 4.9 20.2 - - - +
180D LEU 2.2 32.8 + - - +
181D THR* 4.8 4.0 - - - +
182D ALA 5.0 0.8 - - - +
309D GLU* 3.9 6.1 + - - -
312D SER* 3.1 16.8 + - - +
313D LEU* 2.8 52.8 + - - +
315D ALA* 1.3 76.8 - - + +
317D LEU* 1.3 71.9 + - + +
319D GLU* 3.9 21.4 - - - +
320D LYS* 3.9 20.5 + - - +
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Residues in contact with LEU 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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182D ALA* 4.5 10.3 - - + +
207D VAL* 5.4 0.4 - - + -
248D ILE* 3.8 23.7 - - + +
250D ALA* 4.3 21.8 - - + -
251D LEU* 3.9 23.3 - - + -
313D LEU* 3.0 32.6 + - + +
316D ARG* 1.3 100.1 - - + +
318D TYR* 1.3 61.9 + - - +
319D GLU 3.3 0.4 - - - -
320D LYS* 3.7 9.6 + - - +
321D GLN* 3.1 28.8 + - - +
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Residues in contact with TYR 318 (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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207D VAL 4.2 0.4 - - - -
208D VAL* 3.4 17.7 + - - +
246D LEU* 3.3 35.3 - - + +
247D HIS 4.1 13.3 + - - -
248D ILE* 3.9 29.8 - - + +
314D SER* 3.1 31.8 + - - +
315D ALA* 3.2 4.5 + - - +
317D LEU* 1.3 76.6 - - - +
319D GLU* 1.3 65.1 + - - +
321D GLN* 4.5 13.7 - - + +
322D ILE* 3.2 21.9 + - + +
323D SER 3.4 9.9 + - - +
326D PHE* 3.4 31.2 - + + -
327D ALA* 4.3 12.8 - - + -
330D LEU* 3.5 23.6 - - + -
331D LEU* 6.3 0.4 - - + -
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Residues in contact with GLU 319 (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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315D ALA 2.9 17.2 + - - +
316D ARG* 3.9 15.8 - - - +
318D TYR* 1.3 78.2 - - - +
320D LYS* 1.3 66.9 + - + +
322D ILE 4.1 0.7 - - - -
323D SER* 3.7 26.5 - - - -
324D ASP* 3.8 32.6 + - - +
327D ALA* 4.3 5.1 - - + +
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Residues in contact with LYS 320 (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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316D ARG* 3.9 19.4 + - - +
317D LEU* 3.7 10.9 + - - +
318D TYR 3.3 0.2 - - - -
319D GLU* 1.3 86.9 - - + +
321D GLN* 1.3 66.8 + - - +
322D ILE* 4.7 1.2 - - - +
349D GLU* 5.1 12.1 + - - -
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Residues in contact with GLN 321 (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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247D HIS* 3.2 24.9 + - - +
248D ILE* 4.5 2.7 - - + +
249D ASP* 2.0 52.4 + - + +
317D LEU 3.1 20.0 + - - +
318D TYR* 3.5 12.8 + - + +
320D LYS* 1.3 80.5 - - - +
322D ILE* 1.3 92.2 + - + +
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Residues in contact with ILE 322 (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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355C ILE* 5.0 19.3 - - + +
356C LYS* 5.9 2.7 - - - +
318D TYR* 3.2 10.9 + - + +
319D GLU 4.1 3.4 - - - +
320D LYS 5.0 1.3 - - - +
321D GLN* 1.3 104.1 + - - +
323D SER* 1.3 73.2 + - - +
326D PHE* 4.8 21.5 - - + -
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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