Contacts of the helix formed by residues 308 - 322 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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177B ARG* 5.4 12.1 - - - +
179B ARG* 6.1 0.2 - - - -
212B ARG* 5.8 3.4 - - + -
213B VAL* 4.6 6.8 - - - +
306B THR* 4.4 0.2 - - - +
307B PHE* 1.3 76.6 - - - +
309B GLU* 1.3 63.7 + - - +
310B LEU 2.6 0.5 + - - -
311B ARG* 2.6 62.3 + - + +
312B SER* 3.4 7.5 + - - -
11J T 3.7 28.6 + - - -
12J A 3.3 23.6 + - - -
22K C 3.2 33.1 - - - +
23K T 2.6 22.8 + - - +
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Residues in contact with GLU 309 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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177B ARG* 4.1 14.8 - - - +
178B SER 3.8 7.9 - - - +
179B ARG* 3.4 33.7 + - - -
180B LEU* 3.5 16.5 + - + +
289B PHE* 6.1 0.4 - - + -
305B PRO* 3.3 30.1 - - + -
306B THR* 2.4 30.9 + - - +
308B HIS* 1.3 79.1 - - - +
310B LEU* 1.3 55.5 + - - +
312B SER* 2.5 42.5 + - - -
313B LEU* 2.8 19.9 + - - +
316B ARG* 3.8 1.9 + - - -
11J T 5.2 0.5 + - - -
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Residues in contact with LEU 310 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
180B LEU* 4.1 14.6 - - + -
185B TYR* 3.5 35.0 - - + -
203B MSE 3.6 13.7 - - + +
206B ALA* 4.1 18.6 - - + -
207B VAL* 4.0 16.2 - - + +
289B PHE* 3.8 23.1 - - + -
306B THR 5.2 0.4 - - - +
307B PHE* 2.5 53.7 + - + +
308B HIS 2.6 0.6 + - - -
309B GLU* 1.3 69.8 - - - +
311B ARG* 1.3 58.9 + - - +
313B LEU* 3.8 6.2 - - + +
314B SER* 2.8 28.4 + - - -
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Residues in contact with ARG 311 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
206B ALA* 4.8 1.5 + - - +
210B GLY* 2.8 40.4 + - - +
211B GLN* 3.3 24.3 + - - +
212B ARG* 3.0 46.7 - - - +
213B VAL* 6.4 0.2 - - - -
307B PHE* 4.1 0.4 + - - -
308B HIS* 2.6 35.6 + - + +
310B LEU* 1.3 74.1 - - - +
312B SER* 1.3 55.7 + - - +
314B SER* 3.1 8.1 - - - -
315B ALA* 3.1 26.2 + - - +
331B LEU* 3.0 47.2 + - + +
333B HIS* 4.7 0.6 + - - -
12J A 2.9 27.5 + - - -
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Residues in contact with SER 312 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
179B ARG* 4.4 13.2 - - - -
308B HIS* 3.4 7.7 + - - -
309B GLU* 2.5 44.6 + - - -
311B ARG* 1.3 73.9 - - - +
313B LEU* 1.3 64.8 + - - +
315B ALA* 3.4 6.3 + - - +
316B ARG* 3.1 40.9 + - - -
331B LEU* 6.4 0.4 - - - -
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Residues in contact with LEU 313 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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180B LEU* 3.1 45.1 - - + +
181B THR* 3.5 22.2 - - - +
182B ALA* 3.7 12.3 - - - +
185B TYR* 4.2 9.6 - - + -
207B VAL* 5.3 4.3 - - + -
251B LEU* 5.0 3.1 - - + -
309B GLU 2.8 14.8 + - - +
310B LEU* 3.9 5.6 - - + +
312B SER* 1.3 75.3 - - - +
314B SER* 1.3 64.2 - - - +
316B ARG* 3.0 31.5 + - - +
317B LEU* 3.0 49.7 + - + +
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Residues in contact with SER 314 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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207B VAL* 2.1 42.8 + - - +
210B GLY* 3.2 20.5 - - - -
248B ILE* 5.0 1.3 - - - +
310B LEU 2.8 16.1 + - - -
311B ARG 3.1 13.9 - - - -
312B SER 3.2 0.2 - - - -
313B LEU* 1.3 76.9 - - - +
315B ALA* 1.3 54.9 + - - -
317B LEU* 4.1 1.8 - - - +
318B TYR* 2.7 44.2 + - - -
331B LEU* 5.6 0.7 - - - -
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Residues in contact with ALA 315 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
311B ARG 3.1 14.7 + - - +
312B SER* 3.9 5.2 - - - +
313B LEU 3.2 0.2 - - - -
314B SER* 1.3 76.6 - - - +
316B ARG* 1.3 57.8 + - - +
318B TYR* 3.2 7.3 + - - +
319B GLU* 2.9 32.8 + - - +
327B ALA* 4.0 16.5 - - + +
330B LEU* 6.5 0.2 - - - -
331B LEU* 4.4 26.9 - - + +
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Residues in contact with ARG 316 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
179B ARG* 4.2 19.2 - - - +
180B LEU 2.7 31.1 + - - +
181B THR* 4.6 2.6 - - - +
309B GLU* 3.8 10.1 + - - -
312B SER* 3.1 25.7 + - - +
313B LEU* 3.0 49.1 + - - +
315B ALA* 1.3 75.2 - - - +
317B LEU* 1.3 69.4 + - + +
319B GLU* 3.9 10.3 + - - +
320B LYS* 3.9 32.0 + - - +
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Residues in contact with LEU 317 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
182B ALA* 4.7 13.5 - - + -
207B VAL* 5.2 3.8 - - + -
248B ILE* 4.4 22.9 - - + +
250B ALA* 5.2 12.1 - - + -
251B LEU* 4.2 22.9 - - + -
313B LEU* 3.0 48.8 + - + +
314B SER 4.4 2.0 - - - +
316B ARG* 1.3 82.4 - - + +
318B TYR* 1.3 62.3 + - - +
319B GLU 3.3 0.7 - - - -
320B LYS* 3.7 8.3 + - + +
321B GLN* 3.1 30.5 + - - +
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Residues in contact with TYR 318 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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207B VAL 3.2 2.9 - - - -
208B VAL* 2.3 45.8 + - - +
246B LEU* 3.6 18.5 - - + +
247B HIS 4.6 10.1 - - - -
248B ILE* 3.1 27.8 - - + +
314B SER* 2.7 49.1 + - - +
315B ALA* 3.9 6.3 - - - +
317B LEU* 1.3 77.4 - - - +
319B GLU* 1.3 64.5 + - - +
321B GLN* 4.5 7.4 - - + +
322B ILE* 3.1 27.5 + - + +
323B SER 3.5 9.8 + - - +
326B PHE* 3.6 27.0 - + + -
327B ALA* 4.7 6.7 - - + -
330B LEU* 3.8 16.2 - - + -
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Residues in contact with GLU 319 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
315B ALA 2.9 17.9 + - - +
316B ARG* 4.0 10.7 - - - +
317B LEU 3.3 0.2 - - - -
318B TYR* 1.3 77.6 - - - +
320B LYS* 1.3 67.1 + - + +
322B ILE 4.1 0.9 - - - +
323B SER* 3.7 25.6 + - - -
324B ASP* 3.2 38.7 + - + +
327B ALA* 4.4 5.5 - - + +
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Residues in contact with LYS 320 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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316B ARG* 3.9 22.3 + - - +
317B LEU* 3.7 11.0 + - + +
319B GLU* 1.3 84.3 - - + +
321B GLN* 1.3 64.7 + - - +
322B ILE* 4.7 1.2 - - - +
349B GLU* 5.6 5.1 + - - -
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Residues in contact with GLN 321 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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247B HIS* 3.3 19.7 + - - +
248B ILE* 3.9 3.3 - - + +
249B ASP* 2.9 51.5 + - + +
250B ALA* 5.4 2.5 - - + +
317B LEU 3.1 18.7 + - - +
318B TYR* 3.5 8.2 + - + +
320B LYS* 1.3 79.5 - - - +
322B ILE* 1.3 75.6 + - + +
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Residues in contact with ILE 322 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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355A ILE* 5.5 13.0 - - + -
356A LYS* 4.2 29.2 - - - +
246B LEU* 6.3 1.1 - - + -
247B HIS* 5.8 3.8 - - + +
318B TYR* 3.1 14.0 + - + +
319B GLU 4.1 3.4 - - - +
320B LYS 4.9 1.3 - - - +
321B GLN* 1.3 93.0 - - + +
323B SER* 1.3 67.3 + - - +
326B PHE* 4.4 32.1 - - + -
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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