Contacts of the helix formed by residues 443 - 458 (chain V) in PDB entry 5IJO
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 LEU 443 (chain V).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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436V VAL 4.7 1.7 - - - +
439V MET* 3.0 26.9 + - + -
440V PHE* 3.5 17.5 + - - +
441V PRO 3.6 1.3 - - - -
442V HIS* 1.3 75.6 - - - +
444V LEU* 1.3 62.2 + - - +
445V SER 3.5 2.0 - - - +
446V PRO* 4.4 9.4 - - + +
447V LEU* 4.4 6.9 + - - +
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Residues in contact with LEU 444 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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440V PHE* 5.3 1.1 - - - +
441V PRO* 3.3 19.2 + - + +
442V HIS 3.5 2.7 + - - +
443V LEU* 1.3 72.1 - - - +
445V SER* 1.3 68.0 + - - +
446V PRO 3.5 0.2 - - - -
447V LEU* 3.7 2.1 + - - +
448V LEU* 3.4 24.6 + - - +
564V ARG* 4.2 27.1 - - + -
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Residues in contact with SER 445 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
443V LEU* 3.5 1.4 - - - +
444V LEU* 1.3 80.4 - - - +
446V PRO* 1.3 63.1 - - - +
448V LEU* 4.0 2.3 - - - +
449V GLN* 2.9 28.0 + - - +
567V PRO* 5.4 9.0 - - - +
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Residues in contact with PRO 446 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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404V ILE* 5.4 11.9 - - + -
408V CYS* 6.1 0.7 - - - +
436V VAL* 4.4 15.8 - - + +
443V LEU* 4.4 10.7 - - + +
444V LEU 3.5 0.6 - - - -
445V SER* 1.3 78.8 - - - +
447V LEU* 1.3 63.4 + - - +
449V GLN* 3.9 4.2 - - + +
450V LEU* 3.1 25.6 + - - +
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Residues in contact with LEU 447 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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436V VAL* 3.9 22.3 - - + +
437V CYS* 4.5 4.7 - - + -
440V PHE* 3.6 31.9 - - + -
443V LEU 4.4 2.2 + - - +
444V LEU 3.7 3.7 + - - +
445V SER 3.4 0.4 - - - -
446V PRO* 1.3 78.7 - - - +
448V LEU* 1.3 63.3 + - - +
450V LEU* 3.4 3.8 + - - +
451V LEU* 3.1 24.1 + - - +
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Residues in contact with LEU 448 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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444V LEU* 3.4 17.5 + - + +
445V SER 4.0 1.8 - - - +
446V PRO 3.3 0.2 - - - -
447V LEU* 1.3 80.8 - - - +
449V GLN* 1.3 61.4 + - - +
451V LEU* 3.4 6.9 + - - +
452V ARG* 3.0 23.8 + - - +
567V PRO* 4.5 25.4 - - + +
568V ILE* 5.3 3.1 - - - +
571V LEU* 4.6 10.0 - - + +
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Residues in contact with GLN 449 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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408V CYS* 5.3 12.3 - - + -
445V SER* 2.9 20.1 + - - +
446V PRO* 3.9 4.3 - - + +
448V LEU* 1.3 77.2 - - - +
450V LEU* 1.3 62.0 + - - +
452V ARG* 3.3 7.3 + - - +
453V ALA* 3.0 24.0 + - - +
567V PRO* 5.3 7.4 - - + +
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Residues in contact with LEU 450 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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408V CYS* 5.8 7.6 - - + +
411V LEU* 6.5 0.2 - - - -
433V LEU* 6.0 7.9 - - + -
436V VAL* 5.9 3.8 - - + -
446V PRO 3.1 18.0 + - - +
447V LEU* 3.9 4.7 - - - +
449V GLN* 1.3 76.0 - - - +
451V LEU* 1.3 64.3 + - - +
453V ALA* 3.3 5.4 + - - +
454V LEU* 3.0 25.3 + - - +
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Residues in contact with LEU 451 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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447V LEU 3.1 17.4 + - - +
448V LEU* 3.5 7.4 - - - +
449V GLN 3.3 0.2 - - - -
450V LEU* 1.3 75.8 - - - +
452V ARG* 1.3 63.1 + - - +
454V LEU* 3.4 4.3 + - - +
455V VAL* 3.0 26.9 + - - +
464V VAL* 5.4 6.5 - - + +
571V LEU* 5.9 3.4 - - + -
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Residues in contact with ARG 452 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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448V LEU 3.0 13.8 + - - +
449V GLN* 3.5 7.4 - - - +
451V LEU* 1.3 82.5 - - - +
453V ALA* 1.3 63.6 + - - +
455V VAL* 3.5 9.2 + - - +
456V SER* 3.5 12.3 + - - -
567V PRO 5.8 0.7 - - - +
570V ASP* 5.4 3.6 - - + +
571V LEU* 4.4 22.4 - - + +
574V LYS* 4.5 16.8 - - + +
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Residues in contact with ALA 453 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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408V CYS 5.5 0.9 - - - +
411V LEU* 4.7 12.6 - - + +
412V ALA* 4.5 24.9 - - + +
449V GLN 3.0 15.8 + - - +
450V LEU* 3.8 5.6 - - - +
451V LEU 3.3 0.2 - - - -
452V ARG* 1.3 79.4 - - - +
454V LEU* 1.3 62.5 + - - +
456V SER* 3.5 3.6 + - - -
457V GLY* 3.4 16.3 + - - -
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Residues in contact with LEU 454 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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450V LEU 3.0 17.4 + - - +
451V LEU* 3.9 4.9 - - - +
453V ALA* 1.3 74.8 - - - +
455V VAL* 1.3 58.0 + - - +
457V GLY* 3.1 1.3 + - - -
458V LYS* 2.7 42.2 + - + +
464V VAL* 5.4 8.7 - - + -
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Residues in contact with VAL 455 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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451V LEU 3.0 17.3 + - - +
452V ARG* 3.9 6.3 - - - +
453V ALA 3.3 0.2 - - - -
454V LEU* 1.3 77.9 - - - +
456V SER* 1.3 67.8 + - - +
458V LYS* 3.2 14.8 - - - +
460V THR 6.1 0.4 - - - -
461V ALA* 5.4 9.7 - - + +
464V VAL* 5.1 13.5 - - + -
574V LYS 5.4 2.2 - - - +
575V VAL* 5.2 12.3 - - + +
578V THR* 4.3 17.5 - - - -
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Residues in contact with SER 456 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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417V PRO* 4.3 31.1 - - - +
418V GLU 5.0 2.9 + - - -
419V LEU* 5.4 2.4 - - - +
452V ARG 3.5 8.6 + - - -
453V ALA* 3.5 7.7 + - - -
454V LEU 3.2 0.6 - - - -
455V VAL* 1.3 82.2 - - - +
457V GLY* 1.3 64.9 + - - +
458V LYS 4.1 1.7 - - - +
574V LYS* 5.7 6.2 - - - +
578V THR* 4.6 12.8 - - - -
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Residues in contact with GLY 457 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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417V PRO* 6.0 0.2 - - - -
418V GLU 5.1 9.6 - - - -
419V LEU* 3.6 23.6 - - - +
421V TRP 5.1 7.0 - - - +
453V ALA 3.4 7.7 + - - -
454V LEU* 3.1 4.1 + - - -
456V SER* 1.3 83.2 - - - +
458V LYS* 1.3 60.6 + - - +
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Residues in contact with LYS 458 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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419V LEU* 5.5 0.4 - - - -
454V LEU* 2.7 26.0 + - + +
455V VAL* 3.2 15.3 - - - +
456V SER 4.1 1.6 - - - +
457V GLY* 1.3 73.0 - - - +
459V SER* 1.3 62.8 + - - +
460V THR* 3.0 23.9 + - - +
461V ALA* 3.9 8.1 + - - +
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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