Contacts of the helix formed by residues 297 - 316 (chain B) in PDB entry 3ZFW
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 LYS 297 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
292B TYR* 3.0 32.5 + - + +
295B ARG* 3.2 51.5 - - + +
296B GLY* 1.3 74.9 - - - +
298B TYR* 1.3 56.8 + - - +
300B GLU* 3.3 44.5 - - + +
301B ALA* 3.1 26.8 + - - +
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Residues in contact with TYR 298 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
293B GLY* 3.3 31.2 + - - -
296B GLY* 3.2 27.5 + - - -
297B LYS* 1.3 68.8 - - - +
299B LYS* 1.4 64.7 + - - +
301B ALA* 3.1 5.8 + - - +
302B GLU* 3.1 25.1 + - - +
333B LEU* 3.9 24.3 - - + +
336B ASN* 3.2 58.9 + - + +
337B GLN* 3.7 24.5 + - + -
203Y THR 4.9 4.2 + - - -
205Y LEU* 6.1 0.9 - - + -
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Residues in contact with LYS 299 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
298B TYR* 1.4 76.6 - - - +
300B GLU* 1.3 65.0 + - - +
302B GLU* 4.0 6.9 - - - +
303B PRO* 3.3 18.4 - - - +
337B GLN* 3.3 22.2 - - + +
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Residues in contact with GLU 300 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
292B TYR* 4.2 13.5 - - + -
297B LYS* 3.3 60.6 - - + +
298B TYR 3.9 0.2 + - - -
299B LYS* 1.3 83.2 + - - +
301B ALA* 1.3 57.2 - - - +
302B GLU 3.4 0.9 - - - -
303B PRO* 3.4 14.6 - - - +
304B LEU* 3.3 21.4 - - - +
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Residues in contact with ALA 301 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
289B ALA* 3.5 16.4 - - - +
292B TYR* 3.7 19.7 - - + -
293B GLY 4.2 1.8 - - - +
297B LYS 3.1 16.3 + - - +
298B TYR* 3.1 6.6 + - - +
300B GLU* 1.3 76.1 - - - +
302B GLU* 1.3 63.3 + - - +
303B PRO 3.5 0.2 - - - -
304B LEU* 3.4 10.1 + - - +
305B CYS 3.2 17.7 + - - -
333B LEU* 3.7 25.5 - - + +
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Residues in contact with GLU 302 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
298B TYR 3.1 12.6 + - - +
299B LYS* 4.0 5.5 - - - +
301B ALA* 1.3 73.3 - - - +
303B PRO* 1.4 69.4 - - + +
304B LEU 3.3 0.3 + - - -
305B CYS* 3.3 2.3 + - - +
306B LYS* 3.0 61.4 + - + +
330B LEU* 4.3 10.7 - - + +
333B LEU* 3.9 11.4 - - + +
334B CYS* 3.9 10.7 - - - -
337B GLN* 2.7 33.3 + - - +
339B LYS* 2.9 22.4 + - - -
342B GLU* 3.5 10.4 - - - +
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Residues in contact with PRO 303 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
299B LYS 3.3 19.1 - - - +
300B GLU* 3.4 17.0 - - - +
302B GLU* 1.4 87.7 - - + +
304B LEU* 1.3 54.3 + - + +
306B LYS* 3.8 9.0 - - + +
307B ARG* 3.0 30.1 + - - +
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Residues in contact with LEU 304 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
264B ASN* 5.8 0.9 - - - +
267B LEU* 5.3 1.1 - - + -
285B LEU* 3.7 52.4 - - + +
288B LEU* 3.8 19.3 - - + -
289B ALA* 4.0 4.7 - - + +
292B TYR* 3.6 31.2 - - + -
300B GLU 3.3 24.7 - - - +
301B ALA* 3.4 8.9 + - - +
302B GLU 3.3 0.2 - - - -
303B PRO* 1.3 78.4 - - + +
305B CYS* 1.3 58.4 + - - +
307B ARG* 3.4 7.2 + - - +
308B ALA* 3.1 27.0 + - - +
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Residues in contact with CYS 305 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
285B LEU 5.3 0.7 - - - -
286B ASN* 4.3 4.5 - - - +
289B ALA* 4.1 8.5 - - - +
301B ALA 3.2 12.8 + - - +
302B GLU 3.8 0.7 - - - +
304B LEU* 1.3 74.9 - - - +
306B LYS* 1.4 60.7 + - - +
308B ALA* 3.4 1.6 + - - -
309B LEU* 3.1 26.7 + - - +
326B GLN* 3.2 34.4 + - - +
329B ASN* 4.2 10.1 - - - -
330B LEU* 3.6 24.8 - - + +
333B LEU* 3.8 6.7 - - + -
205Y LEU* 4.1 26.9 - - - -
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Residues in contact with LYS 306 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
302B GLU* 3.0 51.5 + - + +
303B PRO* 3.8 8.3 - - + +
305B CYS* 1.4 74.1 - - - +
307B ARG* 1.4 62.4 + - - +
309B LEU* 3.5 3.9 + - + +
310B GLU* 3.2 32.7 + - - +
330B LEU* 4.0 21.1 - - + -
342B GLU* 5.0 3.6 + - - -
346B TYR* 3.6 20.3 + - - +
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Residues in contact with ARG 307 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
267B LEU* 5.4 1.2 - - - +
271B GLU* 3.2 27.5 + - - -
276B LYS* 3.4 38.3 - - - +
281B VAL* 3.5 23.8 - - - +
285B LEU* 3.6 27.5 - - + +
303B PRO 3.0 17.9 + - - +
304B LEU* 3.6 6.7 - - - +
305B CYS 3.3 0.2 - - - -
306B LYS* 1.4 75.5 - - - +
308B ALA* 1.4 62.5 + - - +
310B GLU* 3.3 7.6 + - + +
311B ILE* 3.2 39.6 + - + +
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Residues in contact with ALA 308 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
282B ALA* 3.5 33.9 - - - +
285B LEU* 4.0 6.5 - - + +
286B ASN 4.3 2.7 - - - +
304B LEU 3.1 16.2 + - - +
305B CYS 3.4 5.6 + - - +
307B ARG* 1.4 72.6 - - - +
309B LEU* 1.3 65.1 + - - +
311B ILE* 3.5 6.6 + - - +
312B ARG* 3.1 29.9 + - - +
326B GLN* 3.7 17.7 - - - +
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Residues in contact with LEU 309 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
305B CYS 3.1 16.6 + - - +
306B LYS* 3.6 5.6 - - + +
308B ALA* 1.3 75.9 - - - +
310B GLU* 1.4 68.7 + - - +
312B ARG* 3.1 5.1 + - - +
313B GLU* 2.9 43.7 + - - +
323B VAL* 3.7 42.4 - - + +
326B GLN* 3.8 19.7 - - + +
327B LEU* 3.8 20.2 - - + +
330B LEU* 4.0 22.7 - - + -
346B TYR* 5.2 2.5 - - + -
349B ARG* 4.7 4.3 - - - +
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Residues in contact with GLU 310 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
277B ASP* 5.4 0.7 - - - -
306B LYS* 3.2 24.6 + - - +
307B ARG* 3.3 9.2 + - + +
309B LEU* 1.4 88.5 - - - +
311B ILE* 1.3 60.9 + - + +
313B GLU* 3.2 21.4 + - - +
314B LYS* 3.1 23.8 + - - +
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Residues in contact with ILE 311 (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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277B ASP* 3.8 52.3 - - - +
278B HIS 3.9 7.4 - - - +
279B PRO* 4.8 1.3 - - + -
281B VAL* 4.3 8.3 - - + -
282B ALA* 3.9 19.3 - - + +
285B LEU* 3.7 26.2 - - + -
307B ARG* 3.2 34.4 + - + +
308B ALA* 3.6 7.4 - - - +
310B GLU* 1.3 76.3 - - - +
312B ARG* 1.4 57.8 + - - +
314B LYS* 3.1 5.2 + - - +
315B VAL* 3.0 31.2 + - + +
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Residues in contact with ARG 312 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
279B PRO* 4.6 4.0 + - + +
282B ALA* 3.8 31.7 + - + +
283B ALA* 3.9 11.9 - - - +
286B ASN* 4.4 1.2 - - - +
308B ALA* 3.1 15.3 + - - +
309B LEU* 3.1 9.4 + - - +
311B ILE* 1.4 75.5 - - + +
313B GLU* 1.4 55.8 + - - +
315B VAL* 4.9 1.6 - - - -
316B LEU* 2.9 47.0 + - + +
317B GLY 3.4 1.0 + - - -
322B ASP* 3.8 35.1 + - - +
323B VAL* 4.0 14.7 - - + +
325B LYS* 5.1 2.0 - - - -
326B GLN* 3.1 44.1 + - - +
208Y ASP* 2.7 36.0 + - - -
210Y SER* 5.1 1.8 + - - -
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Residues in contact with GLU 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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309B LEU* 2.9 29.4 + - - +
310B GLU* 3.2 34.6 - - - +
311B ILE 3.3 0.2 - - - -
312B ARG* 1.4 72.0 - - - +
314B LYS* 1.4 65.5 + - - +
317B GLY* 3.3 26.4 + - - -
318B LYS* 3.9 19.0 + - + -
323B VAL* 3.8 16.9 - - + +
349B ARG* 2.7 37.7 + - - -
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Residues in contact with LYS 314 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
277B ASP* 3.3 46.2 + - + +
310B GLU 3.1 14.2 + - - +
311B ILE* 3.1 9.8 + - - +
313B GLU* 1.4 78.8 - - - +
315B VAL* 1.3 64.7 + - + +
317B GLY 4.9 0.5 + - - -
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Residues in contact with VAL 315 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
277B ASP* 3.4 29.8 - - + +
279B PRO* 4.3 24.7 - - + -
311B ILE* 3.0 19.0 + - + +
312B ARG* 4.3 2.0 - - - +
314B LYS* 1.3 84.6 - - + +
316B LEU* 1.3 72.4 + - + +
317B GLY 3.6 0.2 - - - -
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Residues in contact with LEU 316 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
279B PRO* 5.9 8.3 - - + -
312B ARG* 2.9 35.9 + - + +
315B VAL* 1.3 85.6 - - + +
317B GLY* 1.3 58.6 + - - +
320B HIS* 3.8 44.5 - - + +
322B ASP* 3.8 33.2 - - + +
323B VAL* 4.9 1.1 - - + -
357B ARG* 5.3 2.4 + - - -
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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