Contacts of the helix formed by residues 301 - 305 (chain B) in PDB entry 6F0X
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 ILE 301 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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253B GLN* 5.5 3.1 - - + -
255B GLU* 2.9 45.0 - - - +
299B SER* 2.9 8.4 + - - +
300B ASN* 1.3 101.4 - - + +
302B THR* 1.3 54.4 + - - +
303B GLU* 2.7 18.0 + - + -
304B LYS* 3.0 26.8 + - + +
261C ARG* 3.4 56.8 - - + +
274C ILE* 5.4 2.0 - - + -
307C VAL* 6.3 1.8 - - + -
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Residues in contact with THR 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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427A LYS 5.8 0.4 - - - +
428A LEU* 4.0 22.0 + - - +
429A ALA* 5.0 9.0 - - + -
178B HIS* 3.5 36.3 + - - +
179B GLY* 5.0 11.4 - - - +
180B PRO* 6.1 0.7 - - + -
299B SER* 2.8 12.4 + - - -
300B ASN 3.5 2.7 - - - +
301B ILE* 1.3 74.5 - - - +
303B GLU* 1.3 67.9 + - + +
304B LYS 3.2 0.4 - - - -
305B ILE* 3.1 29.1 + - - +
318B TYR* 6.3 1.3 - - + -
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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
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428A LEU 4.6 7.0 - - - +
429A ALA* 4.9 18.0 - - + +
301B ILE* 2.7 8.9 + - + -
302B THR* 1.3 83.5 - - + +
304B LYS* 1.3 56.7 + - + +
305B ILE 3.7 1.6 + - - -
306B ASP 5.4 0.9 + - - +
262C ASN* 4.6 13.1 + - - -
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Residues in contact with LYS 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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255B GLU* 4.4 7.8 - - - +
259B ALA* 3.1 30.9 - - + +
260B ALA* 6.1 1.8 - - - +
263B ALA* 6.1 4.9 - - - -
301B ILE* 3.0 21.4 + - + +
303B GLU* 1.3 80.3 - - + +
305B ILE* 1.3 61.5 + - - +
306B ASP 3.7 0.4 - - - -
261C ARG 5.1 8.9 + - - +
264C CYS 5.3 2.6 + - - -
265C ARG* 5.2 17.0 + - - +
267C GLY* 5.9 2.4 - - - +
270C PRO* 3.9 19.3 - - - +
274C ILE* 3.2 34.0 - - + +
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Residues in contact with ILE 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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176B LEU* 3.9 23.1 - - + -
178B HIS* 4.8 1.8 - - + -
254B VAL* 5.0 7.6 - - + -
255B GLU* 4.6 7.2 - - + +
258B THR* 3.0 28.1 - - + +
259B ALA* 3.0 14.8 - - - +
299B SER* 3.3 30.5 - - - +
302B THR* 3.1 37.4 + - - +
303B GLU 3.4 3.2 + - - -
304B LYS* 1.3 77.5 - - - +
306B ASP* 1.3 72.3 + - + +
309B PHE* 4.9 9.0 - - + -
310B VAL* 4.5 18.2 - - + +
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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