Contacts of the helix formed by residues 308 - 322 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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177A ARG* 5.9 10.8 - - - +
212A ARG* 4.5 9.4 + - - -
213A VAL* 5.0 6.8 - - + +
235A LYS* 5.5 0.4 - - - -
306A THR* 5.0 0.2 - - - +
307A PHE* 1.3 79.1 - - - +
309A GLU* 1.3 57.4 + - - +
310A LEU 2.6 0.5 + - - -
311A ARG* 2.5 64.1 + - + +
312A SER* 3.6 6.9 + - - -
342A PHE* 4.1 13.6 - + - -
11I T 3.9 43.3 - - - -
12I T 4.3 4.3 - - - -
22J G 4.1 18.9 - - - +
23J C 2.7 21.2 + - - +
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Residues in contact with GLU 309 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
177A ARG* 4.9 9.9 - - + +
178A SER 3.9 9.2 - - - +
179A ARG* 3.2 10.4 - - + +
180A LEU* 2.4 42.3 + - + +
305A PRO* 3.6 22.9 - - + -
306A THR 2.5 32.7 + - - +
308A HIS* 1.3 77.5 - - - +
310A LEU* 1.3 55.3 + - - +
312A SER* 2.8 22.1 + - - -
313A LEU* 3.0 17.7 + - - +
316A ARG* 3.3 9.2 + - - -
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Residues in contact with LEU 310 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
180A LEU* 4.2 16.8 - - + -
185A TYR* 4.0 18.8 - - + -
203A MSE 4.2 22.7 - - + -
206A ALA* 3.9 19.7 - - + -
207A VAL* 3.7 25.7 - - + +
289A PHE* 5.0 6.1 - - + -
306A THR 5.1 0.2 - - - +
307A PHE* 2.4 72.3 + - + +
308A HIS 2.6 0.6 + - - -
309A GLU* 1.3 72.5 - - - +
311A ARG* 1.3 55.4 + - - +
313A LEU* 3.7 6.2 - - + +
314A SER* 2.9 28.8 + - - -
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Residues in contact with ARG 311 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
206A ALA* 4.7 2.0 - - + +
210A GLY* 2.1 41.6 + - - +
211A GLN* 2.9 57.4 - - - +
212A ARG* 3.1 46.0 - - - +
213A VAL 4.7 0.7 - - - +
307A PHE* 5.9 1.3 - - + -
308A HIS* 2.5 40.7 + - + +
310A LEU* 1.3 75.9 - - + +
312A SER* 1.3 55.1 + - - +
314A SER* 3.2 9.5 + - - -
315A ALA* 3.1 26.5 + - - +
331A LEU* 3.0 46.1 + - + +
342A PHE* 5.2 3.0 - - + -
12I T 3.5 2.8 + - - -
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Residues in contact with SER 312 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
179A ARG* 2.1 35.0 + - - -
308A HIS* 3.6 10.0 + - - -
309A GLU* 2.8 24.1 + - - -
311A ARG* 1.3 76.4 - - - +
313A LEU* 1.3 62.8 + - - +
315A ALA* 3.4 6.4 + - - +
316A ARG* 3.1 36.9 + - - +
342A PHE* 3.9 17.3 + - - +
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Residues in contact with LEU 313 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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180A LEU* 3.1 40.4 - - + +
181A THR* 4.2 2.5 - - - +
182A ALA* 3.8 18.8 - - - +
185A TYR* 3.8 38.8 - - + -
207A VAL* 4.4 9.9 - - + -
251A LEU* 4.9 2.5 - - + -
309A GLU 3.0 11.4 + - - +
310A LEU* 3.7 9.9 - - + +
312A SER* 1.3 73.7 - - - +
314A SER* 1.3 64.6 - - - +
316A ARG* 3.0 18.1 + - - +
317A LEU* 3.0 46.7 + - + +
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Residues in contact with SER 314 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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207A VAL* 3.0 33.6 + - - +
210A GLY* 3.0 26.5 - - - -
248A ILE* 4.6 2.0 - - - +
310A LEU 2.9 15.2 + - - -
311A ARG 3.2 10.5 + - - -
313A LEU* 1.3 75.9 - - - +
315A ALA* 1.3 58.4 + - - +
317A LEU* 4.1 2.7 - - - +
318A TYR* 2.7 40.8 + - - -
331A LEU* 5.0 2.8 - - - +
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Residues in contact with ALA 315 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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311A ARG 3.1 9.8 + - - +
312A SER* 3.9 8.5 - - - +
313A LEU 3.2 0.2 - - - -
314A SER* 1.3 77.4 + - - +
316A ARG* 1.3 56.3 + - - +
318A TYR* 3.2 7.6 + - - +
319A GLU* 2.8 35.8 + - - +
327A ALA* 3.8 14.4 - - + +
331A LEU* 4.1 25.6 - - + -
342A PHE* 5.5 10.8 - - + +
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Residues in contact with ARG 316 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
179A ARG* 4.2 15.1 - - - +
180A LEU 2.5 32.9 + - - -
181A THR* 4.8 4.2 - - - +
309A GLU* 3.3 14.4 + - - -
312A SER* 3.1 20.6 + - - +
313A LEU* 3.0 33.0 + - - +
315A ALA* 1.3 76.2 - - - +
317A LEU* 1.3 68.0 + - + +
319A GLU* 3.6 14.1 - - - +
320A LYS* 3.5 31.0 - - - +
342A PHE 4.1 18.8 - - - +
343A ARG* 4.4 20.6 - - + +
344A ASP 4.8 5.6 - - - -
349A GLU* 5.2 7.5 + - - -
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Residues in contact with LEU 317 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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182A ALA* 4.2 19.3 - - + +
207A VAL* 5.9 1.8 - - + -
248A ILE* 4.6 17.2 - - + +
250A ALA* 4.1 26.7 - - + -
251A LEU* 4.1 24.2 - - + -
313A LEU* 3.0 34.6 + - + +
314A SER* 4.6 2.5 - - - +
316A ARG* 1.3 83.0 - - + +
318A TYR* 1.3 60.5 + - - +
319A GLU 3.3 0.4 - - - -
320A LYS* 3.8 6.9 + - + +
321A GLN* 3.1 31.4 + - - +
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Residues in contact with TYR 318 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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207A VAL 3.7 6.7 - - - -
208A VAL* 2.4 38.0 + - - +
210A GLY* 5.0 1.3 - - - -
246A LEU* 3.1 22.4 - - + +
247A HIS 5.3 4.5 - - - -
248A ILE* 3.6 20.7 - - + +
314A SER* 2.7 41.7 + - - +
315A ALA* 3.2 8.3 + - - +
317A LEU* 1.3 76.5 - - - +
319A GLU* 1.3 63.2 + - - +
321A GLN* 4.5 7.4 - - + -
322A ILE* 3.2 25.1 + - + +
323A SER 3.5 10.3 + - - +
326A PHE* 3.5 33.2 - + + -
327A ALA* 4.3 12.6 - - + -
330A LEU* 3.7 17.5 - - + -
331A LEU* 6.5 0.4 - - + -
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Residues in contact with GLU 319 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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315A ALA 2.8 17.2 + - - +
316A ARG* 3.6 14.5 - - - +
318A TYR* 1.3 77.4 - - - +
320A LYS* 1.3 84.3 + - + +
322A ILE 4.2 1.0 - - - +
323A SER* 3.8 27.7 + - - -
324A ASP* 3.7 22.2 + - - +
327A ALA* 4.3 7.3 - - + +
343A ARG* 3.0 53.3 + - - +
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Residues in contact with LYS 320 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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316A ARG* 3.5 26.2 + - - +
317A LEU* 3.8 8.3 + - + +
319A GLU* 1.3 99.7 - - + +
321A GLN* 1.3 66.9 + - - +
322A ILE 5.0 0.9 - - - +
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Residues in contact with GLN 321 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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247A HIS* 2.9 32.8 + - - +
248A ILE* 3.3 10.1 - - - +
249A ASP* 2.8 40.7 + - + +
250A ALA 4.8 2.0 + - - +
317A LEU 3.1 22.2 + - - +
318A TYR* 4.1 7.8 - - + +
319A GLU 3.5 0.2 - - - -
320A LYS* 1.3 80.7 - - - +
322A ILE* 1.3 83.3 + - + +
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Residues in contact with ILE 322 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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246A LEU* 6.2 1.3 - - + -
247A HIS* 5.9 5.4 - - + -
318A TYR* 3.2 11.7 + - + +
319A GLU 4.2 3.0 - - - +
320A LYS 5.0 0.9 - - - +
321A GLN* 1.3 100.9 - - + +
323A SER* 1.3 69.4 + - - +
326A PHE* 4.6 23.1 - - + -
355D ILE* 3.8 38.6 - - + +
356D LYS* 5.9 2.7 - - + -
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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