Contacts of the helix formed by residues 289 - 306 (chain A) in PDB entry 4IYM
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 GLY 289 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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256A PRO* 5.7 0.7 - - - -
287A PRO 3.9 0.9 + - - -
288A VAL* 1.3 79.5 + - - +
290A GLU* 1.3 66.8 + - - -
291A GLU 3.3 2.9 - - - -
292A THR 3.3 1.7 + - - -
293A ALA* 3.2 20.7 + - - +
391A ARG* 6.4 1.1 - - - -
392A ALA 2.9 17.6 + - - -
393A ARG* 4.4 9.1 + - - -
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Residues in contact with GLU 290 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
289A GLY* 1.3 71.3 - - - -
291A GLU* 1.3 63.1 + - - +
293A ALA* 3.3 3.8 + - - +
294A ASN* 3.0 37.8 + - - +
391A ARG* 3.0 45.4 + - - +
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Residues in contact with GLU 291 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
289A GLY 3.3 0.8 - - - -
290A GLU* 1.3 78.2 - - - +
292A THR* 1.3 58.6 + - - +
294A ASN* 3.8 6.9 - - + +
295A ARG* 2.9 59.5 + - + +
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Residues in contact with THR 292 (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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254A ILE* 3.7 39.7 - - + +
255A MSE 4.2 4.3 - - - +
256A PRO* 3.3 22.3 + - + +
260A LEU* 4.2 14.4 - - + +
287A PRO* 4.0 7.2 - - + -
288A VAL 3.1 24.0 + - - -
289A GLY 3.3 1.4 + - - -
291A GLU* 1.3 78.8 - - - +
293A ALA* 1.3 56.8 + - - +
295A ARG* 3.8 3.6 - - - +
296A LEU* 2.9 34.1 + - + +
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Residues in contact with ALA 293 (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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287A PRO* 3.5 31.2 - - + +
289A GLY 3.2 8.9 + - - +
290A GLU* 3.3 7.8 + - - +
292A THR* 1.3 77.3 - - - +
294A ASN* 1.3 59.0 + - - +
296A LEU* 3.7 1.1 - - - +
297A ILE* 2.8 38.8 + - + +
389A VAL* 5.5 0.4 - - + -
391A ARG* 3.6 34.1 - - + +
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Residues in contact with ASN 294 (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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290A GLU* 3.0 27.8 + - - +
291A GLU* 3.8 6.7 - - + +
293A ALA* 1.3 75.4 - - - +
295A ARG* 1.3 58.9 + - + +
297A ILE* 4.0 4.1 - - - +
298A ASP* 3.1 30.7 + - - +
391A ARG* 3.0 30.9 + - - +
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Residues in contact with ARG 295 (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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260A LEU* 3.5 35.0 - - + +
291A GLU* 2.9 43.9 + - + +
292A THR 4.0 0.4 - - - +
294A ASN* 1.3 77.6 - - + +
296A LEU* 1.3 61.9 + - - +
298A ASP* 3.4 6.9 + - - +
299A LYS* 3.3 56.3 + - - +
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Residues in contact with LEU 296 (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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254A ILE* 3.5 37.5 - - + -
260A LEU* 3.9 21.0 - - + +
263A ALA* 4.0 12.3 - - + -
264A ALA* 3.8 31.2 - - + +
267A LEU* 4.0 15.0 - - + -
285A ALA* 5.1 2.7 - - + -
287A PRO* 4.4 14.4 - - + -
292A THR 2.9 18.0 + - - +
293A ALA 3.7 2.5 - - - +
295A ARG* 1.3 74.3 - - - +
297A ILE* 1.3 63.3 + - + +
299A LYS* 3.3 6.1 + - - +
300A LEU* 2.9 33.2 + - + +
389A VAL* 6.2 0.7 - - + -
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Residues in contact with ILE 297 (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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287A PRO* 6.0 0.2 - - + -
293A ALA* 2.8 33.6 + - - +
294A ASN* 4.0 4.9 - - - +
296A LEU* 1.3 74.8 - - + +
298A ASP* 1.3 60.8 - - - +
300A LEU* 4.3 8.1 - - + -
301A VAL* 3.0 49.7 + - + +
346A VAL* 4.9 10.3 - - + -
367A LEU* 4.8 8.3 - - + -
369A ASP* 4.3 22.4 - - + +
389A VAL* 3.7 40.4 - - + -
391A ARG* 4.4 5.4 - - - +
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Residues in contact with ASP 298 (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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294A ASN 3.1 20.2 + - - +
295A ARG* 3.5 9.6 - - - +
296A LEU 3.2 0.4 - - - -
297A ILE* 1.3 75.5 - - - +
299A LYS* 1.3 60.1 + - + +
301A VAL* 4.8 1.1 - - - +
302A PRO* 3.2 23.9 - - - +
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Residues in contact with LYS 299 (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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260A LEU* 3.9 21.8 - - + +
261A ASP* 2.8 43.7 + - - +
264A ALA* 3.9 14.6 - - + -
295A ARG* 3.3 42.4 + - - +
296A LEU* 3.8 6.1 - - - +
297A ILE 3.2 0.2 - - - -
298A ASP* 1.3 80.4 - - + +
300A LEU* 1.3 63.4 + - - +
302A PRO* 3.4 10.2 - - - +
303A MSE 3.6 24.0 - - + +
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Residues in contact with LEU 300 (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 ALA* 4.0 26.2 - - + +
267A LEU* 4.1 24.7 - - + -
268A ILE* 4.2 13.2 - - + +
272A TYR* 5.2 0.2 - - + -
285A ALA* 5.8 0.4 - - + -
296A LEU* 2.9 21.2 + - + +
297A ILE* 3.9 7.9 - - + +
299A LYS* 1.3 75.9 - - - +
301A VAL* 1.3 66.6 + - - +
303A MSE 3.0 17.9 + - + +
304A VAL* 3.1 28.3 + - + +
367A LEU* 4.0 18.2 - - + -
387A LEU* 3.9 25.4 - - + -
389A VAL* 5.3 5.4 - - + -
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Residues in contact with VAL 301 (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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297A ILE* 3.0 38.7 + - + +
298A ASP* 4.8 0.9 - - - +
300A LEU* 1.3 73.5 - - - +
302A PRO* 1.4 70.7 - - + +
304A VAL* 3.1 5.2 + - - +
305A GLU* 3.0 37.7 + - - +
346A VAL* 4.2 14.1 - - + +
347A VAL* 3.8 18.8 - - + +
367A LEU* 4.0 16.2 - - + -
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Residues in contact with PRO 302 (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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298A ASP 3.2 23.1 - - - +
299A LYS* 3.4 11.2 - - - +
301A VAL* 1.4 94.2 - - + +
303A MSE 1.3 56.7 + - + +
305A GLU* 3.3 9.6 + - + +
306A SER* 3.0 33.3 + - - -
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Residues in contact with MSE 303 (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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261A ASP* 4.8 4.9 - - - +
264A ALA* 3.9 32.8 - - + +
265A ASN* 3.3 29.8 - - - +
268A ILE* 3.5 29.3 - - + +
299A LYS* 3.6 24.7 - - + +
300A LEU* 3.0 8.9 + - - +
302A PRO* 1.3 77.2 - - + +
304A VAL* 1.3 62.8 + - - +
306A SER* 3.6 9.3 + - - -
307A LEU* 3.5 16.5 + - - +
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Residues in contact with VAL 304 (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 ILE* 3.7 10.5 - - + -
272A TYR* 3.6 46.0 - - + +
300A LEU* 3.1 27.1 + - + +
301A VAL 3.1 5.1 + - - +
303A MSE 1.3 74.4 - - - +
305A GLU* 1.3 65.4 + - - +
307A LEU* 3.2 23.2 + - + +
347A VAL* 3.8 26.5 - - + -
365A GLY* 4.1 16.8 + - - -
366A CYS 4.9 0.2 - - - -
367A LEU* 4.6 7.2 - - + -
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Residues in contact with GLU 305 (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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301A VAL* 3.0 34.8 + - - +
302A PRO* 3.8 7.8 - - + +
304A VAL* 1.3 77.1 - - - +
306A SER* 1.3 58.3 + - - +
307A LEU 3.6 3.6 + - - +
346A VAL 4.5 5.9 - - - +
347A VAL* 3.8 26.2 - - + +
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Residues in contact with SER 306 (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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302A PRO 3.0 19.0 + - - -
303A MSE 3.6 10.5 + - - -
304A VAL 3.2 0.2 - - - -
305A GLU* 1.3 73.9 - - - +
307A LEU* 1.3 67.8 + - - +
308A ARG* 3.3 3.8 + - - +
318A ASP* 4.4 1.4 - - - +
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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
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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