Contacts of the helix formed by residues 330 - 336 (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 THR 330 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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240C VAL* 5.0 0.9 - - - -
328C ARG 5.0 2.9 - - - +
329C LEU* 1.3 76.4 - - - +
331C PRO* 1.3 75.3 - - - +
332C LEU* 3.8 3.3 + - - +
333C GLU* 3.0 46.9 + - - +
334C ALA* 3.1 11.4 + - - +
369C SER* 4.0 18.9 + - - +
370C ASN* 5.9 0.5 - - - +
373C LEU* 5.6 0.2 - - - +
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Residues in contact with PRO 331 (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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166C PHE* 3.4 24.8 - - + +
169C LEU* 4.0 8.5 - - + -
170C ALA* 3.4 32.8 - - - +
173C HIS* 3.5 34.5 - - + +
240C VAL* 4.2 11.7 - - + -
329C LEU 4.2 2.2 - - - +
330C THR* 1.3 90.8 - - - +
332C LEU* 1.3 60.0 + - - +
334C ALA 3.7 0.6 + - - -
335C CYS* 3.3 26.7 + - - -
369C SER* 5.9 0.4 - - - +
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Residues in contact with LEU 332 (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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167C ARG* 6.3 0.2 - - - -
170C ALA* 4.0 19.3 - - + -
330C THR* 3.1 6.8 + - - +
331C PRO* 1.3 77.3 - - - +
333C GLU* 1.3 66.6 + - - +
334C ALA 3.1 1.3 - - - -
335C CYS* 3.0 10.7 + - + +
336C ALA* 3.0 22.3 + - - +
362C PHE* 4.5 13.7 - - + -
366C GLU* 3.4 26.5 - - + +
367C LEU* 4.0 11.7 - - + -
369C SER* 3.7 24.2 + - - +
370C ASN* 3.8 20.0 - - - +
373C LEU* 4.0 13.9 - - + -
377C LEU* 3.7 24.5 - - + +
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Residues in contact with GLU 333 (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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328C ARG 4.6 1.0 - - - +
329C LEU* 3.5 27.4 - - + +
330C THR* 3.0 44.0 + - - +
332C LEU* 1.3 76.8 - - - +
334C ALA* 1.3 61.6 + - - +
336C ALA* 3.3 13.5 + - - +
337C HIS* 3.4 11.8 + - - +
370C ASN* 6.1 1.9 - - + -
373C LEU* 4.2 19.7 - - + -
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Residues in contact with ALA 334 (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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166C PHE* 3.7 41.1 - - + -
316C LEU* 4.7 2.9 - - + +
320C LEU* 4.5 5.2 - - + -
329C LEU* 4.1 18.6 - - + +
330C THR 3.1 12.0 + - - +
331C PRO 3.8 0.9 - - - +
332C LEU 3.1 0.4 - - - -
333C GLU* 1.3 74.1 - - - +
335C CYS* 1.3 66.3 + - - +
337C HIS* 3.1 11.2 - - - +
340C PHE* 3.0 24.7 - - - -
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Residues in contact with CYS 335 (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* 3.6 42.5 - - + +
166C PHE* 3.4 27.1 - - - -
167C ARG* 3.9 15.5 - - - -
331C PRO 3.3 8.7 + - - +
332C LEU* 3.0 16.1 + - + +
334C ALA* 1.3 81.4 - - - +
336C ALA* 1.3 56.3 + - - +
337C HIS 3.1 3.2 + - - -
340C PHE* 3.7 7.9 - - - -
344C ARG* 2.9 20.8 + - - -
362C PHE* 5.4 1.3 - - + -
377C LEU* 3.7 12.6 - - + -
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Residues in contact with ALA 336 (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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332C LEU 3.0 11.6 + - - +
333C GLU* 3.3 9.4 + - - +
334C ALA 3.2 0.4 - - - -
335C CYS* 1.3 74.8 - - - +
337C HIS* 1.3 62.2 + - - +
338C SER 3.9 0.5 + - - -
341C ASP* 5.2 0.3 - - - +
344C ARG* 4.0 9.9 + - - +
373C LEU* 4.2 20.9 - - + -
376C ILE* 4.1 22.6 - - + +
377C LEU* 3.6 18.4 - - + -
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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