Contacts of the helix formed by residues 301 - 310 (chain B) in PDB entry 5NTN
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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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299B ILE 3.4 3.9 + - - -
300B PHE* 1.3 74.4 - - - +
302B ARG* 1.3 60.1 + - - +
303B GLU* 3.5 8.7 + - - +
304B GLU* 2.8 38.6 + - - +
305B VAL* 3.0 27.5 + - - +
381B LYS* 5.7 0.2 - - - -
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Residues in contact with ARG 302 (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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301B SER* 1.3 73.1 - - - +
303B GLU* 1.3 57.9 + - + +
305B VAL* 3.4 24.0 + - - +
306B THR* 2.9 41.8 + - - +
309B GLN* 5.5 0.6 - - - +
386B GLU* 3.2 31.9 + - - +
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Residues in contact with GLU 303 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
294A ARG* 5.4 5.9 + - - -
301B SER* 3.3 7.9 + - - +
302B ARG* 1.3 79.1 - - + +
304B GLU* 1.3 57.5 + - + +
306B THR* 3.4 7.7 + - - -
307B GLY* 2.9 24.4 + - - -
310B ARG* 4.8 3.6 + - - -
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Residues in contact with GLU 304 (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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300B PHE* 3.4 26.0 - - + -
301B SER* 2.8 42.9 + - - +
303B GLU* 1.3 73.2 - - + +
305B VAL* 1.3 66.0 + - - +
307B GLY* 3.2 3.3 + - - +
308B TYR* 3.1 30.7 + - + -
381B LYS* 2.8 36.0 + - - -
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Residues in contact with VAL 305 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
300B PHE* 3.9 21.1 - - + +
301B SER 3.0 18.1 + - - +
302B ARG* 3.4 37.5 - - - +
304B GLU* 1.3 75.2 - - - +
306B THR* 1.3 58.4 + - - +
308B TYR* 3.2 10.5 + - - +
309B GLN* 3.0 37.1 + - - +
383B GLY* 5.5 3.6 - - - -
384B GLY 5.6 0.7 - - - +
386B GLU* 3.9 22.9 - - + +
387B LEU* 4.3 19.7 - - + -
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Residues in contact with THR 306 (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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302B ARG* 2.9 27.7 + - - +
303B GLU* 3.6 9.3 - - - -
304B GLU 3.3 0.2 - - - -
305B VAL* 1.3 77.3 - - - +
307B GLY* 1.3 55.5 - - - +
309B GLN* 3.2 16.3 + - + +
310B ARG* 3.0 56.6 + - + +
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Residues in contact with GLY 307 (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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303B GLU 2.9 15.5 + - - -
304B GLU* 3.2 5.3 + - - -
306B THR* 1.3 75.0 - - - +
308B TYR* 1.3 61.6 + - - +
310B ARG* 3.4 18.8 + - - +
311B LYS* 3.4 25.6 + - - +
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Residues in contact with TYR 308 (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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300B PHE* 3.6 32.1 - + - -
304B GLU* 3.1 26.1 + - + -
305B VAL 3.2 6.9 + - - +
307B GLY* 1.3 72.8 - - - +
309B GLN* 1.3 65.6 + - - +
311B LYS* 3.3 44.3 + - + +
316B MET* 3.9 21.8 - - + +
319B ARG* 4.6 1.9 + - - -
378B PHE* 3.7 13.7 - + - -
379B GLU* 2.5 43.7 + - - +
387B LEU* 3.6 36.5 - - + +
390B ALA* 3.8 9.2 - - - +
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Residues in contact with GLN 309 (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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302B ARG* 5.5 1.2 + - - +
305B VAL* 3.0 21.0 + - + +
306B THR* 3.2 20.1 + - + +
308B TYR* 1.3 76.2 - - - +
310B ARG* 1.3 60.4 + - + +
311B LYS 3.6 1.6 + - - +
386B GLU* 2.8 48.8 + - - +
387B LEU 4.7 2.0 - - - +
389B ARG* 3.6 38.6 + - + +
390B ALA* 3.9 15.4 + - - +
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Residues in contact with ARG 310 (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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303B GLU 4.8 3.2 + - - -
306B THR* 3.0 35.1 + - + +
307B GLY* 3.9 23.9 - - - +
308B TYR 3.2 0.4 - - - -
309B GLN* 1.3 77.1 - - + +
311B LYS* 1.3 65.6 + - - +
312B SER 3.7 1.0 + - - -
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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