Contacts of the helix formed by residues 596 - 609 (chain A) 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 SER 596 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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452A LEU 5.2 0.5 + - - -
455A VAL* 5.4 2.1 - - - +
458A PHE* 3.6 42.4 - - - +
459A GLN 3.5 5.4 - - - -
460A GLN* 4.1 1.3 - - - +
594A LEU* 3.2 9.2 + - - +
595A GLY* 1.3 73.3 - - - -
597A VAL* 1.3 65.0 + - - +
598A GLU* 4.0 2.8 + - - +
599A ARG* 3.0 29.5 + - - +
600A MET* 3.0 21.2 + - - +
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Residues in contact with VAL 597 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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353A TYR* 3.7 48.9 - - + +
356A LEU* 4.2 11.4 - - + -
357A ILE* 3.9 23.8 - - + -
437A PHE* 5.3 6.1 - - + -
459A GLN* 2.9 24.9 + - + +
460A GLN 5.3 1.3 - - - -
461A ASP* 5.4 1.6 - - + +
594A LEU* 5.1 13.4 - - + +
595A GLY 4.3 0.4 + - - -
596A SER* 1.3 69.5 - - - +
598A GLU* 1.3 61.8 + - - +
600A MET* 3.4 7.6 + - - +
601A ILE* 2.9 36.3 + - + +
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Residues in contact with GLU 598 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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343A CYS* 5.1 2.4 - - + +
345A PHE* 4.1 11.7 - - + -
353A TYR* 2.8 29.6 + - - -
452A LEU* 3.6 43.1 - - + +
455A VAL* 5.0 4.0 - - + -
457A ARG* 3.3 26.2 + - - +
458A PHE* 3.4 20.0 - - + +
459A GLN 3.1 15.4 + - - -
596A SER* 4.1 5.2 - - - +
597A VAL* 1.3 77.6 + - - +
599A ARG* 1.3 56.9 + - - +
601A ILE* 3.1 10.7 + - - +
602A ALA 2.9 24.4 + - - -
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Residues in contact with ARG 599 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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452A LEU 3.9 9.8 + - - +
453A THR* 3.9 32.7 + - - +
556A HIS* 5.1 1.2 - - - +
557A GLN* 2.6 36.3 + - - +
558A CYS* 3.6 18.6 - - - +
594A LEU 4.8 2.2 + - - +
595A GLY* 5.6 2.4 - - - -
596A SER* 3.0 24.0 + - - +
598A GLU* 1.3 79.3 - - - +
600A MET* 1.3 62.9 + - - +
602A ALA* 3.2 4.3 + - - +
603A ILE* 3.0 38.1 + - + +
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Residues in contact with MET 600 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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356A LEU* 4.3 10.8 - - + -
487A TYR* 5.2 3.1 - - - -
490A PHE* 4.2 7.4 - - + -
492A PHE* 3.7 24.5 - - + -
548A ILE* 4.3 8.7 - - + -
558A CYS* 4.8 6.5 - - - -
594A LEU* 3.6 47.5 + - + +
596A SER 3.0 16.0 + - - +
597A VAL* 3.7 5.4 - - - +
599A ARG* 1.3 76.4 - - - +
601A ILE* 1.3 57.7 + - - +
603A ILE* 3.4 15.7 + - + -
604A LEU* 2.9 64.3 + - + +
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Residues in contact with ILE 601 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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333A TYR* 4.1 10.5 - - + -
345A PHE* 3.8 23.8 - - + -
349A GLY* 4.5 2.2 - - - +
352A ILE* 3.9 18.4 - - + -
353A TYR* 3.9 21.5 - - + +
356A LEU* 3.6 17.0 - - + -
452A LEU* 3.9 17.3 - - + -
597A VAL* 2.9 36.3 + - + +
598A GLU* 3.1 5.1 + - - +
600A MET* 1.3 73.8 - - - +
602A ALA* 1.3 58.4 + - - +
604A LEU* 3.8 5.0 - - - +
605A THR* 2.7 46.1 + - - +
612A TRP* 4.5 2.5 - - + -
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Residues in contact with ALA 602 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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323A HIS* 3.6 28.7 - - + +
452A LEU* 3.8 19.1 - - + -
453A THR* 4.1 18.6 - - + -
598A GLU 2.9 12.4 + - - +
599A ARG 3.5 9.0 - - - +
601A ILE* 1.3 78.4 - - - +
603A ILE* 1.3 59.2 + - + +
605A THR* 3.3 2.9 + - - -
606A GLU* 2.9 31.5 + - - +
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Residues in contact with ILE 603 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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453A THR* 6.1 2.5 - - + -
492A PHE* 4.5 12.8 - - + -
548A ILE* 4.6 3.1 - - + -
550A ASP* 5.0 2.6 - - + +
556A HIS* 3.7 47.6 - - + +
558A CYS* 3.6 31.6 - - - -
599A ARG* 3.0 31.3 + - + +
600A MET* 3.9 17.0 - - + +
602A ALA* 1.3 77.5 - - + +
604A LEU* 1.3 57.3 + - - +
606A GLU* 3.3 11.2 + - + +
607A ASN* 2.8 28.4 + - + +
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Residues in contact with LEU 604 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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352A ILE* 6.1 0.2 - - + -
356A LEU* 4.2 9.2 - - + -
490A PHE* 3.6 30.7 - - + -
492A PHE* 3.6 32.1 - - + -
600A MET* 2.9 35.8 + - + +
601A ILE* 4.0 2.2 - - - +
603A ILE* 1.3 72.4 - - - +
605A THR* 1.3 61.0 + - - +
607A ASN* 4.1 2.5 - - + -
608A TYR* 2.9 64.4 + - + +
612A TRP* 4.0 10.5 - - + -
616A LEU* 3.7 17.5 - - + -
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Residues in contact with THR 605 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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323A HIS* 3.5 31.9 - - - +
326A ILE* 3.6 36.6 - - + +
327A GLY 4.5 1.6 - - - +
332A LEU* 4.6 2.3 - - + +
333A TYR* 3.9 10.7 + - + +
601A ILE* 2.7 29.7 + - - +
602A ALA 3.5 4.7 - - - -
604A LEU* 1.3 74.9 - - - +
606A GLU* 1.3 63.3 + - - +
609A GLY 3.4 15.8 + - - -
610A GLY 3.9 1.6 + - - +
612A TRP* 3.5 24.2 - - + -
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Residues in contact with GLU 606 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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322A ASP* 2.8 45.9 + - - +
323A HIS* 4.2 16.7 - - + +
453A THR* 5.8 4.4 - - - +
550A ASP* 5.5 2.3 - - - +
556A HIS* 4.5 17.2 - - - -
602A ALA* 2.9 18.1 + - - +
603A ILE* 3.5 9.6 - - - +
604A LEU 3.2 0.2 - - - -
605A THR* 1.3 80.2 - - - +
607A ASN* 1.3 62.3 + - - +
609A GLY* 3.9 6.1 + - - -
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Residues in contact with ASN 607 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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490A PHE 5.2 1.0 + - - -
492A PHE* 3.7 19.9 - - + -
550A ASP* 3.2 17.3 - - + +
551A ALA* 2.8 45.8 + - - +
552A ILE 4.8 0.2 + - - -
603A ILE* 2.8 18.1 + - + +
604A LEU* 3.3 6.7 + - - +
606A GLU* 1.3 78.6 - - - +
608A TYR* 1.3 89.5 + - - +
609A GLY* 3.5 0.5 + - - -
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Residues in contact with TYR 608 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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489A VAL 5.1 0.9 + - - -
490A PHE* 3.7 40.4 + - - -
604A LEU* 2.9 46.8 + - + +
607A ASN* 1.3 95.0 - - - +
609A GLY* 1.3 58.2 - - - +
610A GLY* 4.2 2.7 - - - +
611A LYS* 3.0 50.1 + - - +
612A TRP* 3.8 18.6 - + + -
613A PRO* 3.7 30.0 - - + +
615A TRP* 5.7 0.2 - - - -
616A LEU* 4.1 7.0 - - + -
717A LYS* 6.2 0.2 - - - +
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Residues in contact with GLY 609 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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326A ILE* 3.8 17.7 - - - +
605A THR 3.4 11.0 + - - -
606A GLU 3.9 4.5 + - - -
607A ASN 3.3 4.6 + - - -
608A TYR* 1.3 77.7 - - - +
610A GLY* 1.3 56.6 + - - +
611A LYS* 3.3 2.2 + - - +
669A GLN* 4.8 5.5 + - - -
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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