Contacts of the helix formed by residues 361 - 371 (chain C) in PDB entry 4LEO
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 ASP 361 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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326C SER* 5.2 0.2 + - - -
359C ALA 3.7 3.0 + - - +
360C LEU* 1.3 84.7 - - - +
362C PRO* 1.3 64.1 - - - +
363C GLU* 3.6 29.9 + - - +
364C LYS* 2.8 53.3 + - + +
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Residues in contact with PRO 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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349C LEU* 5.8 0.7 - - + -
360C LEU* 3.2 10.9 - - + +
361C ASP* 1.3 92.3 - - - +
363C GLU* 1.3 58.2 + - + +
365C LEU* 3.1 37.8 + - + +
366C ASN* 4.1 0.5 + - - -
384C PRO* 4.1 16.2 - - + -
386C HIS* 3.5 38.1 - - + +
387C MET* 3.3 14.0 - - + +
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Residues in contact with GLU 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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361C ASP* 3.0 21.2 + - - +
362C PRO* 1.3 78.7 - - + +
364C LYS* 1.3 59.8 + - - +
365C LEU 3.2 0.2 - - - -
366C ASN* 2.9 31.5 + - - +
386C HIS* 6.3 0.2 - - - +
387C MET* 5.2 0.4 - - - -
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Residues in contact with LYS 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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326C SER* 4.7 8.8 + - - +
329C ILE* 3.3 45.0 - - + +
330C ASP* 3.5 27.6 + - - +
360C LEU* 4.7 1.6 - - + -
361C ASP* 2.8 37.3 + - + +
363C GLU* 1.3 73.6 - - - +
365C LEU* 1.3 62.5 + - - +
366C ASN 3.1 3.2 + - - -
367C VAL* 3.3 15.6 + - - +
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Residues in contact with LEU 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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329C ILE* 4.2 11.7 - - + -
344C PHE* 3.9 28.7 - - + -
349C LEU* 5.0 3.8 - - + -
360C LEU* 3.9 26.5 - - + -
362C PRO* 3.1 16.8 + - + +
364C LYS* 1.3 74.3 - - - +
366C ASN* 1.3 56.2 + - - +
367C VAL 2.9 11.0 + - - -
368C PHE* 3.3 10.4 + - + -
383C TRP* 4.1 14.1 - - + -
384C PRO* 3.7 34.8 - - + -
387C MET* 3.8 14.4 - - + -
392C VAL* 3.2 33.2 - - + +
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Residues in contact with ASN 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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362C PRO 4.1 2.8 + - - -
363C GLU* 2.9 37.4 + - - +
364C LYS 3.1 1.2 - - - -
365C LEU* 1.3 76.2 - - - +
367C VAL* 1.3 60.5 + - - +
368C PHE 3.2 1.6 + - - -
369C ARG* 2.9 55.6 + - - +
370C THR* 6.0 0.3 - - - +
387C MET* 4.6 7.7 - - - +
392C VAL* 3.8 11.3 - - - +
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Residues in contact with VAL 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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329C ILE* 3.7 30.7 - - + +
332C PHE* 3.3 36.7 - - + +
333C VAL* 3.6 22.9 - - + +
334C ASN 4.8 1.0 + - - +
364C LYS 3.3 19.1 + - - +
365C LEU 2.9 1.2 - - - -
366C ASN* 1.3 78.9 - - - +
368C PHE* 1.3 72.8 + - + +
369C ARG 3.2 1.9 + - - -
370C THR* 3.6 17.0 + - - +
371C VAL* 4.7 0.5 - - - +
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Residues in contact with PHE 368 (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 VAL* 4.3 9.0 - - + -
329C ILE* 3.5 29.4 - - + -
332C PHE* 3.9 31.4 - + + -
338C ILE* 4.4 0.2 - - + -
342C LEU* 3.7 33.9 - - + -
344C PHE* 4.0 24.9 - + - -
365C LEU* 3.3 22.0 - - + -
366C ASN 3.2 1.8 - - - -
367C VAL* 1.3 79.6 - - + +
369C ARG* 1.3 60.8 + - - +
370C THR 3.1 3.6 - - - -
371C VAL* 3.2 33.8 + - + +
392C VAL* 3.2 28.0 - - + +
393C PHE* 3.8 18.4 - + + -
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Residues in contact with ARG 369 (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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366C ASN* 2.9 47.6 + - - +
367C VAL 3.2 1.6 - - - -
368C PHE* 1.3 79.3 - - - +
370C THR* 1.3 61.2 + - + +
391C SER* 3.3 41.7 + - - +
392C VAL* 3.2 21.2 - - - +
394C SER* 3.7 5.4 + - - +
395C ASN* 2.8 34.9 + - - +
705C NAG 3.3 36.7 + - - +
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Residues in contact with THR 370 (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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307C LEU* 4.6 19.8 - - + +
334C ASN* 3.7 18.6 - - - +
335C CYS 2.7 33.4 + - - -
336C THR* 3.3 19.2 - - - +
366C ASN 6.0 0.2 - - - +
367C VAL 3.6 12.5 + - - +
369C ARG* 1.3 80.8 - - + +
371C VAL* 1.3 62.6 + - - +
372C ARG* 3.3 9.7 + - - +
395C ASN* 4.6 4.4 + - - +
705C NAG 4.6 14.1 - - - +
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Residues in contact with VAL 371 (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 PHE 5.4 0.4 - - - +
335C CYS* 3.3 21.5 - - + +
336C THR 3.5 3.4 - - - +
338C ILE* 4.0 31.4 - - + -
367C VAL 4.7 1.1 - - - +
368C PHE* 3.2 37.5 + - + +
370C THR* 1.3 76.9 - - - +
372C ARG* 1.3 61.2 + - - +
373C GLU 3.8 22.7 - - - +
374C ILE* 4.2 10.8 - - + -
393C PHE* 5.0 5.5 - - + -
395C ASN* 3.3 4.3 - - - +
396C LEU* 3.2 27.5 + - + +
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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