Contacts of the helix formed by residues 443 - 454 (chain B) in PDB entry 5WWT
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 ARG 443 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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441B GLU 4.0 3.0 + - - -
442B ALA* 1.3 73.6 - - - +
444B ARG* 1.3 64.8 + - - +
445B GLU* 3.1 43.0 + - - +
446B ASP* 3.1 41.5 + - - +
447B MET* 3.3 7.7 + - - +
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Residues in contact with ARG 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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91A ASP* 6.0 0.4 + - - -
87B LEU* 4.5 25.7 - - + +
88B GLN* 3.3 29.5 + - - +
90B PRO* 4.7 6.3 - - - +
442B ALA 3.7 2.9 + - - -
443B ARG* 1.3 76.7 - - - +
445B GLU* 1.3 69.2 + - - +
447B MET* 3.1 11.9 + - - +
448B LEU* 2.9 56.1 + - + +
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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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443B ARG* 3.1 47.6 + - - +
444B ARG* 1.3 85.4 + - - +
446B ASP* 1.3 59.0 + - - +
448B LEU* 3.8 13.2 - - + +
449B ARG* 2.9 30.0 + - - +
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Residues in contact with ASP 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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442B ALA* 5.8 2.2 - - + -
443B ARG* 3.1 37.5 + - - +
444B ARG 3.1 0.2 - - - -
445B GLU* 1.3 77.8 - - - +
447B MET* 1.3 60.6 + - + +
449B ARG* 3.6 29.9 + - - +
450B LEU* 2.9 33.1 + - - +
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Residues in contact with MET 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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52B PHE* 3.4 24.4 - - + -
85B PRO* 4.4 15.9 - - + -
87B LEU* 3.7 33.4 - - + -
99B PRO* 4.8 3.4 - - + -
439B LEU* 3.6 36.8 - - + +
442B ALA* 3.7 26.5 - - + +
443B ARG 3.3 10.3 + - - +
444B ARG* 3.1 13.6 + - - +
446B ASP* 1.3 78.5 - - - +
448B LEU* 1.3 58.3 + - - +
450B LEU* 3.2 9.0 + - + +
451B ALA* 2.9 25.6 + - - +
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Residues in contact with LEU 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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87B LEU* 4.2 18.4 - - + -
88B GLN 4.8 0.9 - - - +
89B HIS* 4.9 2.8 + - + +
90B PRO* 3.7 35.4 - - + -
97B LEU* 3.9 24.7 - - + -
444B ARG* 2.9 49.9 + - + +
445B GLU* 3.8 11.9 - - + +
446B ASP 3.3 0.2 - - - -
447B MET* 1.3 77.0 - - - +
449B ARG* 1.3 58.2 + - - +
451B ALA* 3.3 4.7 + - - +
452B ASN* 2.9 40.9 + - - +
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Residues in contact with ARG 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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429B VAL* 3.5 27.5 - - - +
430B PRO* 6.1 0.4 - - - +
445B GLU 2.9 17.9 + - - +
446B ASP* 3.6 32.5 + - - +
448B LEU* 1.3 76.0 - - - +
450B LEU* 1.3 63.7 + - - +
452B ASN* 3.2 8.7 + - + +
453B LYS* 2.9 56.4 + - + +
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Residues in contact with LEU 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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51B SER* 3.8 8.2 + - - +
52B PHE* 3.7 17.0 - - + -
429B VAL* 4.2 13.5 - - + -
430B PRO 4.7 1.3 - - - +
432B PRO* 3.6 43.7 - - + -
434B THR* 5.4 2.9 - - - +
446B ASP 2.9 20.7 + - - +
447B MET* 3.2 10.7 + - + +
449B ARG* 1.3 83.6 - - - +
451B ALA* 1.3 55.8 + - - +
453B LYS* 5.0 1.1 - - - -
454B ASP* 2.7 47.6 + - + +
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Residues in contact with ALA 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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52B PHE* 3.7 28.8 - - + +
54B THR* 5.7 0.4 - - + -
97B LEU* 3.8 31.4 - - + -
221B LEU* 3.3 20.1 - - + +
447B MET 2.9 16.1 + - - +
448B LEU 3.7 4.9 - - - +
450B LEU* 1.3 76.4 - - - +
452B ASN* 1.3 62.4 + - - +
454B ASP 4.5 3.0 - - - +
455B SER* 4.2 12.3 - - - -
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Residues in contact with ASN 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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89B HIS* 2.7 35.9 + - - -
91B ASP* 5.1 4.2 + - - -
221B LEU* 3.6 8.0 - - - +
403B ILE* 3.5 29.0 - - + +
404B GLY* 5.2 0.3 - - - -
424B PHE* 3.8 26.2 - - - -
448B LEU* 2.9 28.3 + - - +
449B ARG* 3.6 8.6 - - + +
450B LEU 3.2 0.2 - - - -
451B ALA* 1.3 78.4 - - - +
453B LYS* 1.3 68.0 + - + +
455B SER* 4.2 1.6 + - - -
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Residues in contact with LYS 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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403B ILE 4.5 15.7 - - - +
404B GLY* 5.7 1.1 - - - -
405B GLY* 5.6 8.3 - - - +
424B PHE* 5.7 0.5 - - - -
425B ASP 3.5 21.3 + - - +
426B PRO* 4.5 1.0 - - - +
428B ALA* 4.1 17.8 - - + +
429B VAL* 3.6 33.3 - - + +
449B ARG* 2.9 35.6 + - + +
452B ASN* 1.3 86.6 - - + +
454B ASP* 1.3 61.5 + - - +
455B SER* 2.9 13.0 + - - -
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Residues in contact with ASP 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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45B HIS* 4.8 0.7 - - - -
49B PRO 4.4 0.9 - - - +
50B PRO* 3.8 12.5 - - - +
51B SER* 2.5 41.6 + - - +
52B PHE* 5.0 2.6 + - - +
332B ARG* 2.7 39.8 + - - +
426B PRO 4.6 5.3 - - - +
429B VAL* 3.9 8.9 - - + +
430B PRO 5.4 0.4 - - - -
431B LEU* 4.0 6.6 - - - +
432B PRO* 3.8 13.6 - - - +
450B LEU* 2.7 34.3 + - + +
451B ALA* 4.5 3.9 - - - +
453B LYS* 1.3 68.7 - - - +
455B SER* 1.3 57.9 + - - +
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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