Contacts of the helix formed by residues 361 - 367 (chain C) in PDB entry 1JPW
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 GLY 361 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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653B THR* 5.1 2.7 - - - +
656B ALA* 4.8 8.7 - - - -
657B ALA 5.7 0.2 - - - -
325C VAL* 3.6 3.8 - - - +
329C ARG* 4.7 2.5 + - - -
358C VAL 3.2 4.7 + - - -
359C GLU 3.2 5.6 + - - -
360C ALA* 1.3 81.1 - - - +
362C GLY* 1.3 60.8 + - - +
364C GLN* 3.2 27.8 - - - +
365C ALA* 3.2 27.2 + - - +
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Residues in contact with GLY 362 (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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325C VAL* 3.9 19.2 - - - +
357C ILE* 2.8 26.5 + - - -
358C VAL 3.9 1.4 + - - -
360C ALA 3.7 0.4 - - - -
361C GLY* 1.3 76.1 - - - +
363C MET* 1.3 59.9 + - - +
365C ALA* 3.7 1.0 - - - +
366C LEU* 2.8 43.4 + - - +
388C LEU* 5.0 0.9 - - - -
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Residues in contact with MET 363 (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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357C ILE 4.5 0.8 + - - -
358C VAL* 4.3 15.9 - - + +
361C GLY 3.4 0.4 - - - -
362C GLY* 1.3 75.7 - - - +
364C GLN* 1.3 59.4 + - - +
367C GLY* 3.1 24.8 + - - -
385C LEU* 3.6 36.1 - - + +
388C LEU* 3.9 28.8 - - - +
389C SER* 4.3 3.4 - - - -
392C ALA* 3.8 21.3 - - + -
398C MET* 3.4 24.7 - - + -
401C LEU* 3.9 21.5 - - + +
423C ILE* 5.0 1.8 - - + -
427C LEU* 3.6 33.0 - - + -
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Residues in contact with GLN 364 (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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644B LEU* 4.6 2.8 - - + +
649B GLU* 5.1 2.3 - - - +
652B ALA* 4.7 5.2 - - + +
653B THR* 2.9 41.1 + - + +
656B ALA* 3.3 30.8 - - + +
358C VAL 4.6 2.4 - - - +
361C GLY* 3.2 23.1 - - - +
363C MET* 1.3 81.7 + - - +
365C ALA* 1.3 60.4 + - - +
367C GLY* 3.8 2.6 + - - -
368C LEU* 3.6 13.2 + - - +
395C GLN* 5.3 6.8 + - - +
396C GLU 3.8 20.2 + - - -
397C GLY 3.8 12.4 + - - +
398C MET* 3.6 20.8 - - + +
401C LEU* 5.8 4.3 - - + -
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Residues in contact with ALA 365 (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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653B THR* 4.0 8.0 - - - +
325C VAL* 3.7 28.9 - - + +
328C MET* 3.9 16.0 - - + +
329C ARG* 4.0 12.1 - - + +
344C LEU* 6.4 0.2 - - + -
361C GLY 3.2 18.2 + - - +
362C GLY* 3.2 4.0 + - - +
364C GLN* 1.3 76.3 - - - +
366C LEU* 1.3 60.6 + - + +
368C LEU* 3.2 19.6 - - - +
369C HIS* 3.6 13.5 + - - -
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Residues in contact with LEU 366 (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 MET* 4.0 23.3 - - + -
341C SER* 5.0 3.8 - - - -
344C LEU* 4.1 21.8 - - + -
357C ILE* 5.3 0.9 - - + -
362C GLY* 2.8 25.0 + - - +
365C ALA* 1.3 75.4 - - + +
367C GLY* 1.3 58.3 + - - +
368C LEU 3.0 7.9 + - - -
369C HIS 3.4 8.8 + - - -
370C LEU* 4.0 3.1 + - - +
381C CYS* 3.5 39.0 - - + +
384C THR* 3.3 34.8 - - + -
385C LEU* 3.8 24.2 - - + -
388C LEU* 4.0 15.3 - - + -
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Residues in contact with GLY 367 (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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649B GLU* 4.3 10.8 - - - +
363C MET 3.1 11.8 + - - -
364C GLN* 3.8 4.7 + - - -
365C ALA 3.5 0.2 - - - -
366C LEU* 1.3 74.8 - - - +
368C LEU* 1.3 61.2 + - - +
369C HIS 3.2 1.6 - - - -
370C LEU* 3.6 33.8 + - - +
385C LEU* 4.2 0.8 - - - +
401C LEU* 3.8 17.0 - - - +
404C THR* 4.6 8.3 + - - +
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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