Contacts of the helix formed by residues 306 - 311 (chain C) in PDB entry 1EZF
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 ASN 306 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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256C VAL* 4.6 1.1 - - - -
259C LEU* 3.5 18.2 - - - +
302C ALA 3.0 23.2 + - - +
303C CYS* 2.9 20.8 + - - +
304C TYR 3.9 1.8 - - - +
305C ASN* 1.3 74.8 - - - +
307C GLN* 1.3 64.6 + - - +
308C GLN* 2.9 35.7 + - - +
309C VAL* 3.2 12.6 + - + +
310C PHE* 4.5 0.3 - - - -
314C VAL* 4.9 9.3 - - - +
348C ARG* 4.5 3.7 - - - +
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Residues in contact with GLN 307 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
252C ILE* 3.9 35.2 - - + +
253C ASP* 5.0 5.0 - - - +
256C VAL* 3.9 25.3 - - + +
305C ASN 4.0 3.9 + - - +
306C ASN* 1.3 72.8 + - - +
308C GLN* 1.3 72.4 + - - +
310C PHE* 2.9 22.8 + - - +
311C LYS* 3.6 20.9 + - + +
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Residues in contact with GLN 308 (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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306C ASN* 2.9 24.6 + - - +
307C GLN* 1.3 84.2 - - - +
309C VAL* 1.3 53.5 + - - +
310C PHE 3.1 0.2 - - - -
311C LYS* 2.8 27.5 + - - +
312C GLY 2.7 36.4 + - - +
313C ALA 5.7 0.2 - - - +
314C VAL* 4.3 19.5 - - + -
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Residues in contact with VAL 309 (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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217C ILE 3.7 22.9 - - - +
218C ARG* 4.6 8.1 - - - +
220C TYR* 4.4 8.0 - - + -
221C LEU* 4.1 15.4 + - - +
231C TRP* 4.9 0.7 - - + -
259C LEU* 4.1 15.7 - - + -
303C CYS* 3.7 41.5 - - + +
306C ASN* 3.2 17.0 + - + +
307C GLN 2.9 1.0 + - - -
308C GLN* 1.3 78.8 - - - +
310C PHE* 1.3 73.5 + - + +
312C GLY 3.5 14.6 + - - +
314C VAL* 6.5 0.2 - - + -
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Residues in contact with PHE 310 (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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220C TYR* 3.4 29.6 - + + -
221C LEU* 3.7 19.1 - - - +
231C TRP* 3.4 36.8 - + - -
246C PHE* 3.9 18.8 - - + +
247C ALA* 4.6 9.0 - - - +
252C ILE* 4.6 11.0 - - + -
255C ALA* 3.0 52.9 - - + -
256C VAL* 3.8 8.3 - - + -
259C LEU* 3.7 23.8 - - + -
307C GLN 2.9 15.0 + - - +
309C VAL* 1.3 82.8 - - + +
311C LYS* 1.3 61.8 + - - +
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Residues in contact with LYS 311 (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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221C LEU* 3.4 12.1 - - - +
249C PRO* 5.3 15.6 - - + +
252C ILE* 5.2 9.2 - - + -
307C GLN* 3.8 29.8 - - - +
308C GLN* 2.8 32.6 + - - +
310C PHE* 1.3 82.3 - - + +
312C GLY* 1.3 57.5 + - - +
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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