Contacts of the helix formed by residues 308 - 327 (chain A) in PDB entry 1ZGA
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 ASP 308 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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306A SER* 3.0 13.9 + - - +
307A ASP* 1.3 78.2 - - - +
309A ARG* 1.3 60.7 + - - +
310A GLY* 3.5 5.4 + - - -
311A LEU* 3.0 46.4 + - + +
312A THR* 3.2 12.6 + - - -
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Residues in contact with ARG 309 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
304A GLU 3.7 20.4 + - - -
306A SER 4.2 11.6 + - - -
307A ASP* 3.2 10.6 + - - +
308A ASP* 1.3 71.7 - - - +
310A GLY* 1.3 58.2 + - - +
312A THR* 3.0 13.3 + - - +
313A GLU* 2.8 31.0 + - - +
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Residues in contact with GLY 310 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
308A ASP* 3.2 6.2 + - - -
309A ARG* 1.3 79.5 - - - +
311A LEU* 1.3 57.1 + - - +
313A GLU* 3.4 13.1 + - - +
314A LEU* 2.9 28.2 + - - +
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Residues in contact with LEU 311 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
306A SER* 5.1 5.8 - - - +
308A ASP* 3.0 36.7 + - + +
310A GLY* 1.3 73.0 - - - +
312A THR* 1.3 62.9 + - - +
314A LEU* 3.2 8.7 + - + +
315A GLN* 2.8 55.6 + - - +
352A PRO* 5.4 12.1 - - + -
355A GLY 3.5 24.9 - - - +
356A PHE* 3.8 13.2 - - + -
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Residues in contact with THR 312 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
302A ILE* 4.2 10.3 - - + -
303A ASP 3.0 20.3 + - - +
304A GLU* 3.9 26.2 + - + +
306A SER* 3.9 6.6 + - - -
308A ASP 3.2 9.3 + - - -
309A ARG* 3.0 15.8 + - - +
311A LEU* 1.3 78.8 - - - +
313A GLU* 1.3 53.7 + - - +
315A GLN* 3.1 12.4 + - - +
316A LEU* 2.7 58.1 + - + +
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Residues in contact with GLU 313 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23A HIS* 4.2 22.5 + - - -
26A ASN* 4.6 8.0 + - - -
309A ARG 2.8 12.8 + - - +
310A GLY* 3.5 15.2 - - - +
312A THR* 1.3 78.0 - - - +
314A LEU* 1.3 51.0 + - - +
316A LEU* 3.2 10.3 + - + +
317A ASP* 2.6 55.2 + - - +
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Residues in contact with LEU 314 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
310A GLY 2.9 14.9 + - - +
311A LEU* 3.5 12.3 - - + +
313A GLU* 1.3 76.4 - - - +
315A GLN* 1.3 58.0 + - - +
317A ASP* 3.2 13.7 + - + +
318A TYR* 2.9 29.1 + - + +
355A GLY* 4.5 7.0 - - - +
356A PHE* 3.7 44.9 - - + -
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Residues in contact with GLN 315 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
300A ILE* 4.9 6.1 - - + +
301A SER 3.3 16.5 + - - +
302A ILE* 3.3 41.8 - - + +
303A ASP* 3.6 7.7 - - - +
311A LEU* 2.8 34.6 + - - +
312A THR* 3.5 16.4 + - - +
314A LEU* 1.3 77.7 - - - +
316A LEU* 1.3 57.7 + - - +
318A TYR* 3.3 7.5 + - - +
319A ASP* 2.9 27.2 + - - +
330A GLU* 5.5 0.3 - - - +
356A PHE* 3.2 38.4 - - + +
357A LYS 5.3 0.2 - - - +
358A SER* 5.0 1.6 + - - -
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Residues in contact with LEU 316 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
302A ILE* 4.0 27.1 - - + -
304A GLU* 5.3 11.7 - - + +
312A THR* 2.7 40.3 + - + +
313A GLU* 3.6 7.9 - - + +
315A GLN* 1.3 70.1 - - - +
317A ASP* 1.3 67.8 + - - +
319A ASP* 3.1 12.6 + - + +
320A LEU* 2.9 24.6 + - - +
332A THR* 6.2 1.1 - - + -
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Residues in contact with ASP 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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313A GLU* 2.6 48.0 + - - +
314A LEU* 3.2 15.1 + - + +
316A LEU* 1.3 73.3 - - - +
318A TYR* 1.3 63.3 + - - +
320A LEU* 3.0 22.0 + - - +
321A VAL* 3.1 17.5 + - + +
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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
----------------------------------------------------------
300A ILE* 3.4 32.7 - - + +
314A LEU* 2.9 18.3 + - + +
315A GLN 3.6 4.5 - - - +
317A ASP* 1.3 76.8 - - - +
319A ASP* 1.3 63.8 + - - +
321A VAL* 3.0 14.8 + - + +
322A MET* 3.0 62.2 + - + +
330A GLU* 4.0 5.2 - - + -
356A PHE* 3.5 34.5 - + + -
357A LYS* 4.9 6.5 + - - -
365A HMK 3.6 39.8 - + - -
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Residues in contact with ASP 319 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
302A ILE* 4.1 12.1 - - + -
315A GLN 2.9 15.2 + - - +
316A LEU* 3.1 18.6 + - - +
318A TYR* 1.3 76.6 - - - +
320A LEU* 1.3 66.4 + - - +
322A MET* 3.3 4.3 + - - +
323A LEU* 2.9 29.0 + - - +
328A GLY 4.5 0.7 - - - +
329A LYS* 4.0 5.9 - - - +
330A GLU* 3.1 46.3 + - + +
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Residues in contact with LEU 320 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
135A TRP* 4.4 25.4 - - + -
316A LEU 2.9 12.8 + - - +
317A ASP* 3.0 15.4 + - - +
319A ASP* 1.3 80.2 + - - +
321A VAL* 1.3 61.4 + - + +
323A LEU* 3.4 23.2 - - + +
324A THR* 2.8 36.2 + - + +
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Residues in contact with VAL 321 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
131A SER* 6.4 0.4 - - - -
135A TRP* 6.0 2.9 - - + -
317A ASP* 3.1 15.4 + - + +
318A TYR* 3.0 16.7 + - + +
320A LEU* 1.3 73.5 - - + +
322A MET* 1.3 78.8 + - + +
324A THR* 3.3 6.2 + - - -
325A MET* 2.9 51.5 + - + +
365A HMK 4.0 13.9 - - - +
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Residues in contact with MET 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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268A HIS* 6.3 2.7 - - - -
318A TYR* 3.0 50.2 + - + +
319A ASP* 3.5 8.7 - - - +
321A VAL* 1.3 81.2 - - + +
323A LEU* 1.3 58.5 - - - +
326A PHE* 2.9 34.4 + - + +
327A LEU 2.9 21.0 + - - -
328A GLY* 3.0 22.5 + - - +
329A LYS* 4.6 0.7 - - - +
330A GLU* 3.5 19.5 - - + +
365A HMK 3.5 37.0 - - - +
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Residues in contact with LEU 323 (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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141A TRP* 4.4 16.3 - - + -
319A ASP* 2.9 17.7 + - - +
320A LEU* 3.4 28.5 - - + +
321A VAL 3.1 0.2 - - - -
322A MET* 1.3 77.1 - - - +
324A THR* 1.3 61.3 + - + +
327A LEU* 2.9 55.3 + - + +
328A GLY 3.7 12.5 + - - +
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Residues in contact with THR 324 (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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134A MET* 3.5 18.7 - - - +
135A TRP* 3.6 31.0 - - + -
141A TRP* 3.9 18.2 - - + -
149A THR* 3.5 0.9 - - - -
150A LEU* 2.7 49.1 + - + +
151A PHE 3.1 9.0 + - - -
320A LEU* 2.8 27.8 + - + +
321A VAL* 3.3 11.8 + - - -
323A LEU* 1.3 77.2 - - + +
325A MET* 1.3 56.9 + - - +
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Residues in contact with MET 325 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
130A SER 4.4 5.8 - - - +
131A SER* 3.9 18.8 - - - +
134A MET* 3.4 29.8 - - + +
149A THR* 3.4 16.3 + - - +
151A PHE* 4.4 6.6 - - + +
159A PHE* 4.3 25.2 + - + +
321A VAL* 2.9 34.3 + - + +
324A THR* 1.3 80.6 - - - +
326A PHE* 1.3 91.3 + - + +
365A HMK 3.3 35.9 - - + -
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Residues in contact with PHE 326 (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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149A THR* 3.6 8.3 - - - +
159A PHE* 3.6 36.1 - + + -
160A TRP* 4.0 35.4 - + + +
175A PHE* 4.7 5.4 - + - -
322A MET* 2.9 48.3 + - + +
325A MET* 1.3 104.9 - - + +
327A LEU* 1.3 74.3 + - - +
328A GLY* 3.2 7.3 + - - +
365A HMK 4.1 12.3 - + - -
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Residues in contact with LEU 327 (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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141A TRP* 4.3 7.6 - - + -
147A GLU* 4.4 16.6 - - + +
148A GLN* 3.4 43.3 - - - +
149A THR* 3.8 10.1 - - + +
152A GLU* 5.5 0.2 - - - +
322A MET 2.9 3.4 + - - -
323A LEU* 2.9 38.2 + - + +
325A MET 3.8 0.2 - - - -
326A PHE* 1.3 81.8 - - - +
328A GLY* 1.3 64.1 + - - +
329A LYS* 5.8 0.3 - - - +
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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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
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