Contacts of the helix formed by residues 252 - 259 (chain C) in PDB entry 1G59
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 SER 252 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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13C ASP* 3.6 30.3 - - - +
14C PRO 3.6 5.8 + - - -
15C HIS* 4.9 0.2 - - - +
246C LYS* 5.7 4.0 - - - +
250C HIS* 3.6 1.2 - - - +
251C THR* 1.3 81.0 + - - +
253C LEU* 1.3 59.1 + - - +
254C ASP* 3.0 25.8 + - - +
255C TRP* 3.0 27.7 + - - +
256C TYR* 3.2 14.3 - - - -
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Residues in contact with LEU 253 (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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14C PRO* 2.9 25.0 + - + +
15C HIS 3.7 16.8 - - - +
16C VAL* 4.0 19.1 - - + -
19C ALA* 3.9 15.7 - - + +
59C ALA* 4.1 22.2 - - + +
62C TRP* 4.5 9.7 - - + -
63C LEU* 4.0 14.6 - - + -
251C THR 3.5 0.2 + - - -
252C SER* 1.3 72.1 - - - +
254C ASP* 1.3 58.7 + - - +
256C TYR* 3.1 12.6 + - + +
257C LYS* 3.0 29.9 + - - +
266C LEU* 3.5 31.4 - - + -
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Residues in contact with ASP 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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14C PRO* 3.2 21.8 - - - +
55C ARG* 3.3 35.7 + - - +
59C ALA* 5.3 2.4 - - - +
252C SER* 3.0 11.1 + - - +
253C LEU* 1.3 79.8 - - - +
255C TRP* 1.3 57.8 + - - +
257C LYS* 4.0 7.8 - - - +
258C ALA* 3.2 22.5 + - - +
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Residues in contact with TRP 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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250C HIS* 3.2 58.1 + + + -
252C SER* 3.0 21.2 + - - +
254C ASP* 1.3 77.8 - - - +
256C TYR* 1.3 100.0 + + - +
258C ALA* 3.0 8.1 + - + +
259C GLU* 2.8 63.5 + - + +
261C PHE* 3.9 15.0 - + - -
307C LEU* 4.0 13.0 - - + -
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Residues in contact with TYR 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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16C VAL* 4.4 12.3 - - + +
62C TRP* 4.5 3.8 - - + -
249C SER* 5.7 0.5 - - - -
250C HIS* 2.6 34.3 + - - +
251C THR 4.4 2.9 - - - -
252C SER 3.2 25.4 - - - -
253C LEU* 3.1 19.2 + - + +
255C TRP* 1.3 100.9 - + - +
257C LYS* 1.3 64.0 + - - +
259C GLU 3.3 6.1 + - - -
261C PHE* 3.2 38.2 + + + +
266C LEU* 4.6 15.5 - - + -
305C PHE* 3.1 30.4 - + - -
307C LEU* 4.3 6.1 - - + +
310C LEU* 3.7 31.9 - - + -
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Residues in contact with LYS 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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62C TRP* 3.5 54.7 - - + +
253C LEU 3.0 14.9 + - - +
254C ASP* 4.1 7.9 - - - +
256C TYR* 1.3 76.4 - - - +
258C ALA* 1.3 65.3 + - - +
260C GLY* 3.2 13.5 + - - -
261C PHE 4.1 2.2 + - - +
334C PHE* 3.9 8.8 - - - -
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Residues in contact with ALA 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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254C ASP 3.2 13.9 + - - +
255C TRP* 3.0 13.2 + - + +
257C LYS* 1.3 82.8 - - - +
259C GLU* 1.3 66.3 + - - +
260C GLY 3.1 4.6 + - - -
334C PHE* 3.5 13.2 - - - -
363C LYS* 3.5 8.7 - - - +
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Residues in contact with GLU 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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255C TRP* 2.8 54.3 + - + +
256C TYR 3.3 0.8 + - - -
258C ALA* 1.3 82.7 - - - +
260C GLY* 1.3 63.3 + - - +
261C PHE* 3.4 23.5 + - + -
361C THR* 3.5 19.8 + - - +
363C LYS* 3.1 40.4 + - + +
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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