Contacts of the helix formed by residues 325 - 346 (chain A) in PDB entry 4ZGA
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 MET 325 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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178A TYR* 3.9 15.9 - - + +
311A PRO* 4.8 7.9 - - - +
314A SER* 3.4 37.5 - - - +
315A GLY* 3.6 20.2 - - - +
318A TYR* 3.4 28.5 - - + -
319A GLY 3.9 4.5 - - - +
320A PRO 3.4 20.0 - - - +
322A GLY 3.3 17.5 - - - +
323A PRO 3.0 0.8 - - - -
324A GLU* 1.3 78.0 - - - +
326A THR* 1.3 66.2 + - - +
327A ASN 3.3 0.9 - - - -
328A PRO* 3.6 7.4 - - + +
329A LEU* 3.1 37.2 + - + +
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Residues in contact with THR 326 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
185A VAL* 3.3 43.3 - - + +
323A PRO* 3.3 17.9 + - - +
324A GLU 3.4 0.4 - - - -
325A MET* 1.3 77.4 - - - +
327A ASN* 1.3 52.0 + - - +
329A LEU* 3.1 7.2 + - - +
330A ARG* 2.7 31.2 + - + -
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Residues in contact with ASN 327 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
324A GLU* 4.1 5.5 + - - +
325A MET 3.3 0.2 - - - -
326A THR* 1.3 78.7 - - - +
328A PRO* 1.3 62.1 - - + +
330A ARG* 2.8 11.7 + - - +
331A GLU* 2.7 42.5 + - + +
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Residues in contact with PRO 328 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
310A GLN* 4.0 26.3 - - - +
311A PRO* 5.3 7.0 - - + -
314A SER* 3.9 25.8 - - - +
318A TYR* 5.9 0.7 - - + -
324A GLU 3.2 21.8 - - - +
325A MET* 3.7 9.6 - - - +
327A ASN* 1.3 92.3 - - + +
329A LEU* 1.3 59.0 + - + +
331A GLU* 3.4 10.3 + - + +
332A ILE* 3.0 27.7 + - - +
906A SCN 4.9 2.3 - - - -
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Residues in contact with LEU 329 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
174A PHE* 3.6 30.5 - - + -
178A TYR* 4.1 35.7 - - + +
181A LYS* 4.9 9.4 - - + -
185A VAL* 4.3 3.4 - - + -
186A MET* 3.4 33.5 - - + +
311A PRO* 3.7 24.7 - - + -
325A MET* 3.1 28.7 + - + +
326A THR* 3.5 6.7 - - - +
328A PRO* 1.3 74.4 - - + +
330A ARG* 1.3 65.5 + - - +
332A ILE* 4.0 5.8 - - + +
333A ASP* 3.1 16.3 + - - +
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Residues in contact with ARG 330 (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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185A VAL* 3.9 21.1 - - + +
326A THR* 2.7 13.8 + - + +
327A ASN* 2.8 17.6 + - - +
329A LEU* 1.3 74.5 - - - +
331A GLU* 1.3 65.9 + - + +
333A ASP* 2.8 14.4 + - - +
334A LYS* 2.9 13.8 + - - +
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Residues in contact with GLU 331 (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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283A GLU* 5.4 3.3 - - - +
327A ASN* 2.7 24.8 + - + +
328A PRO* 3.4 11.0 + - + +
330A ARG* 1.3 75.0 - - - +
332A ILE* 1.3 63.4 + - - +
334A LYS* 3.2 11.8 + - - +
335A ILE* 3.1 23.7 + - - +
906A SCN 3.8 17.0 - - - -
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Residues in contact with ILE 332 (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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169A PHE* 4.6 4.0 - - + -
171A VAL* 5.1 12.6 - - + -
174A PHE* 5.6 4.0 - - + -
189A ILE* 4.4 10.3 - - + -
310A GLN* 5.5 5.4 - - + +
311A PRO* 6.2 1.1 - - + -
328A PRO 3.0 16.9 + - - +
329A LEU* 4.0 10.3 - - + +
331A GLU* 1.3 74.8 - - - +
333A ASP* 1.3 63.3 + - - +
335A ILE* 3.1 5.1 + - - +
336A VAL* 3.1 25.2 + - + +
356A PHE* 5.9 0.7 - - + -
906A SCN 3.9 23.5 - - - +
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Residues in contact with ASP 333 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
185A VAL 3.8 3.6 - - - +
186A MET* 3.2 18.0 - - - -
187A PRO* 3.0 20.8 - - - +
188A ASN* 2.8 21.0 + - - +
189A ILE* 2.5 48.3 + - + +
329A LEU 3.1 14.8 + - - +
330A ARG 2.8 8.9 + - - +
332A ILE* 1.3 77.5 - - - +
334A LYS* 1.3 60.9 + - - +
336A VAL* 3.6 0.8 + - - -
337A GLY 3.1 17.0 + - - -
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Residues in contact with LYS 334 (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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188A ASN* 5.0 1.8 - - - +
330A ARG 2.9 10.5 + - - +
331A GLU* 3.2 16.1 + - - +
333A ASP* 1.3 76.9 - - - +
335A ILE* 1.3 58.7 + - + +
337A GLY* 3.0 4.9 + - - -
338A GLN* 2.8 39.1 + - + +
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Residues in contact with ILE 335 (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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169A PHE* 4.1 10.5 - - + -
282A HIS* 3.6 16.2 - - + +
283A GLU* 3.4 38.1 - - + +
286A ILE* 3.5 29.1 - - + +
306A PHE* 4.1 11.2 - - + -
331A GLU* 3.1 16.0 + - - +
332A ILE 3.1 7.2 + - - +
334A LYS* 1.3 72.3 - - + +
336A VAL* 1.3 65.8 + - - +
338A GLN* 3.4 12.1 + - - +
339A LEU* 3.0 19.9 + - - +
906A SCN 3.9 21.5 - - - +
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Residues in contact with VAL 336 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
169A PHE* 3.7 34.5 - - + -
188A ASN* 4.1 11.4 - - + -
189A ILE* 3.8 19.5 - - + +
192A LEU* 3.7 30.5 - - + -
332A ILE 3.1 14.7 + - - +
333A ASP 3.8 7.0 - - - +
335A ILE* 1.3 73.2 - - - +
337A GLY* 1.3 53.0 + - - +
339A LEU* 2.8 12.5 + - + +
340A MET* 2.7 41.2 + - + -
356A PHE* 4.2 7.9 - - + -
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Residues in contact with GLY 337 (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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145A VAL* 5.3 0.2 - - - -
188A ASN* 2.9 32.6 - - - +
333A ASP 3.1 5.3 + - - -
334A LYS 3.0 7.7 + - - -
336A VAL* 1.3 74.5 - - - +
338A GLN* 1.3 56.3 + - - -
340A MET* 3.2 1.2 + - - +
341A ASP* 2.6 47.2 + - - +
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Residues in contact with GLN 338 (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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101A TRP* 4.8 14.8 + - - +
132A THR* 3.4 31.6 - - + +
283A GLU* 3.3 47.3 + - - +
286A ILE* 4.3 8.0 - - + +
287A LEU* 5.8 1.2 - - - +
334A LYS* 2.8 26.6 + - - +
335A ILE* 3.4 18.6 - - - +
337A GLY* 1.3 69.6 - - - +
339A LEU* 1.3 53.3 + - - +
341A ASP* 3.4 4.1 + - - +
342A GLY* 2.6 36.7 + - - -
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Residues in contact with LEU 339 (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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167A ILE* 4.5 28.3 - - + -
169A PHE* 4.2 21.3 - - + -
286A ILE* 3.6 32.7 - - + +
289A ILE* 5.1 7.9 - - + -
290A LEU* 4.1 15.3 - - + -
306A PHE* 6.2 0.4 - - + -
335A ILE 3.0 7.6 + - - +
336A VAL* 2.8 17.5 + - + +
338A GLN* 1.3 75.7 - - - +
340A MET* 1.3 68.9 + - + +
342A GLY* 3.1 2.1 + - - +
343A LEU* 2.8 37.6 + - + +
354A VAL* 4.9 14.1 - - + -
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Residues in contact with MET 340 (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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144A TRP* 3.6 66.3 - - + +
188A ASN* 4.7 2.0 - - - +
192A LEU* 4.1 10.3 - - + -
336A VAL* 2.7 35.5 + - + +
337A GLY 4.1 2.0 - - - +
339A LEU* 1.3 76.7 - - + +
341A ASP* 1.3 66.3 + - - +
343A LEU* 3.6 25.5 + - + +
344A LYS* 3.3 20.3 + - - +
349A HIS* 4.5 9.5 - - + +
354A VAL* 4.1 15.3 - - + -
491A TYR* 3.8 18.6 - - + -
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Residues in contact with ASP 341 (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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132A THR* 3.7 21.3 + - - +
133A ASN* 4.9 4.4 - - - +
143A HIS* 2.9 40.4 + - - +
144A TRP* 3.3 22.2 + - - +
145A VAL* 4.6 3.3 - - - +
337A GLY* 2.6 31.1 + - - +
338A GLN* 3.4 6.0 + - - +
340A MET* 1.3 71.4 - - - +
342A GLY* 1.3 58.2 + - - +
344A LYS* 3.1 10.0 + - - +
345A GLN* 2.9 28.8 + - - +
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Residues in contact with GLY 342 (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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132A THR* 4.1 9.2 - - - -
290A LEU* 3.5 25.3 - - - +
338A GLN 2.6 19.5 + - - -
339A LEU 3.4 2.2 - - - -
341A ASP* 1.3 74.3 - - - +
343A LEU* 1.3 62.4 + - - +
345A GLN* 3.4 11.6 + - - +
346A LEU* 3.3 22.5 + - - +
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Residues in contact with LEU 343 (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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167A ILE* 4.3 4.9 - - + -
290A LEU* 3.8 17.0 - - + -
293A LEU* 4.0 18.6 - - + -
339A LEU* 2.8 26.2 + - + +
340A MET* 4.0 29.6 - - + +
341A ASP 3.2 0.2 - - - -
342A GLY* 1.3 70.8 - - - +
344A LYS* 1.3 58.5 + - - +
346A LEU* 2.7 24.1 + - - +
348A LEU* 3.0 34.0 + - + -
349A HIS* 3.7 20.2 - - - +
352A VAL* 4.1 29.2 - - + +
354A VAL* 4.4 7.4 - - + -
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Residues in contact with LYS 344 (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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135A GLN* 4.6 0.8 - - - +
141A GLU* 3.5 32.3 + - - +
142A SER* 2.7 32.4 + - - +
143A HIS* 5.2 0.2 - - - -
144A TRP* 3.9 16.6 - - + +
147A ASP* 2.3 35.1 + - - +
340A MET 3.3 11.5 + - - +
341A ASP* 3.1 10.5 + - - +
343A LEU* 1.3 76.3 - - - +
345A GLN* 1.3 56.6 + - - +
347A LYS* 2.7 24.6 + - - +
349A HIS* 3.2 38.4 + - + +
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Residues in contact with GLN 345 (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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125A LEU* 5.9 6.3 - - + -
130A CYS* 3.5 30.7 + - - +
131A CYS 3.5 8.1 + - - -
132A THR* 3.8 17.6 - - - +
134A TYR* 3.5 16.0 - - - +
135A GLN* 3.1 50.7 + - + +
290A LEU* 6.0 1.0 - - - +
341A ASP 2.9 12.4 + - - +
342A GLY* 3.4 14.9 + - - +
344A LYS* 1.3 78.9 - - - +
346A LEU* 1.3 68.2 + - + +
347A LYS* 3.4 1.0 + - - +
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Residues in contact with LEU 346 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
125A LEU* 5.4 11.0 - - + +
128A GLY* 6.1 2.5 - - - -
158A PRO* 5.2 3.1 - - - +
290A LEU* 3.3 38.6 - - + +
293A LEU* 4.4 1.6 - - + -
294A THR* 3.9 21.1 - - + -
342A GLY 3.3 12.3 + - - +
343A LEU 2.7 12.8 + - - +
345A GLN* 1.3 81.8 - - + +
347A LYS* 1.3 70.8 + - - +
348A LEU* 3.2 34.2 + - + +
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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
------------------------------------------------------------
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