Contacts of the helix formed by residues 338 - 348 (chain C) in PDB entry 5EWL
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 THR 338 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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316C LEU* 3.9 24.9 - - + -
321C ASN 4.2 1.9 + - - -
322C ILE* 4.0 25.7 - - + -
323C THR* 2.7 37.0 + - - +
336C TRP* 3.2 26.1 - - + -
337C LYS* 1.4 74.5 - - - +
339C GLY* 1.3 64.9 + - - +
340C PRO* 3.5 0.4 - - - -
341C LEU* 3.1 10.9 + - + +
342C PHE* 2.9 21.4 + - + +
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Residues in contact with GLY 339 (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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115C ARG* 3.4 25.9 - - - +
117C PRO* 4.7 0.9 - - - +
136C SER* 5.6 0.2 - - - -
336C TRP* 3.0 31.4 + - - -
338C THR* 1.3 76.0 - - - +
340C PRO* 1.4 61.9 - - - +
342C PHE* 3.1 2.8 + - - +
343C LYS* 2.9 27.8 + - - +
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Residues in contact with PRO 340 (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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115C ARG* 4.4 15.0 - - + +
335C ILE* 4.4 12.1 - - + -
336C TRP 3.5 11.9 - - - +
337C LYS 3.5 12.8 - - - +
339C GLY* 1.4 85.7 - - - +
341C LEU* 1.4 59.0 + - - +
343C LYS* 3.5 2.5 + - + +
344C ARG 3.1 16.5 + - - -
207D MET 4.6 5.4 - - - +
208D SER 3.4 23.1 - - - +
209D LEU* 3.5 21.0 - - - +
210D ASP* 3.3 17.3 + - + +
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Residues in contact with LEU 341 (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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316C LEU* 3.8 11.2 - - + -
319C MET* 3.8 27.4 - - + -
320C GLU 5.6 0.7 - - - +
322C ILE* 3.7 29.4 - - + -
337C LYS 5.0 1.5 + - - +
338C THR* 3.1 13.4 + - + +
340C PRO* 1.4 74.3 - - - +
342C PHE* 1.4 60.7 + - - +
344C ARG* 3.0 9.5 + - + +
345C VAL* 2.9 35.8 + - + +
210D ASP* 3.3 36.4 - - + +
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Residues in contact with PHE 342 (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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88C TYR* 3.2 33.7 - - + -
89C ALA* 4.1 4.3 - - + -
117C PRO* 3.7 11.4 - - + -
309C VAL* 4.4 5.6 - - + -
312C ALA* 3.7 31.9 - - + -
313C ILE* 3.4 26.7 - - + -
316C LEU* 3.9 30.1 - - + -
336C TRP* 3.6 17.9 - + + -
338C THR 2.9 16.4 + - - +
339C GLY 3.6 3.6 - - - +
341C LEU* 1.4 77.3 - - - +
343C LYS* 1.4 54.3 + - - +
345C VAL* 3.4 4.5 + - + -
346C LEU* 3.0 52.1 + - + +
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Residues in contact with LYS 343 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117C PRO* 4.5 7.2 - - + +
131C LYS* 4.2 15.7 - - - +
134C HIS 5.3 0.8 + - - -
135C LEU 3.2 22.4 + - - +
136C SER* 3.9 27.4 - - - +
137C PHE 4.8 4.0 + - - +
138C LEU* 4.8 9.6 - - + -
339C GLY 2.9 12.8 + - - +
340C PRO* 3.6 9.0 - - + +
341C LEU 3.2 0.4 - - - -
342C PHE* 1.4 74.0 - - - +
344C ARG* 1.4 62.7 + - - +
346C LEU* 3.1 8.9 + - - +
347C MET* 2.9 49.9 + - + +
208D SER* 2.9 41.3 + - - +
209D LEU* 3.9 11.4 - - + -
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Residues in contact with ARG 344 (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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340C PRO 3.1 10.0 + - - +
341C LEU* 3.0 13.0 + - + +
343C LYS* 1.4 74.1 - - - +
345C VAL* 1.4 55.4 + - + +
347C MET* 3.4 5.4 + - + +
348C SER* 2.9 37.7 + - - +
209D LEU* 3.6 41.5 - - + +
210D ASP* 2.9 46.5 + - - +
211D ASP* 5.0 0.8 + - - +
213D ASP* 2.9 31.1 + - - -
215D LYS* 5.5 3.0 - - - +
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Residues in contact with VAL 345 (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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312C ALA* 3.6 33.9 - - + +
315C GLU* 3.8 28.6 - - + +
316C LEU* 4.3 12.8 - - + +
319C MET* 4.5 15.0 - - + -
341C LEU* 2.9 35.2 + - + +
342C PHE* 3.6 10.8 - - + +
344C ARG* 1.4 74.4 - - + +
346C LEU* 1.4 61.5 + - - +
348C SER* 3.1 16.8 + - - -
349C SER* 3.2 16.2 + - - -
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Residues in contact with LEU 346 (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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89C ALA* 5.1 1.1 - - + -
117C PRO* 3.7 31.4 - - + -
119C ILE* 4.1 16.2 - - + -
138C LEU* 3.7 15.3 - - + -
308C VAL* 4.4 11.9 - - + -
309C VAL* 4.2 24.2 - - + -
312C ALA* 3.6 18.8 - - + -
342C PHE* 3.0 38.5 + - + +
343C LYS* 3.5 6.5 - - - +
345C VAL* 1.4 72.0 - - - +
347C MET* 1.3 60.4 + - - +
349C SER* 2.9 27.3 + - - -
361C PHE* 3.6 10.9 - - - -
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Residues in contact with MET 347 (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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131C LYS* 5.6 2.9 - - + +
138C LEU* 3.9 13.0 - - + +
343C LYS* 2.9 55.1 + - + +
344C ARG* 3.5 7.9 - - + +
346C LEU* 1.3 71.9 - - - +
348C SER* 1.3 57.5 + - - +
349C SER 3.4 1.8 + - - +
361C PHE* 3.8 28.3 + - - +
362C ASN 4.2 4.8 - - - +
363C GLU* 3.7 26.0 - - - +
364C ASP* 4.6 1.8 - - - -
365C GLY* 3.6 29.6 - - - +
206D ASP* 5.7 2.5 - - - +
209D LEU* 4.4 14.1 - - + -
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Residues in contact with SER 348 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
315C GLU* 5.0 6.8 + - - +
344C ARG* 2.9 24.2 + - - +
345C VAL* 3.1 10.4 + - - -
346C LEU 3.1 0.2 - - - -
347C MET* 1.3 75.9 - - - +
349C SER* 1.4 59.4 + - - +
350C LYS* 3.9 11.0 + - - +
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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