Contacts of the helix formed by residues 319 - 331 (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 319 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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283C VAL* 4.2 1.4 - - - +
316C LEU 3.2 10.3 + - - -
317C ALA 3.0 6.2 + - - -
318C SER* 1.3 81.5 - - - +
320C GLY* 1.3 63.1 + - - +
321C PRO* 3.3 5.4 - - - -
322C GLN* 3.5 27.9 - - - +
323C ALA* 4.0 3.6 + - - +
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Residues in contact with GLY 320 (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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283C VAL* 3.4 22.4 - - - -
286C LEU* 4.2 1.1 - - - +
315C ILE* 2.7 27.5 + - - -
318C SER 3.3 2.0 - - - -
319C GLY* 1.3 74.1 - - - +
321C PRO* 1.3 62.8 - - - +
323C ALA* 3.2 4.8 + - - +
324C LEU* 3.0 31.5 + - - +
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Residues in contact with PRO 321 (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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315C ILE* 3.2 12.8 - - + +
316C LEU* 3.6 18.8 - - + +
319C GLY* 3.3 6.7 - - - -
320C GLY* 1.3 91.1 - - - +
322C GLN* 1.3 57.0 + - - +
323C ALA 3.1 0.3 + - - -
324C LEU* 3.2 10.5 + - + +
325C VAL* 3.0 36.4 + - - +
344C LEU* 4.5 3.1 - - + +
347C LEU* 4.9 5.2 - - + -
353C ASN* 3.4 24.5 - - - +
356C ALA* 4.2 19.3 - - + +
357C ILE* 4.4 11.4 - - + -
360C ALA* 5.0 0.7 - - - -
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Residues in contact with GLN 322 (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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660B PHE* 4.0 27.0 - - + -
661B ARG* 3.7 31.9 - - - +
319C GLY* 3.5 19.7 + - - +
321C PRO* 1.3 76.6 - - - +
323C ALA* 1.3 72.0 + - - +
325C VAL* 4.1 2.6 - - - +
326C ASN* 3.3 19.6 + - - +
329C ARG* 4.7 3.0 + - - +
356C ALA 5.2 0.2 + - - -
360C ALA* 3.9 14.3 - - + +
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Residues in contact with ALA 323 (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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283C VAL* 5.0 3.4 - - + +
286C LEU* 3.8 29.6 - - + +
319C GLY 4.2 5.2 - - - +
320C GLY* 3.2 10.7 + - - +
321C PRO 3.0 1.0 - - - -
322C GLN* 1.3 92.7 - - - +
324C LEU* 1.3 65.8 + - - +
325C VAL 3.3 0.2 - - - -
326C ASN* 3.1 7.2 + - - +
327C ILE* 3.1 26.8 + - - +
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Residues in contact with LEU 324 (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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286C LEU* 3.9 19.1 - - + -
298C THR* 4.4 13.0 - - + -
301C LEU* 4.7 3.4 - - + -
315C ILE* 5.1 3.4 - - + -
320C GLY 3.0 21.5 + - - +
321C PRO* 3.7 2.2 - - + +
323C ALA* 1.3 75.8 - - - +
325C VAL* 1.3 64.4 + - - +
327C ILE* 2.9 18.9 + - + +
328C MET* 3.1 16.4 + - - +
340C THR* 3.6 23.4 - - + +
343C VAL* 3.3 36.8 - - + -
344C LEU* 3.7 27.8 - - + -
347C LEU* 3.8 15.0 - - + -
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Residues in contact with VAL 325 (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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321C PRO 3.0 22.4 + - - +
322C GLN* 4.1 6.7 - - - +
324C LEU* 1.3 77.5 - - - +
326C ASN* 1.3 59.7 + - - +
328C MET* 3.2 13.4 + - - +
329C ARG* 3.2 36.5 + - - +
344C LEU* 4.3 8.9 - - + +
357C ILE* 4.1 22.2 - - + +
360C ALA* 4.0 9.0 - - + +
361C GLY 3.6 27.8 - - - +
362C GLY* 3.9 17.9 - - - -
365C ALA* 3.7 4.2 - - + +
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Residues in contact with ASN 326 (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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619B CYS* 4.0 3.2 - - - -
620B GLU* 4.9 4.9 + - - +
623B GLN* 5.2 3.1 + - - -
654B TYR* 5.5 0.4 - - - -
661B ARG* 3.0 29.4 - - - +
322C GLN 3.3 17.4 + - - +
323C ALA* 3.1 9.0 + - - +
325C VAL* 1.3 76.4 - - - +
327C ILE* 1.3 67.8 + - - +
329C ARG* 2.6 39.2 + - - +
330C THR* 3.0 33.9 + - - -
331C TYR* 5.7 1.6 - - - -
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Residues in contact with ILE 327 (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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286C LEU* 4.5 17.5 - - + +
294C LEU* 4.5 18.4 - - + -
298C THR* 4.1 24.5 - - + -
323C ALA 3.1 14.6 + - - +
324C LEU* 2.9 18.9 + - + +
326C ASN* 1.3 77.0 - - + +
328C MET* 1.3 66.1 + - - +
329C ARG 3.0 1.4 + - - -
331C TYR* 3.2 42.8 + - + +
336C LEU* 3.6 35.4 - - + -
337C LEU* 4.3 3.2 - - + +
340C THR* 3.7 11.9 - - + +
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Residues in contact with MET 328 (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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324C LEU 3.4 12.3 - - - +
325C VAL* 3.3 9.4 - - - +
327C ILE* 1.3 78.3 - - - +
329C ARG* 1.3 58.9 + - - +
331C TYR 4.4 1.0 - - - +
337C LEU* 3.7 29.7 - - + +
340C THR* 3.6 28.7 - - + -
341C SER* 4.0 11.4 - - - -
344C LEU* 3.8 18.2 - - + -
365C ALA* 3.9 17.9 - - + +
366C LEU* 4.0 22.2 - - + -
368C LEU* 3.9 3.5 - - - +
369C HIS* 2.9 46.0 + - + -
377C LEU* 4.8 1.1 - - + -
381C CYS* 4.2 6.7 - - - -
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Residues in contact with ARG 329 (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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619B CYS* 3.7 13.9 - - - -
653B THR* 3.4 36.3 + - + +
654B TYR* 3.6 31.1 + - + -
657B ALA* 3.4 23.3 - - - +
660B PHE* 5.9 1.8 - - - -
661B ARG* 3.8 13.3 - - - +
322C GLN* 4.7 3.4 + - - +
325C VAL* 3.2 24.3 + - - +
326C ASN* 2.6 46.7 + - - +
327C ILE 3.0 0.4 - - - -
328C MET* 1.3 79.8 - - - +
330C THR* 1.3 62.9 + - - +
331C TYR 4.8 0.9 - - - +
360C ALA* 3.5 23.2 + - - +
361C GLY* 4.7 2.6 + - - -
365C ALA* 4.0 6.1 - - + -
368C LEU* 4.3 12.3 - - - +
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Residues in contact with THR 330 (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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578B HIS* 5.5 1.5 + - - +
582B ARG* 3.1 50.8 + - + +
620B GLU* 3.8 14.5 + - - +
654B TYR* 3.7 16.9 + - - +
326C ASN* 3.0 26.6 + - - -
329C ARG* 1.3 77.8 - - - +
331C TYR* 1.3 84.8 + - + +
332C THR* 4.2 4.9 + - - +
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Residues in contact with TYR 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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582B ARG* 3.4 36.2 - - - +
287C ASN 5.3 0.3 + - - -
288C LYS 3.9 14.6 + - - -
289C THR* 4.0 18.9 - - - +
291C VAL* 3.6 20.9 - - + -
294C LEU* 3.8 20.0 - - + -
326C ASN* 5.7 1.6 - - - -
327C ILE* 3.2 29.5 + - + +
328C MET 4.4 1.7 - - - +
329C ARG 4.8 0.7 - - - +
330C THR* 1.3 93.6 - - + +
332C THR* 1.3 64.9 + - - +
333C TYR 3.7 4.5 - - - +
336C LEU* 3.6 29.4 - - + -
337C LEU* 3.7 20.8 - - + +
369C HIS* 4.3 6.1 - - - -
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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