Contacts of the helix formed by residues 267 - 280 (chain A) in PDB entry 4Z9L
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 267 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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227A ARG* 4.7 14.1 - - - +
265A GLY 3.3 2.3 - - - -
266A ARG* 1.3 86.0 - - - +
268A TYR* 1.4 52.5 + - - +
269A ILE* 3.1 16.9 + - + +
270A ASP* 2.9 32.3 + - - +
271A GLN* 2.8 36.2 + - - +
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Residues in contact with TYR 268 (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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227A ARG* 3.6 37.6 - - + +
230A ARG* 3.0 36.0 + - + -
234A VAL* 4.2 11.1 + - - +
235A ILE* 3.7 58.7 - - + +
267A ASP* 1.4 70.0 - - - +
269A ILE* 1.4 60.1 + - + +
271A GLN* 3.3 7.7 - - + +
272A TRP* 2.9 30.7 + - - +
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Residues in contact with ILE 269 (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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267A ASP* 3.1 11.1 + - + +
268A TYR* 1.4 77.2 - - + +
270A ASP* 1.3 62.7 + - - +
272A TRP* 3.2 7.9 + - - +
273A ASN* 3.1 34.9 + - - +
297A TYR* 3.3 46.3 + - + +
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Residues in contact with ASP 270 (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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264A PRO 3.8 1.6 - - - +
265A GLY* 3.3 3.7 - - - -
266A ARG* 3.0 29.8 + - - +
267A ASP* 2.9 27.2 + - - +
269A ILE* 1.3 72.5 - - - +
271A GLN* 1.4 61.5 - - - +
273A ASN* 3.2 14.1 + - - +
274A LYS* 2.9 57.9 + - - +
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Residues in contact with GLN 271 (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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227A ARG* 3.4 37.4 + - - +
228A TYR* 3.3 20.7 - - - +
230A ARG 5.1 0.7 - - - +
235A ILE* 3.7 29.2 - - + +
263A PHE* 3.0 32.2 + - - +
265A GLY* 3.9 18.3 + - - +
267A ASP 2.8 20.9 + - - +
268A TYR* 3.3 12.6 - - + +
270A ASP* 1.4 70.8 - - - +
272A TRP* 1.4 61.5 + - - +
274A LYS* 3.3 6.4 + - - +
275A VAL* 3.2 28.3 + - + +
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Residues in contact with TRP 272 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
232A PRO* 3.7 27.4 - - + -
235A ILE* 4.4 13.4 - - + +
236A LEU* 3.9 26.7 - - + -
268A TYR 2.9 20.4 + - - +
269A ILE* 3.6 6.1 - - - +
271A GLN* 1.4 71.5 - - - +
273A ASN* 1.4 66.6 + - - +
275A VAL* 3.4 18.6 + - + +
276A ILE* 3.1 54.2 + - + +
282A PRO* 4.1 9.4 - - + -
286A PHE* 4.1 3.1 - + - -
297A TYR* 4.6 19.7 - + + -
298A VAL* 3.9 41.1 + - + +
301A ARG* 5.0 5.3 - - + +
342A ILE* 3.7 24.2 - - + -
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Residues in contact with ASN 273 (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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269A ILE* 3.1 32.6 + - - +
270A ASP* 3.2 14.1 + - - +
272A TRP* 1.4 80.6 - - - +
274A LYS* 1.4 56.7 + - + +
276A ILE* 3.4 17.0 - - + +
277A GLU* 2.9 49.2 + - + +
297A TYR* 4.7 6.6 + - - -
301A ARG* 5.1 3.1 - - - +
302A PRO* 5.1 8.7 - - - +
304A TYR* 6.4 0.2 - - + -
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Residues in contact with LYS 274 (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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263A PHE* 3.6 21.2 - - + -
264A PRO* 3.7 39.4 + - + -
265A GLY 4.7 0.4 - - - +
270A ASP* 2.9 49.2 + - - +
271A GLN 3.7 5.8 - - - +
273A ASN* 1.4 71.6 - - + +
275A VAL* 1.4 65.6 + - - +
277A GLU* 3.8 18.7 + - - +
278A GLN* 3.5 32.8 + - - +
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Residues in contact with VAL 275 (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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232A PRO* 5.0 0.9 - - + -
235A ILE* 5.0 8.7 - - + -
247A TRP* 3.9 20.2 - - + -
263A PHE* 3.7 32.1 - - + -
271A GLN* 3.2 20.3 + - - +
272A TRP* 3.6 25.1 - - + +
273A ASN 3.3 0.2 - - - -
274A LYS* 1.4 75.5 - - - +
276A ILE* 1.4 58.3 + - - +
278A GLN* 3.3 2.3 + - - +
279A LEU* 2.9 31.9 + - + +
342A ILE* 3.8 31.0 - - + -
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Residues in contact with ILE 276 (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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272A TRP* 3.1 51.9 + - + +
273A ASN* 3.4 20.4 - - - +
275A VAL* 1.4 74.2 - - + +
277A GLU* 1.4 62.8 + - - +
280A GLY* 2.8 47.4 + - - +
281A THR* 4.5 8.3 - - + +
282A PRO* 4.4 6.7 - - + -
301A ARG* 4.2 19.3 - - + -
302A PRO* 3.4 26.9 - - + +
304A TYR* 3.4 18.3 - - + +
342A ILE* 4.8 0.2 - - + -
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Residues in contact with GLU 277 (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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273A ASN* 2.9 37.5 + - - +
274A LYS* 3.9 24.7 - - - +
275A VAL 3.3 0.2 - - - -
276A ILE* 1.4 75.2 - - - +
278A GLN* 1.3 63.2 - - + +
304A TYR* 3.6 46.5 + - + +
306A GLY* 4.8 4.2 - - - -
307A LEU* 4.7 9.5 - - - +
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Residues in contact with GLN 278 (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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258A ARG* 2.8 39.4 + - - +
262A LEU* 3.0 25.6 + - - +
263A PHE* 3.7 14.6 - - + -
264A PRO* 5.5 0.4 - - - +
274A LYS* 3.5 23.7 + - - +
275A VAL 3.3 2.9 + - - +
276A ILE 3.2 0.2 - - - -
277A GLU* 1.3 82.6 - - + +
279A LEU* 1.3 57.4 + - + +
280A GLY 3.5 0.4 - - - -
307A LEU* 2.8 44.0 + - + +
312A LEU* 3.5 17.3 - - + +
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Residues in contact with LEU 279 (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 TRP* 3.5 30.3 - - + -
263A PHE* 4.2 17.0 - - + -
275A VAL* 2.9 16.8 + - + +
278A GLN* 1.3 72.7 - - + +
280A GLY* 1.3 61.2 + - - +
305A ALA 4.3 2.6 - - - +
306A GLY* 3.6 8.5 - - - -
307A LEU 4.5 4.9 + - - +
309A PHE* 3.8 20.6 - - + -
312A LEU* 3.6 28.0 - - + -
340A LEU* 3.5 25.6 - - + +
342A ILE* 4.1 18.5 - - + +
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Residues in contact with GLY 280 (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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276A ILE* 2.8 25.9 + - - -
279A LEU* 1.3 82.8 - - - +
281A THR* 1.3 65.8 + - - -
304A TYR 3.3 12.3 - - - -
305A ALA 3.9 2.5 - - - -
306A GLY* 3.4 13.7 - - - -
342A ILE* 3.3 19.9 - - - +
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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