Contacts of the helix formed by residues 307 - 315 (chain B) in PDB entry 4YVF
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 307 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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280B ASP* 5.7 3.5 - - - +
282B ILE 2.9 21.4 + - - +
283B LEU* 4.1 22.9 - - + +
284B GLY 4.5 2.9 + - - -
287B PHE* 3.7 9.4 - - + -
305B GLU 4.0 0.8 + - - -
306B ILE* 1.3 70.6 - - - +
308B VAL* 1.3 60.8 + - - +
309B LYS* 3.7 10.2 + - - +
310B TRP* 3.1 44.3 + - + +
311B LEU* 3.6 3.8 + - - +
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Residues in contact with VAL 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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303B ASP* 5.3 4.0 - - + +
306B ILE* 2.8 26.3 + - + +
307B ASP* 1.3 70.2 - - - +
309B LYS* 1.3 66.0 + - - +
311B LEU* 3.2 9.0 + - + +
312B ASN* 3.0 30.1 + - - +
328B TYR* 3.9 10.8 - - + +
338B LEU* 3.6 26.0 - - + -
341B GLU* 3.6 25.1 - - + +
342B GLY* 3.6 16.8 - - - -
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Residues in contact with LYS 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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307B ASP* 3.2 9.6 - - - +
308B VAL* 1.3 81.0 - - - +
310B TRP* 1.3 62.2 + - - +
312B ASN* 3.3 10.5 + - + +
313B GLU* 2.9 58.5 + - + +
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Residues in contact with TRP 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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284B GLY* 3.4 28.6 - - - +
287B PHE* 3.7 25.4 - + + -
288B GLU* 3.8 35.4 - - + -
307B ASP* 3.1 34.1 + - + +
308B VAL 3.2 0.6 - - - -
309B LYS* 1.3 80.0 - - - +
311B LEU* 1.3 73.6 + - + +
313B GLU* 3.2 4.2 + - - -
314B ASN* 2.8 79.6 + - + +
330B LEU* 4.4 15.3 - - + -
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Residues in contact with LEU 311 (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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287B PHE* 3.6 43.3 - - + -
307B ASP 3.6 1.5 + - - +
308B VAL* 3.2 13.5 + - - +
310B TRP* 1.3 99.5 - - + +
312B ASN* 1.3 58.5 + - - +
315B ALA* 2.9 35.0 + - - +
328B TYR* 3.6 39.7 - - + -
330B LEU* 4.1 17.5 - - + -
336B ILE* 4.5 7.9 - - + -
338B LEU* 4.1 21.3 - - + -
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Residues in contact with ASN 312 (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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308B VAL* 3.0 23.8 + - - +
309B LYS* 3.6 11.1 - - + +
311B LEU* 1.3 78.1 - - - +
313B GLU* 1.3 62.2 + - + +
314B ASN 3.8 0.2 + - - -
315B ALA* 4.8 3.9 + - - +
318B LYS* 3.7 15.7 + - - +
328B TYR* 2.6 32.3 + - - -
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Residues in contact with GLU 313 (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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309B LYS* 2.9 52.3 + - + +
310B TRP* 4.8 2.9 - - - -
312B ASN* 1.3 81.2 - - + +
314B ASN* 1.3 73.5 + - - +
315B ALA 5.0 1.1 - - - -
331B LYS* 5.1 1.6 + - - -
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Residues in contact with ASN 314 (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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310B TRP* 2.8 78.1 + - + +
313B GLU* 1.3 91.1 + - - +
315B ALA* 1.3 67.0 + - - +
316B VAL 3.8 0.3 + - - -
330B LEU* 5.0 2.1 - - - +
331B LYS* 3.0 40.6 + - + +
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Residues in contact with ALA 315 (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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311B LEU* 2.9 19.1 + - - +
312B ASN 5.1 3.0 - - - +
313B GLU 5.0 1.0 - - - -
314B ASN* 1.3 83.3 + - - +
316B VAL* 1.3 62.7 + - - +
317B GLU* 3.3 18.4 - - - +
318B LYS* 5.5 0.7 - - + -
328B TYR* 3.6 13.5 - - + -
329B ARG 3.2 13.7 - - - +
330B LEU* 4.0 16.5 - - + +
331B LYS* 5.1 1.1 + - - -
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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