Contacts of the helix formed by residues 299 - 309 (chain B) in PDB entry 5NV6
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 299 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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295B ARG* 2.9 18.9 + - + +
296B ILE 2.9 16.5 - - - +
297B LEU 4.7 0.2 - - - -
298B GLY* 1.3 73.4 - - - +
300B PRO* 1.4 64.9 - - - +
301B GLU* 3.2 20.3 - - - +
302B ALA* 3.2 22.7 + - + +
303B LEU* 3.1 15.3 + - - +
487B ARG* 2.8 35.3 + - - +
488B TYR* 3.8 16.6 + - - +
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Residues in contact with PRO 300 (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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262B ALA 5.9 2.9 - - - +
263B SER* 4.8 4.2 + - - -
298B GLY 3.6 7.9 - - - +
299B ASP* 1.4 91.4 - - - +
301B GLU* 1.3 71.7 + - - +
303B LEU* 3.9 9.2 - - + +
304B ARG* 3.0 31.7 + - - +
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Residues in contact with GLU 301 (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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299B ASP* 3.2 11.7 - - - +
300B PRO* 1.3 92.6 - - - +
302B ALA* 1.4 56.2 + - - +
304B ARG* 3.6 4.3 + - - +
305B ASP* 3.2 35.9 + - - +
487B ARG* 3.1 41.1 + - - +
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Residues in contact with ALA 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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295B ARG* 5.6 2.7 - - - +
296B ILE* 4.1 16.3 - - + +
299B ASP* 3.2 27.0 + - + +
300B PRO 3.4 0.4 - - - -
301B GLU* 1.4 74.9 - - - +
303B LEU* 1.4 60.1 + - - +
305B ASP* 3.4 6.1 + - - +
306B LEU* 2.9 29.6 + - - +
376B ALA* 3.6 32.6 - - + +
487B ARG* 4.3 6.5 - - + +
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Residues in contact with LEU 303 (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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259B ALA* 3.5 35.4 - - + +
262B ALA* 3.8 15.5 - - + +
263B SER* 3.8 21.5 - - - +
296B ILE* 3.4 18.8 + - + +
297B LEU* 3.8 38.1 - - + +
299B ASP 3.1 18.8 + - - +
300B PRO* 3.9 7.4 - - + +
302B ALA* 1.4 72.1 - - - +
304B ARG* 1.4 60.4 + - - +
306B LEU* 3.3 6.5 + - + +
307B LEU* 3.0 38.1 + - + +
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Residues in contact with ARG 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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263B SER* 2.8 44.7 + - - +
264B GLY 4.5 6.6 + - - -
265B LEU* 3.8 30.4 - - - +
300B PRO 3.0 19.0 + - - +
301B GLU* 3.8 5.6 - - - +
303B LEU* 1.4 74.6 - - - +
305B ASP* 1.4 59.1 + - - +
307B LEU* 3.9 1.2 - - - -
308B ASN* 2.9 52.6 + - - +
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Residues in contact with ASP 305 (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 GLU* 3.2 22.1 + - - +
302B ALA* 3.6 6.5 - - - +
303B LEU 3.3 0.2 - - - -
304B ARG* 1.4 76.1 - - - +
306B LEU* 1.4 62.7 + - - +
308B ASN* 4.5 3.9 + - - -
309B ASN* 3.1 20.6 + - - +
331B GLU* 3.3 24.2 - - + +
373B PRO* 3.4 6.2 - - + +
375B SER* 3.2 44.0 + - - +
376B ALA* 4.4 1.3 - - + -
487B ARG* 5.0 2.1 - - - -
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Residues in contact with LEU 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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285B PHE* 4.3 17.3 - - + -
293B LEU* 6.1 0.9 - - + -
296B ILE* 3.7 25.4 - - + -
297B LEU* 5.9 1.1 - - + -
302B ALA 2.9 18.0 + - - +
303B LEU* 3.6 13.5 - - + +
305B ASP* 1.4 76.1 - - - +
307B LEU* 1.3 60.5 + - + +
309B ASN* 3.3 10.0 + - - +
310B HIS* 2.8 33.0 + - + -
370B LEU* 3.8 25.8 - - + -
371B LEU 3.9 5.6 - - - +
372B ILE* 3.8 42.6 - - + -
373B PRO* 3.8 8.3 - - + +
376B ALA* 5.0 0.7 - - + -
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Residues in contact with LEU 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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256B LEU* 3.8 28.7 - - + -
259B ALA* 3.5 39.9 - - + +
260B VAL* 3.9 11.0 - - + +
263B SER* 3.6 20.6 - - - -
265B LEU* 3.8 20.4 - - + -
277B LEU* 5.1 0.9 - - - +
280B PRO* 6.0 0.9 - - + -
285B PHE* 5.4 2.5 - - + -
303B LEU* 3.0 24.2 + - + +
304B ARG 4.1 0.2 - - - +
306B LEU* 1.3 79.8 - - + +
308B ASN* 1.4 62.1 + - - +
310B HIS* 3.2 19.0 + - + +
311B ILE* 3.4 20.4 - - + +
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Residues in contact with ASN 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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265B LEU* 4.3 14.7 - - - +
268B MET* 5.1 0.2 - - - +
304B ARG* 2.9 43.1 + - - +
305B ASP* 4.0 3.8 + - - +
306B LEU 3.4 0.2 - - - -
307B LEU* 1.4 75.1 - - - +
309B ASN* 1.3 55.6 + - - +
310B HIS 3.2 0.7 - - - -
311B ILE* 3.3 23.7 + - - +
330B LEU* 3.1 50.4 + - - +
331B GLU* 3.5 22.8 - - + +
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Residues in contact with ASN 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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278B LEU* 5.0 0.2 - - - +
305B ASP 3.1 17.8 + - - +
306B LEU 3.5 8.5 - - - +
307B LEU 3.2 0.6 - - - -
308B ASN* 1.3 75.1 - - - +
310B HIS* 1.3 58.5 + - - +
311B ILE 3.6 0.4 - - - -
329B THR* 3.0 37.9 + - - +
331B GLU* 3.7 4.6 - - + +
333B THR* 3.3 24.6 + - - +
335B LEU* 4.2 5.9 - - - +
371B LEU* 2.8 50.5 + - - +
372B ILE 4.1 0.8 + - - -
373B PRO* 3.8 18.3 - - + +
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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