Contacts of the helix formed by residues 337 - 345 (chain C) in PDB entry 4J1R
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 HIS 337 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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312C GLU* 3.3 26.5 - - - -
315C ALA* 4.1 11.2 + - + +
316C LEU* 3.6 36.5 + - + -
319C ARG* 5.0 5.4 - - + +
329C LEU* 4.6 9.2 - - + -
333C GLU 3.4 4.6 + - - +
334C ALA 3.1 19.3 + - - +
335C CYS 3.1 3.4 - - - -
336C ALA* 1.3 79.6 - - - +
338C SER* 1.3 65.8 + - - +
339C PHE* 2.9 30.3 + - - +
340C PHE* 3.0 16.7 + - + -
341C ASP* 4.2 0.2 - - - -
344C ARG* 2.8 23.0 + - - -
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Residues in contact with SER 338 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
159C LYS* 5.7 0.2 + - - -
312C GLU* 4.5 15.7 - - - +
336C ALA 3.9 0.8 + - - -
337C HIS* 1.3 81.3 + - - +
339C PHE* 1.3 64.0 + - - +
340C PHE 3.1 0.2 - - - -
341C ASP* 3.2 36.0 + - - +
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Residues in contact with PHE 339 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
155C VAL* 4.1 11.7 - - + -
158C VAL* 4.0 18.8 - - + -
159C LYS* 3.3 61.1 + - + +
162C MET* 4.9 0.7 - - + -
247C LEU* 4.3 15.7 - - + -
251C LEU* 5.4 1.1 - - + -
312C GLU* 3.9 20.9 - - + +
313C ALA* 3.6 38.1 - - + -
316C LEU* 3.6 14.1 - - + -
337C HIS* 2.9 19.0 + - + +
338C SER* 1.3 78.4 - - - +
340C PHE* 1.3 96.7 + + + +
341C ASP 3.4 0.8 + - - -
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Residues in contact with PHE 340 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
159C LYS* 3.1 31.6 - - - -
162C MET* 3.8 16.8 - - + -
163C TYR* 3.5 26.2 - + + -
166C PHE* 3.9 13.9 - + - -
316C LEU* 3.7 16.8 - - + -
334C ALA 3.0 31.4 - - - -
335C CYS* 3.7 18.2 - - - +
337C HIS* 3.0 11.8 + - + +
339C PHE* 1.3 102.1 - + - +
341C ASP* 1.3 61.1 + - - +
342C GLU* 3.2 3.8 - - - -
343C LEU* 3.0 28.9 + - + +
344C ARG* 3.5 12.6 + - - +
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Residues in contact with ASP 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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336C ALA 5.2 0.2 - - - +
337C HIS 3.6 2.1 - - - +
338C SER* 3.2 34.1 + - - +
339C PHE 3.4 0.6 - - - -
340C PHE* 1.3 77.8 - - - +
342C GLU* 1.3 62.6 + - - +
344C ARG* 2.7 50.7 + - - +
345C ASP* 3.4 9.5 + - - +
376C ILE* 6.0 0.5 - - - +
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Residues in contact with GLU 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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155C VAL* 5.4 0.5 - - - +
156C ILE* 3.5 33.9 - - + +
159C LYS* 2.5 49.7 + - + +
341C ASP* 1.3 78.8 - - - +
343C LEU* 1.3 60.2 + - - +
345C ASP* 3.5 14.0 - - + +
348C VAL* 3.5 23.5 - - + +
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Residues in contact with LEU 343 (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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156C ILE* 4.1 22.9 - - + -
159C LYS* 3.5 38.1 - - + +
160C LEU* 4.0 27.8 - - + +
163C TYR* 3.9 19.5 - - + -
340C PHE* 3.0 27.0 + - + +
342C GLU* 1.3 78.2 - - - +
344C ARG* 1.3 62.4 + - + +
345C ASP 3.3 1.1 + - - +
348C VAL* 3.8 21.5 - - + +
356C THR* 5.4 2.2 + - + -
359C LEU* 4.4 15.4 - - + +
360C PHE* 3.3 18.0 - - + -
381C HIS* 5.5 0.3 + - - -
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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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163C TYR* 4.2 9.9 - - + -
335C CYS 2.9 23.8 + - - -
336C ALA* 4.0 9.3 + - - +
337C HIS 2.8 23.4 + - - -
340C PHE* 3.5 17.6 + - - +
341C ASP* 2.7 38.8 + - - +
343C LEU* 1.3 78.1 - - + +
345C ASP* 1.3 59.2 - - - +
346C PRO* 3.6 1.6 - - - +
360C PHE* 3.6 25.1 - - + -
376C ILE* 3.2 32.8 + - - +
377C LEU* 4.1 10.4 + - - +
379C PRO* 3.7 12.7 - - + +
381C HIS* 2.9 24.4 + - - -
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Residues in contact with ASP 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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341C ASP 3.4 6.7 + - - +
342C GLU* 3.5 17.5 - - + +
343C LEU 3.3 1.3 - - - +
344C ARG* 1.3 77.3 - - - +
346C PRO* 1.3 79.7 - - - +
347C ASN* 3.1 33.7 + - - +
348C VAL* 3.1 27.4 + - + +
381C HIS* 4.0 2.2 + - - -
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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