Contacts of the helix formed by residues 597 - 609 (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 VAL 597 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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353C TYR* 3.8 47.1 - - + +
356C LEU* 4.4 6.7 - - + +
357C ILE* 4.0 22.9 - - + -
437C PHE* 5.2 7.2 - - + -
459C GLN* 2.9 22.3 + - + +
460C GLN 5.3 1.8 - - - -
461C ASP 5.4 0.2 - - - +
594C LEU* 4.4 19.0 - - + +
595C GLY 4.1 0.2 + - - -
596C SER* 1.3 71.2 - - - +
598C GLU* 1.3 70.1 + - - +
600C MET* 3.4 5.7 + - - +
601C ILE* 2.9 33.0 + - + +
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Residues in contact with GLU 598 (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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343C CYS* 5.3 3.6 - - + -
345C PHE* 4.5 12.4 - - + -
353C TYR* 2.8 29.0 + - - -
452C LEU* 3.6 37.4 - - + +
455C VAL* 5.0 4.7 - - + -
457C ARG* 3.0 29.3 + - - +
458C PHE* 3.2 20.7 - - + +
459C GLN 3.3 13.9 + - - -
596C SER* 4.4 4.9 - - - -
597C VAL* 1.3 75.5 + - - +
599C ARG* 1.3 57.2 + - - +
601C ILE* 3.3 6.7 + - - +
602C ALA* 2.9 28.2 + - - +
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Residues in contact with ARG 599 (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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452C LEU 4.1 9.4 + - - +
453C THR* 4.3 32.0 + - + +
556C HIS* 4.1 22.6 + - - +
557C GLN* 2.9 42.8 + - - +
558C CYS* 4.1 9.1 - - - +
594C LEU 4.7 1.3 - - - +
595C GLY* 5.9 1.3 - - - -
596C SER* 3.3 29.9 + - - +
597C VAL 3.3 0.4 - - - -
598C GLU* 1.3 80.8 - - - +
600C MET* 1.3 57.4 + - - +
602C ALA* 3.0 6.5 + - - +
603C ILE* 2.9 46.4 + - - +
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Residues in contact with MET 600 (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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356C LEU* 4.4 7.9 - - + -
487C TYR* 4.9 6.1 - - + -
490C PHE* 4.4 10.1 - - + -
492C PHE* 4.2 9.6 - - + -
548C ILE* 4.1 12.8 - - + -
558C CYS* 3.8 28.5 - - + -
594C LEU* 3.8 40.9 + - + +
596C SER 3.0 15.6 + - - +
597C VAL* 3.9 3.8 - - - +
599C ARG* 1.3 76.4 - - - +
601C ILE* 1.3 58.5 + - - +
603C ILE* 3.3 8.0 + - + +
604C LEU* 2.9 66.9 + - + +
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Residues in contact with ILE 601 (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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333C TYR* 3.8 22.0 - - + -
345C PHE* 3.7 23.3 - - + -
349C GLY 4.6 0.7 - - - +
352C ILE* 4.1 12.8 - - + -
353C TYR* 4.0 22.0 - - + +
356C LEU* 3.6 16.8 - - + -
452C LEU* 3.8 8.5 - - + -
597C VAL* 2.9 37.1 + - + +
598C GLU 3.5 4.3 - - - +
600C MET* 1.3 76.2 - - - +
602C ALA* 1.3 54.0 + - - +
604C LEU* 4.1 4.8 - - - +
605C THR* 2.4 48.1 + - - +
612C TRP* 4.5 6.9 - - + -
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Residues in contact with ALA 602 (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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323C HIS* 3.6 31.7 - - + +
452C LEU* 3.5 29.6 - - + +
453C THR* 4.0 23.9 - - + +
598C GLU 2.9 7.4 + - - +
599C ARG 3.3 9.9 - - - +
601C ILE* 1.3 77.6 - - - +
603C ILE* 1.3 61.4 + - - +
605C THR* 4.2 3.6 - - - -
606C GLU* 3.6 14.6 + - - +
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Residues in contact with ILE 603 (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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453C THR* 5.9 4.0 - - + -
492C PHE* 4.2 24.2 - - + -
548C ILE* 4.4 6.1 - - + -
550C ASP* 5.3 1.8 - - + -
556C HIS* 3.9 52.3 - - + +
558C CYS* 3.9 21.5 - - - -
599C ARG* 2.9 35.2 + - - +
600C MET* 3.7 11.0 - - + +
602C ALA* 1.3 76.7 - - + +
604C LEU* 1.3 60.3 + - - +
606C GLU* 3.4 5.7 + - - +
607C ASN* 2.9 31.3 + - + +
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Residues in contact with LEU 604 (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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356C LEU* 4.3 11.2 - - + -
490C PHE* 3.8 22.2 - - + -
492C PHE* 3.8 33.2 - - + -
600C MET* 2.9 42.6 + - + +
601C ILE* 4.1 2.2 - - - +
603C ILE* 1.3 70.5 - - - +
605C THR* 1.3 60.3 + - - +
607C ASN* 4.1 3.6 - - - +
608C TYR* 2.9 64.7 + - + +
612C TRP* 4.0 12.5 - - + -
616C LEU* 4.1 14.6 - - + -
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Residues in contact with THR 605 (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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323C HIS* 3.6 25.1 - - - +
326C ILE* 3.4 25.3 - - + +
327C GLY 4.6 0.9 - - - +
332C LEU* 4.7 2.5 - - + -
333C TYR* 2.9 28.2 + - + +
601C ILE* 2.4 32.0 + - - +
602C ALA 4.0 0.2 - - - -
604C LEU* 1.3 77.8 - - - +
606C GLU* 1.3 60.3 + - - +
609C GLY 3.3 15.4 + - - -
610C GLY 3.4 8.7 + - - -
612C TRP* 3.8 22.6 - - + -
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Residues in contact with GLU 606 (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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322C ASP* 3.8 21.5 + - + +
323C HIS* 3.4 45.4 + - + +
326C ILE* 4.5 6.5 - - - +
453C THR* 5.7 2.7 - - - +
554C ARG* 5.7 3.5 + - - -
556C HIS* 5.7 5.2 - - - -
602C ALA 3.6 9.5 + - - +
603C ILE* 3.4 7.0 + - - +
604C LEU 3.3 0.2 - - - -
605C THR* 1.3 74.1 - - - +
607C ASN* 1.3 65.7 + - - +
609C GLY* 3.5 10.0 + - - -
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Residues in contact with ASN 607 (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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490C PHE 5.1 1.6 + - - -
492C PHE* 3.5 26.1 - - + -
550C ASP* 3.2 14.2 - - + +
551C ALA* 2.7 47.6 + - - +
603C ILE 2.9 20.2 + - - +
604C LEU* 4.0 6.5 - - - +
606C GLU* 1.3 79.9 - - - +
608C TYR* 1.3 81.1 + - - +
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Residues in contact with TYR 608 (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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489C VAL 4.9 1.7 + - - -
490C PHE* 3.6 32.5 + - - -
604C LEU* 2.9 55.0 + - + +
605C THR* 5.4 0.2 - - - -
607C ASN* 1.3 91.3 - - - +
609C GLY* 1.3 61.4 + - - +
610C GLY 3.3 2.0 - - - +
611C LYS* 3.0 42.7 + - - +
612C TRP* 3.9 11.2 - + + -
613C PRO* 3.5 35.9 - - + +
615C TRP* 5.6 0.9 + - - -
616C LEU* 4.0 8.2 - - + +
717C LYS* 5.8 3.8 - - + +
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Residues in contact with GLY 609 (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 ILE* 4.2 12.9 - - - +
605C THR 3.3 10.5 + - - -
606C GLU 3.5 8.2 + - - -
607C ASN 3.3 3.2 - - - -
608C TYR* 1.3 75.2 - - - +
610C GLY* 1.3 59.6 + - - +
611C LYS* 3.1 6.5 + - - +
669C GLN* 4.6 5.9 + - - -
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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