Contacts of the helix formed by residues 301 - 311 (chain D) in PDB entry 5NTI
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 SER 301 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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295C GLN* 4.9 2.1 + - - -
299D ILE 3.5 2.9 + - - -
300D PHE* 1.3 75.7 - - - +
302D ARG* 1.3 60.0 + - - +
303D GLU* 3.2 18.7 + - - +
304D GLU* 2.8 39.1 + - - +
305D VAL* 3.0 28.7 + - - +
381D LYS* 5.6 0.9 - - - -
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Residues in contact with ARG 302 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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301D SER* 1.3 73.4 - - - +
303D GLU* 1.3 62.7 + - - +
305D VAL* 3.5 29.5 + - - +
306D THR* 2.7 49.1 + - - +
309D GLN* 4.0 9.5 + - - +
386D GLU* 3.2 25.3 + - - -
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Residues in contact with GLU 303 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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291C ASP* 5.4 8.4 - - - +
294C ARG* 5.3 11.0 + - - +
295C GLN* 5.7 3.8 - - - +
301D SER* 3.2 20.8 + - - +
302D ARG* 1.3 85.8 + - + +
304D GLU* 1.3 58.9 + - + +
306D THR* 3.5 8.7 + - - -
307D GLY* 3.0 22.7 + - - -
310D ARG* 4.5 6.2 + - - +
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Residues in contact with GLU 304 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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295C GLN* 3.5 32.7 + - - +
298C ASN* 4.0 4.9 + - - -
380C GLY* 4.3 7.1 - - - +
300D PHE* 3.4 27.7 - - + -
301D SER* 2.8 45.4 + - - +
303D GLU* 1.3 75.2 - - - +
305D VAL* 1.3 64.1 + - - +
307D GLY* 3.2 3.7 + - - +
308D TYR* 3.2 30.7 + - + -
381D LYS* 3.2 28.5 + - - +
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Residues in contact with VAL 305 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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300D PHE* 4.2 18.4 - - + +
301D SER 3.0 22.7 + - - +
302D ARG* 3.5 31.6 - - - +
304D GLU* 1.3 71.4 - - - +
306D THR* 1.3 65.6 + - - +
308D TYR* 3.2 5.2 + - - +
309D GLN* 3.0 40.5 + - + +
383D GLY* 6.0 0.7 - - - -
386D GLU* 3.7 28.9 - - + +
387D LEU* 4.3 18.8 - - + +
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Residues in contact with THR 306 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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302D ARG* 2.7 37.0 + - - +
303D GLU* 3.5 9.0 - - - -
305D VAL* 1.3 76.2 - - - +
307D GLY* 1.3 56.4 + - - +
309D GLN* 3.1 14.5 + - + +
310D ARG* 2.9 46.7 + - + +
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Residues in contact with GLY 307 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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291C ASP* 5.9 1.1 - - - -
303D GLU 3.0 14.3 + - - -
304D GLU* 3.2 6.8 + - - -
306D THR* 1.3 74.5 - - - +
308D TYR* 1.3 60.7 + - - +
310D ARG* 3.2 34.8 + - - +
311D LYS* 3.2 19.7 + - - +
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Residues in contact with TYR 308 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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379C GLU 6.1 0.3 - - - -
380C GLY* 6.1 0.7 - - - -
300D PHE* 3.7 32.1 - + - -
304D GLU* 3.2 26.2 + - + -
305D VAL 3.2 6.9 + - - +
307D GLY* 1.3 75.3 - - - +
309D GLN* 1.3 61.0 + - - +
311D LYS* 3.4 37.2 - - - +
316D MET* 3.7 29.0 - - + +
319D ARG* 5.2 2.5 + - + -
378D PHE* 3.9 15.3 - + - -
379D GLU* 2.6 43.7 + - - +
387D LEU* 3.5 35.1 - - + +
390D ALA* 3.7 11.1 - - - +
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Residues in contact with GLN 309 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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302D ARG* 4.0 9.2 + - - +
305D VAL* 3.0 36.1 + - - +
306D THR* 3.6 13.7 + - + +
308D TYR* 1.3 75.6 - - - +
310D ARG* 1.3 62.2 + - - +
311D LYS 3.2 6.0 - - - +
386D GLU* 3.1 31.4 + - - +
387D LEU 4.8 1.6 - - - +
389D ARG* 3.1 53.6 + - + +
390D ALA* 4.3 7.3 + - - +
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Residues in contact with ARG 310 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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288C ARG* 4.0 28.2 - - - +
291C ASP* 4.4 15.2 + - - -
303D GLU* 4.5 5.9 + - - +
306D THR* 2.9 24.6 + - + +
307D GLY* 3.2 36.0 + - - +
309D GLN* 1.3 74.3 - - - +
311D LYS* 1.3 65.2 + - + +
312D SER* 3.6 1.9 + - - -
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Residues in contact with LYS 311 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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286C GLN* 5.0 12.5 + - - +
287C LEU* 6.1 2.8 - - - +
307D GLY 3.2 15.1 + - - +
308D TYR* 3.4 39.9 - - + +
309D GLN 3.2 3.1 - - - +
310D ARG* 1.3 81.2 - - + +
312D SER* 1.3 69.5 + - - +
313D MET 3.8 0.3 + - - -
315D GLU* 3.3 33.8 + - + +
316D MET* 4.7 10.8 - - + +
319D ARG* 3.7 24.7 - - - +
390D ALA* 3.2 19.2 - - + +
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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
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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