Contacts of the helix formed by residues 412 - 421 (chain C) in PDB entry 4P3N
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 ASN 412 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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374C THR* 5.3 1.1 + - - +
409C LYS* 2.4 40.6 + - - +
411C MET* 1.3 73.6 - - - +
413C CYS* 1.3 66.3 + - - +
414C PRO* 3.5 0.9 - - - -
415C GLY* 3.2 13.7 + - - -
416C HIS* 3.2 31.0 + - + +
436C ASP* 3.7 23.4 + - - +
438C GLY* 4.2 6.5 + - - -
440C LEU* 3.5 16.4 - - - +
460C GLN* 5.3 0.6 - - - +
462C ASP* 3.2 38.8 + - - +
464C HIS* 4.2 0.2 - - - -
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Residues in contact with CYS 413 (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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388C HIS* 5.6 1.6 - - + -
411C MET* 3.9 28.5 - - - -
412C ASN* 1.3 77.0 - - - +
414C PRO* 1.3 70.3 - - + +
416C HIS* 3.1 5.8 + - - +
417C CYS* 2.9 26.2 + - - -
462C ASP* 4.7 3.6 - - - -
464C HIS* 2.9 37.4 - - + +
567C LEU* 4.0 9.6 - - + -
590C HIS* 3.2 27.1 - - + -
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Residues in contact with PRO 414 (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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382C LEU* 3.7 22.9 - - + -
383C TRP* 3.6 22.2 - - + -
386C SER* 3.6 18.8 - - - -
388C HIS* 4.2 7.9 - - + -
411C MET 3.9 12.3 - - - +
412C ASN 3.5 3.6 - - - -
413C CYS* 1.3 94.5 - - + +
415C GLY* 1.3 56.2 + - - +
417C CYS* 3.0 9.4 + - + +
418C LEU* 2.9 30.9 + - - +
567C LEU* 5.6 1.6 - - + -
571C PHE* 3.8 23.1 - - + -
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Residues in contact with GLY 415 (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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374C THR* 5.0 3.4 - - - -
378C PHE* 4.4 16.8 - - - -
382C LEU* 4.7 2.2 - - - +
412C ASN 3.2 7.7 + - - -
414C PRO* 1.3 78.5 - - - +
416C HIS* 1.3 60.4 + - - +
418C LEU* 3.1 10.3 + - - +
419C MET* 2.9 29.5 + - - +
344D PHE* 3.5 20.5 - - - -
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Residues in contact with HIS 416 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
372C VAL* 3.7 13.7 - - + +
374C THR* 3.9 17.3 - - + -
412C ASN* 3.2 18.8 + - + +
413C CYS 3.1 9.5 + - - +
415C GLY* 1.3 73.4 - - - +
417C CYS* 1.3 60.8 + - - +
419C MET* 3.1 9.7 + - - +
420C PHE* 2.9 27.5 + - - +
434C LEU* 3.8 29.3 + - + +
436C ASP* 3.0 42.8 + - + +
462C ASP 4.8 1.3 - - - -
464C HIS* 3.0 29.2 + + + +
466C PHE* 4.0 15.9 - - + -
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Residues in contact with CYS 417 (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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413C CYS* 2.9 18.2 + - - -
414C PRO 3.2 9.0 - - - +
416C HIS* 1.3 76.4 - - - +
418C LEU* 1.3 56.5 + - - +
420C PHE* 3.2 3.2 + - - +
421C ASP* 2.9 30.2 + - - +
466C PHE* 4.7 2.9 - - - -
567C LEU* 3.7 21.3 - - - -
571C PHE* 3.8 27.4 - - + -
573C LEU* 3.5 18.5 - - + +
588C ILE* 3.6 30.5 - - - -
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Residues in contact with LEU 418 (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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378C PHE* 4.9 2.7 - - + -
382C LEU* 3.8 21.1 - - + -
414C PRO 2.9 15.6 + - - +
415C GLY* 3.3 10.1 - - - +
417C CYS* 1.3 76.2 - - - +
419C MET* 1.3 55.3 + - - +
421C ASP* 3.3 10.6 + - + +
422C HIS* 2.9 27.7 + - - +
571C PHE* 4.0 22.7 - - + -
334D PHE* 4.1 4.7 - - + -
336D HIS* 3.8 48.9 - - + +
338D LEU* 4.1 8.1 - - + -
344D PHE* 4.1 20.6 - - + -
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Residues in contact with MET 419 (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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372C VAL* 3.6 23.8 - - + -
374C THR* 3.6 27.1 - - - -
415C GLY 2.9 19.0 + - - +
416C HIS* 3.1 12.5 + - - +
418C LEU* 1.3 74.5 - - - +
420C PHE* 1.3 56.3 + - - +
422C HIS* 3.3 9.0 - - - +
425C ARG* 2.4 30.9 + - - -
434C LEU* 4.3 11.9 - - + -
334D PHE* 4.0 14.4 - - + -
344D PHE* 3.5 16.2 - - + -
345D PHE 3.5 28.9 - - - +
346D LEU* 3.7 28.0 - - + +
347D PRO* 4.9 0.2 - - + -
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Residues in contact with PHE 420 (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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416C HIS 2.9 12.2 + - - +
417C CYS* 3.2 7.2 + - - +
419C MET* 1.3 76.1 - - - +
421C ASP* 1.3 60.5 - - - +
422C HIS 3.2 0.6 + - - -
423C ARG 3.5 6.1 - - - +
425C ARG* 2.6 54.1 + - + +
430C LEU* 4.1 16.4 - - + -
432C LEU* 3.9 11.0 - - + -
434C LEU* 4.9 1.7 - - + +
466C PHE* 3.5 48.0 - + + -
573C LEU* 3.9 29.6 - - + -
574C THR 3.3 26.9 - - - -
575C TYR* 4.6 4.3 - - + -
586C PRO* 4.0 17.0 - - + -
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Residues in contact with ASP 421 (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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417C CYS 2.9 18.0 + - - +
418C LEU* 3.5 11.0 - - + +
419C MET 3.2 0.4 - - - -
420C PHE* 1.3 75.8 - - - +
422C HIS* 1.3 63.8 + - - +
423C ARG* 3.3 7.0 + - - +
571C PHE* 4.2 12.0 - - + +
572C ASN 4.2 11.5 - - - +
573C LEU* 3.6 18.3 - - + +
574C THR* 5.2 1.9 + - - -
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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