Contacts of the helix formed by residues 253 - 260 (chain C) in PDB entry 6E07
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 PHE 253 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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144C PRO* 6.3 0.9 - - + -
171C LYS* 6.5 1.3 - - + -
173C PHE 5.5 2.2 - - - -
174C GLY 4.6 9.2 - - - -
175C ARG* 3.7 35.0 - - + -
249C TYR* 3.4 22.4 - - + -
250C PHE* 2.8 10.5 + - + +
251C ASP 4.6 0.7 - - - -
252C GLU* 1.3 98.5 - - + +
254C GLY* 1.3 68.3 + - - +
256C ILE* 5.8 0.2 - - - +
257C ARG* 2.8 54.4 + - + +
258C ASP* 4.8 10.5 - - + +
334C THR* 4.9 0.2 - - - -
469C LEU* 5.6 0.5 - - - +
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Residues in contact with GLY 254 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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250C PHE* 3.0 19.9 + - - -
253C PHE* 1.3 82.7 - - - +
255C ILE* 1.3 60.8 + - - -
256C ILE 3.3 2.4 + - - -
257C ARG 3.4 0.2 + - - -
258C ASP* 3.0 24.4 + - - +
334C THR* 3.5 27.6 - - - +
335C ALA* 3.8 2.2 - - - -
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Residues in contact with ILE 255 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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237C PHE* 5.4 1.3 - - + -
250C PHE* 3.5 12.0 - - + -
254C GLY* 1.3 70.7 - - - -
256C ILE* 1.3 69.8 + - + +
258C ASP* 4.1 3.6 - - - +
259C VAL* 3.1 37.0 + - + +
260C MET 3.6 4.3 + - - -
335C ALA* 3.1 25.1 + - + +
336C THR* 3.8 20.9 - - - +
337C PHE 3.6 26.0 - - - +
338C ALA* 3.7 12.8 - - + -
358C CYS* 3.7 21.5 - - - +
359C GLY* 4.3 8.3 - - - +
360C LYS* 4.1 19.5 - - + +
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Residues in contact with ILE 256 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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254C GLY 3.3 1.2 + - - -
255C ILE* 1.3 78.3 - - + +
257C ARG* 1.3 60.0 + - - +
260C MET* 3.1 18.6 + - + -
261C GLN* 2.9 31.2 + - + +
305C LEU* 4.1 22.0 - - + -
335C ALA* 6.1 1.1 - - + -
338C ALA* 3.8 20.9 - - + -
340C VAL* 4.7 5.4 - - + -
465C PHE* 3.9 32.3 - - + -
468C LEU* 4.0 24.2 - - + -
469C LEU* 4.1 20.9 - - + -
472C ILE* 4.4 11.4 - - + -
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Residues in contact with ARG 257 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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173C PHE* 6.0 2.8 - - - +
174C GLY 4.7 2.5 - - - -
175C ARG* 2.9 31.9 + - - +
176C ASP* 5.6 3.0 - - - +
252C GLU 3.9 9.8 + - - -
253C PHE* 2.8 65.0 + - + +
254C GLY 3.4 1.8 + - - -
256C ILE* 1.3 79.4 - - - +
258C ASP* 1.3 63.4 + - - +
259C VAL 3.4 0.7 + - - -
261C GLN* 3.8 24.2 - - - +
262C ASN* 3.7 13.7 + - - +
462C TRP* 4.6 3.8 - - - -
469C LEU* 4.0 44.3 - - + +
473C GLU* 3.8 28.3 + - - +
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Residues in contact with ASP 258 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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171C LYS* 6.0 0.2 + - - -
250C PHE* 3.7 17.9 - - + -
253C PHE* 4.8 8.6 - - + +
254C GLY 3.0 17.1 + - - +
255C ILE* 3.8 10.4 - - + +
256C ILE 3.3 0.4 - - - -
257C ARG* 1.3 78.0 - - - +
259C VAL* 1.3 71.0 + - + +
262C ASN* 3.2 15.9 + - - -
263C HIS* 4.0 5.7 - - - -
360C LYS* 3.4 24.9 + - - -
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Residues in contact with VAL 259 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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237C PHE* 3.7 45.3 - - + -
255C ILE* 3.1 16.1 + - + +
257C ARG 3.3 0.2 - - - -
258C ASP* 1.3 99.0 - - + +
260C MET* 1.3 59.5 + - - +
262C ASN* 3.0 14.7 + - - +
263C HIS* 3.2 28.2 + - + +
264C LEU* 3.2 11.2 + - + -
358C CYS* 3.6 29.6 - - + -
360C LYS* 5.4 0.9 - - - +
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Residues in contact with MET 260 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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255C ILE 3.6 0.8 + - - -
256C ILE* 3.1 21.3 + - + +
259C VAL* 1.3 77.0 - - - +
261C GLN* 1.3 66.0 + - - +
262C ASN 3.2 2.1 + - - -
264C LEU* 3.6 8.7 + - + -
265C LEU* 3.1 27.2 + - - +
338C ALA* 3.8 15.3 - - + +
340C VAL* 3.5 34.5 - - + -
356C LEU* 3.6 46.8 - - + +
358C CYS* 3.6 26.0 - - - -
465C PHE* 3.8 19.5 - - + -
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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