Contacts of the helix formed by residues 443 - 454 (chain B) in PDB entry 1JQI
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 PRO 443 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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429B LEU* 5.7 0.2 - - + -
436B LEU* 3.9 24.0 - - + -
441B LEU* 3.3 8.7 - - + +
442B PHE* 1.3 86.5 - - + +
444B THR* 1.3 64.9 + - - +
445B SER 3.4 1.8 - - - -
446B GLN* 3.3 26.4 + - + +
447B VAL* 3.0 32.3 + - + +
488B THR* 3.6 22.2 - - + +
491B ILE* 4.0 15.0 - - + -
611B ALA* 4.2 8.3 - - + +
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Residues in contact with THR 444 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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441B LEU* 5.6 0.5 - - - +
442B PHE* 2.9 35.8 + - + +
443B PRO* 1.3 71.0 - - - +
445B SER* 1.3 64.9 + - - +
447B VAL* 3.4 2.3 + - - +
448B LYS* 3.2 22.6 + - + +
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Residues in contact with SER 445 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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443B PRO 3.4 0.4 - - - -
444B THR* 1.3 79.6 - - - +
446B GLN* 1.3 76.5 + - - +
448B LYS* 3.4 6.5 + - - +
449B LYS* 3.2 37.0 + - - +
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Residues in contact with GLN 446 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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424B PHE* 4.9 3.1 - - + -
428B GLU* 4.0 27.8 - - + +
429B LEU* 3.9 29.4 - - + -
432B ILE* 3.6 20.6 - - + +
436B LEU* 5.7 0.2 - - - +
443B PRO* 3.5 32.4 + - + +
445B SER* 1.3 87.2 - - - +
447B VAL* 1.3 65.5 + - + +
449B LYS* 3.2 9.7 + - - +
450B MET* 3.0 30.8 + - - +
488B THR* 5.5 0.4 - - + -
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Residues in contact with VAL 447 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
442B PHE* 3.8 27.4 - - + -
443B PRO* 3.0 31.5 + - + +
444B THR 3.9 4.3 - - - +
446B GLN* 1.3 75.6 - - - +
448B LYS* 1.3 58.3 + - - +
450B MET* 3.3 15.1 + - - +
451B GLY 2.9 23.4 + - - -
456B LEU* 3.6 27.7 - - + +
488B THR* 5.2 2.0 - - + -
491B ILE* 4.3 15.0 - - + -
522B GLY 4.6 7.0 - - - +
525B ILE* 4.3 15.9 - - + -
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Residues in contact with LYS 448 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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444B THR* 3.2 11.1 + - + +
445B SER* 3.6 10.5 - - - +
447B VAL* 1.3 80.3 - - - +
449B LYS* 1.3 56.8 + - + +
451B GLY* 2.9 3.9 + - - +
452B GLU* 2.8 54.9 + - - +
521B ASN* 2.9 44.9 + - - +
522B GLY* 4.0 14.3 + - - +
523B ASP* 3.2 20.4 + - - +
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Residues in contact with LYS 449 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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424B PHE* 3.9 19.3 - - + -
428B GLU* 3.2 34.8 - - + +
445B SER* 3.2 22.7 + - - +
446B GLN* 3.2 12.2 + - - +
448B LYS* 1.3 79.0 - - + +
450B MET* 1.3 59.0 + - - +
452B GLU* 3.0 19.6 + - - +
453B LEU* 2.9 29.5 + - - +
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Residues in contact with MET 450 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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424B PHE* 3.6 27.1 - - + -
446B GLN* 3.0 20.9 + - - +
447B VAL* 3.5 15.3 - - - +
449B LYS* 1.3 72.3 - - - +
451B GLY* 1.3 64.3 + - - +
453B LEU* 3.2 8.3 + - - +
454B GLY 3.1 3.5 + - - -
455B LEU* 2.9 40.5 + - + +
456B LEU* 4.3 9.2 - - + -
481B ILE* 4.0 11.7 - - + -
488B THR* 3.3 35.0 - - + +
492B MET* 3.5 42.2 - - + -
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Residues in contact with GLY 451 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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447B VAL 2.9 10.9 + - - -
448B LYS 2.9 4.9 + - - -
450B MET* 1.3 77.7 - - - +
452B GLU* 1.3 54.8 + - - +
454B GLY* 2.9 20.8 + - - -
456B LEU* 3.7 25.1 - - - +
520B THR 3.7 9.5 - - - +
521B ASN* 3.6 22.6 - - - -
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Residues in contact with GLU 452 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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448B LYS* 2.8 50.0 + - - +
449B LYS* 3.3 18.0 - - - +
451B GLY* 1.3 77.2 - - - +
453B LEU* 1.3 59.0 + - - +
454B GLY* 3.1 0.7 + - - -
521B ASN* 3.8 3.3 + - + +
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Residues in contact with LEU 453 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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420B THR* 4.3 24.2 - - + -
421B CYS* 6.1 0.4 - - - -
424B PHE* 3.7 41.1 - - + -
449B LYS 2.9 11.7 + - - +
450B MET* 3.6 9.9 - - - +
451B GLY 3.2 0.6 - - - -
452B GLU* 1.3 76.3 - - - +
454B GLY* 1.3 60.9 + - - +
455B LEU* 4.1 25.3 - - + +
467B ALA* 5.2 2.3 - - - +
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Residues in contact with GLY 454 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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451B GLY 2.9 16.1 + - - -
452B GLU 3.1 1.6 - - - -
453B LEU* 1.3 81.0 - - - +
455B LEU* 1.3 62.3 + - - +
456B LEU 3.3 3.7 + - - -
457B ALA* 3.8 3.3 + - - -
458B MET* 3.5 12.4 + - - +
467B ALA* 3.4 31.5 - - - +
469B LEU* 5.5 0.2 - - - +
520B THR 5.1 4.5 - - - -
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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