Contacts of the helix formed by residues 444 - 461 (chain B) in PDB entry 4D1Q
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 GLN 444 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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441B HIS 3.8 13.4 + - - +
442B MET* 2.5 21.7 + - - +
443B GLN* 1.3 87.3 - - + +
445B GLU* 1.3 78.5 + - - +
446B LYS* 2.5 24.1 + - + +
447B VAL* 2.8 11.4 + - - +
448B ALA 4.3 0.2 + - - -
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Residues in contact with GLU 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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444B GLN* 1.3 93.8 - - - +
446B LYS* 1.3 71.0 + - + +
447B VAL 3.3 0.4 - - - -
448B ALA* 3.4 18.0 + - - +
449B GLN* 3.4 21.3 + - + +
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Residues in contact with LYS 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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430B TYR* 3.2 57.2 + - + -
442B MET* 3.3 45.4 - - + +
444B GLN* 2.5 14.4 + - + +
445B GLU* 1.3 79.0 + - - +
447B VAL* 1.3 57.6 + - - +
449B GLN* 3.0 28.9 + - + +
450B ILE* 2.8 34.0 + - + +
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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
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434B PHE* 4.2 25.8 - - + -
439B ALA 6.0 0.2 - - - +
442B MET 3.3 8.3 + - - +
443B GLN* 4.1 21.5 - - - +
444B GLN 2.8 13.2 + - - +
446B LYS* 1.3 71.3 - - - +
448B ALA* 1.3 71.8 + - + +
450B ILE* 4.1 7.8 - - + +
451B LYS* 3.0 24.6 + - - +
524B PHE* 4.2 8.3 - - + -
528B ARG* 3.6 43.5 - - - +
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Residues in contact with ALA 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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445B GLU* 3.4 14.8 + - + +
446B LYS 3.3 0.6 - - - -
447B VAL* 1.3 85.3 - - + +
449B GLN* 1.3 64.0 + - + +
451B LYS* 3.6 4.7 + - - +
452B GLU* 3.3 19.3 + - - +
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Residues in contact with GLN 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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427B ILE* 4.9 14.8 - - + +
430B TYR* 5.9 2.2 - - - -
445B GLU* 3.4 18.1 - - + +
446B LYS* 3.0 33.0 + - + +
448B ALA* 1.3 76.3 - - + +
450B ILE* 1.3 65.8 + - - +
452B GLU* 3.1 19.2 - - - +
453B PHE* 3.0 22.1 + - - +
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Residues in contact with ILE 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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427B ILE* 4.3 14.6 - - + +
430B TYR* 4.0 18.2 - - + +
431B THR* 3.8 24.5 - - + +
434B PHE* 3.4 55.9 - - + -
442B MET* 4.5 11.4 - - + -
446B LYS* 2.8 31.5 + - + +
447B VAL* 3.3 11.0 + - + +
449B GLN* 1.3 69.1 - - + +
451B LYS* 1.3 70.9 + - - +
453B PHE* 3.1 3.5 + - - +
454B CYS* 2.8 20.8 + - - -
524B PHE* 4.1 0.7 - - + -
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Residues in contact with LYS 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 3.0 13.3 + - - +
448B ALA* 3.9 4.5 - - - +
450B ILE* 1.3 72.3 - - - +
452B GLU* 1.3 67.1 + - - +
453B PHE 2.7 2.3 + - - -
454B CYS* 2.7 14.9 + - - -
455B LEU* 2.9 37.1 + - + -
521B SER* 4.0 24.5 - - - +
524B PHE* 3.4 38.1 - - + -
525B GLU* 3.1 41.6 + - - +
528B ARG* 6.0 0.7 - - - +
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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 ALA 3.3 11.5 + - - +
449B GLN* 3.1 19.7 + - - +
451B LYS* 1.3 78.8 - - - +
453B PHE* 1.3 59.6 + - - +
455B LEU* 3.8 12.3 + - - +
456B SER* 3.3 24.2 + - - +
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Residues in contact with PHE 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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427B ILE* 3.6 33.2 - - + -
428B TRP* 3.9 42.6 - + - -
431B THR* 3.6 36.6 - - + -
449B GLN 3.0 11.2 + - - +
450B ILE 3.3 7.2 - - - +
451B LYS 2.7 3.6 + - - -
452B GLU* 1.3 69.9 + - - +
454B CYS* 1.3 69.8 + - - +
455B LEU 3.1 1.3 - - - -
456B SER* 3.0 10.2 + - - -
457B LYS* 2.9 44.1 + - + +
557B LEU* 5.3 2.7 - - + -
561B LEU* 4.4 10.3 - - + -
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Residues in contact with CYS 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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431B THR* 3.6 15.0 - - - -
435B PHE* 3.4 34.8 - - - -
450B ILE* 2.8 21.6 + - - +
451B LYS 2.7 11.9 + - - +
453B PHE* 1.3 72.6 - - - +
455B LEU* 1.3 64.7 + - + +
457B LYS* 3.7 2.0 - - - +
458B MET* 2.9 38.0 + - + +
524B PHE* 4.2 15.5 - - + -
554B LEU* 4.8 1.1 - - + -
557B LEU* 3.4 17.3 - - + -
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Residues in contact with LEU 455 (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 LYS* 2.9 51.5 + - + +
452B GLU* 3.8 11.9 - - - +
454B CYS* 1.3 76.0 - - + +
456B SER* 1.3 56.3 + - - +
458B MET* 2.8 44.4 + - + +
459B GLU* 3.1 21.6 + - + +
520B PRO* 3.9 18.4 - - + +
521B SER* 4.0 19.5 - - - +
524B PHE* 5.1 2.0 - - + -
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Residues in contact with SER 456 (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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452B GLU* 3.3 12.9 + - - +
453B PHE* 3.0 11.7 + - - -
455B LEU* 1.3 78.2 - - - +
457B LYS* 1.3 62.5 + - - +
459B GLU* 3.6 10.0 + - - +
460B ASP* 3.2 28.7 + - - +
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Residues in contact with LYS 457 (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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173B ASP* 4.0 20.9 - - - +
244B LYS* 6.2 1.1 - - - +
261B ILE* 5.7 4.2 - - - +
428B TRP* 3.5 33.4 - - + -
453B PHE* 2.9 39.2 + - + +
454B CYS* 4.0 4.5 - - - +
456B SER* 1.3 77.1 - - - +
458B MET* 1.3 64.6 + - - +
459B GLU 3.3 0.4 + - - -
460B ASP* 3.7 32.8 + - - +
461B LEU* 3.7 10.0 + - - +
557B LEU* 3.9 28.2 - - + +
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Residues in contact with MET 458 (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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454B CYS* 2.9 35.4 + - + +
455B LEU* 2.8 17.4 + - + +
457B LYS* 1.3 71.0 - - - +
459B GLU* 1.3 66.4 + - - +
461B LEU* 3.6 10.4 + - + +
462B GLU* 3.5 23.5 + - - +
520B PRO* 3.6 39.3 - - + +
523B GLU* 5.5 0.7 - - - -
524B PHE* 5.4 1.6 - - + -
553B LYS* 3.3 40.5 - - + +
554B LEU* 3.3 35.2 - - + -
557B LEU* 4.5 9.9 - - + -
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Residues in contact with GLU 459 (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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455B LEU* 3.1 25.9 + - + +
456B SER* 3.8 10.1 - - - +
457B LYS 3.3 0.2 - - - -
458B MET* 1.3 76.1 - - - +
460B ASP* 1.3 59.3 + - - +
461B LEU 3.1 1.3 - - - -
462B GLU* 2.7 53.1 + - - +
463B LEU* 4.8 0.7 - - - +
520B PRO* 3.8 24.9 - - - +
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Residues in contact with ASP 460 (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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173B ASP* 4.3 16.7 - - - +
456B SER* 3.2 16.2 + - - +
457B LYS* 3.7 32.3 + - - +
459B GLU* 1.3 78.6 - - - +
461B LEU* 1.3 56.7 + - - +
463B LEU* 3.0 31.8 - - - +
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Residues in contact with LEU 461 (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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171B GLU 4.8 3.1 - - - +
172B LYS* 3.8 38.4 - - + +
173B ASP* 4.2 12.8 - - + -
457B LYS 3.7 9.1 + - - +
458B MET* 3.6 11.9 + - + +
459B GLU 3.1 1.0 - - - -
460B ASP* 1.3 74.1 - - + +
462B GLU* 1.3 56.4 + - - +
463B LEU 3.0 7.0 - - - -
464B ILE* 3.1 38.9 - - + +
553B LYS 5.6 2.0 - - - +
556B LYS* 3.7 48.7 + - + +
557B LEU* 5.0 7.0 - - - +
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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