Contacts of the helix formed by residues 291 - 302 (chain A) in PDB entry 4N78
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 ASN 291 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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243A ASN* 4.4 3.6 + - - -
246A VAL* 5.3 4.9 - - + +
285A ASP* 3.9 2.4 - - - +
290A ILE* 1.3 74.6 - - - +
292A LEU* 1.3 63.6 + - - +
293A SER* 3.1 26.3 + - - -
294A LYS* 3.3 47.3 + - + +
295A ILE* 3.5 17.0 + - - +
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Residues in contact with LEU 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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271A LEU* 3.9 30.1 - - + -
281A ILE* 3.8 11.4 - - + +
282A TYR* 3.7 33.2 - - + -
285A ASP* 3.0 40.9 + - + +
290A ILE* 3.7 20.9 - - + -
291A ASN* 1.3 72.1 - - - +
293A SER* 1.3 57.3 + - - +
295A ILE* 3.5 5.7 + - + +
296A ASP* 2.9 30.9 + - - +
331A ARG* 4.3 9.9 - - + +
332A TRP* 3.7 18.8 - - + -
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Residues in contact with SER 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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285A ASP* 4.6 1.8 + - - -
291A ASN* 3.1 11.8 + - - -
292A LEU* 1.3 78.5 - - - +
294A LYS* 1.3 58.2 + - - +
296A ASP* 3.3 8.8 + - - +
297A LYS* 2.9 27.4 + - - +
331A ARG* 5.2 7.3 + - - -
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Residues in contact with LYS 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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246A VAL* 3.9 16.9 - - + +
250A GLU* 3.1 30.9 + - - -
291A ASN* 3.3 35.2 + - + +
293A SER* 1.3 78.4 - - - +
295A ILE* 1.3 64.7 + - - +
297A LYS* 3.0 15.3 + - - +
298A TYR* 2.9 57.5 + - + +
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Residues in contact with ILE 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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242A VAL* 3.7 27.6 - - + -
246A VAL* 3.7 20.9 - - + -
267A MET* 4.4 10.8 - - + -
271A LEU* 3.6 35.2 - - + -
290A ILE* 5.9 1.3 - - + -
291A ASN 3.8 13.0 - - - +
292A LEU* 3.5 10.9 + - + +
293A SER 3.3 0.6 - - - -
294A LYS* 1.3 75.9 - - - +
296A ASP* 1.3 57.7 + - - +
298A TYR* 3.2 9.9 + - - +
299A PHE* 3.0 59.5 + - + -
332A TRP* 4.8 3.6 - - + -
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Residues in contact with ASP 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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292A LEU 2.9 19.0 + - - +
293A SER* 3.4 8.3 - - - +
295A ILE* 1.3 78.0 - - - +
297A LYS* 1.3 58.1 + - - +
299A PHE 3.4 0.5 + - - -
300A LYS* 3.0 28.6 + - - +
331A ARG 4.5 4.6 - - - +
332A TRP* 3.2 29.9 - - + -
333A THR* 2.6 50.4 + - - +
334A CYS* 3.2 14.7 + - - +
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Residues in contact with LYS 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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250A GLU* 6.3 0.8 - - - +
293A SER 2.9 13.1 + - - +
294A LYS* 3.4 15.4 - - - +
296A ASP* 1.3 78.9 + - - +
298A TYR* 1.3 86.8 + - + +
300A LYS* 3.4 8.4 + - + +
301A GLN* 3.1 32.2 + - + +
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Residues in contact with TYR 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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246A VAL* 3.8 23.1 + - + -
249A TYR* 3.7 37.3 + + + -
250A GLU* 3.2 33.2 - - + +
264A LEU* 3.9 18.2 - - + +
267A MET* 3.9 15.5 - - + -
294A LYS* 2.9 42.7 + - + +
295A ILE* 3.6 10.3 - - - +
297A LYS* 1.3 101.1 + - - +
299A PHE* 1.3 59.8 + - + +
301A GLN* 3.4 8.9 + - - +
302A LEU* 2.9 31.9 + - - +
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Residues in contact with PHE 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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264A LEU* 3.7 24.2 - - + -
267A MET* 4.2 3.4 - - + -
268A GLY* 3.7 32.8 - - - -
295A ILE* 3.0 39.4 + - + +
296A ASP* 5.4 0.2 - - - -
298A TYR* 1.3 80.0 - - + +
300A LYS* 1.3 60.8 + - - +
302A LEU 2.9 21.5 - - - +
303A GLN* 3.3 12.3 - - - +
315A LEU* 3.6 51.4 - - + -
316A ALA* 5.1 2.5 - - + +
319A ILE* 4.1 23.3 - - + -
332A TRP* 5.7 0.2 - + - -
334A CYS* 3.6 23.5 - - + +
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Residues in contact with LYS 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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296A ASP 3.0 17.8 + - - +
297A LYS* 3.8 7.9 - - + +
298A TYR 3.2 0.4 - - - -
299A PHE* 1.3 79.1 - - - +
301A GLN* 1.3 58.4 + - - +
303A GLN* 3.6 14.5 - - - +
333A THR* 3.2 46.0 + - - +
334A CYS* 3.5 12.1 - - + +
336A SER* 4.4 9.3 + - - +
342A GLN* 2.9 32.0 + - - +
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Residues in contact with GLN 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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249A TYR* 5.6 7.9 + - - +
297A LYS* 3.1 26.2 + - + +
298A TYR* 3.9 7.8 - - - +
300A LYS* 1.3 78.4 - - - +
302A LEU* 1.3 61.6 + - + +
303A GLN 4.2 0.2 + - - -
342A GLN* 3.2 15.8 - - - +
343A TYR* 3.0 37.4 + - + +
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Residues in contact with LEU 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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249A TYR* 4.0 15.7 - - - +
260A LYS* 4.1 7.9 - - - +
261A HIS* 4.3 1.3 - - + -
264A LEU* 3.6 24.2 - - + -
298A TYR 2.9 15.4 + - - +
299A PHE 2.9 10.4 - - - +
301A GLN* 1.3 81.2 - - + +
303A GLN* 1.3 60.4 + - - +
304A VAL 3.9 15.0 - - - +
305A VAL* 3.8 18.2 - - + -
315A LEU* 3.3 18.9 - - - +
410A GLU* 3.5 45.8 - - + +
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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