Contacts of the helix formed by residues 438 - 450 (chain B) in PDB entry 4MZ7
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 438 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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393B ALA* 3.6 38.8 - - + +
396B TYR* 4.0 22.7 - - + +
397B ILE* 4.1 20.6 - - + -
429B GLU* 5.1 2.2 - - + +
430B ILE* 5.0 6.1 - - + +
433B SER* 3.5 33.7 - - - +
435B ASP* 2.9 23.0 + - + +
437B LYS* 1.3 78.7 - - - +
439B LYS* 1.3 57.1 + - - +
440B ASP 3.3 2.9 - - - -
441B ALA* 3.3 6.6 + - + +
442B ARG* 2.8 31.2 + - + +
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Residues in contact with LYS 439 (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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435B ASP 3.5 2.2 + - - -
436B PRO* 3.2 20.6 + - + +
437B LYS 3.3 0.6 - - - -
438B LEU* 1.3 78.6 - - - +
440B ASP* 1.3 65.5 + - - +
442B ARG* 3.6 28.6 + - - +
443B GLU* 2.8 44.0 + - + +
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Residues in contact with ASP 440 (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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392B LYS* 3.8 27.7 - - + +
437B LYS 4.8 4.6 + - - +
438B LEU 3.3 0.2 - - - -
439B LYS* 1.3 81.0 - - - +
441B ALA* 1.3 66.3 + - - +
443B GLU* 3.4 7.9 + - - +
444B ILE* 3.3 25.6 + - - +
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Residues in contact with ALA 441 (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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389B ALA* 3.4 32.5 - - - +
392B LYS* 3.8 16.7 + - + +
393B ALA* 3.7 21.1 - - + +
430B ILE* 3.8 11.0 - - + -
438B LEU* 3.3 11.7 + - + +
440B ASP* 1.3 77.8 - - - +
442B ARG* 1.3 63.0 + - - +
444B ILE* 3.1 15.6 + - - +
445B LEU* 3.3 10.0 + - - +
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Residues in contact with ARG 442 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
430B ILE* 3.7 20.6 - - - +
431B LEU* 3.8 13.4 - - - +
433B SER* 2.9 55.6 + - - -
434B THR* 3.7 9.9 + - - +
435B ASP 3.1 24.5 + - - -
436B PRO* 4.6 1.8 - - - +
438B LEU 2.8 25.7 + - - +
439B LYS* 3.6 34.5 + - - +
441B ALA* 1.3 73.0 - - - +
443B GLU* 1.3 57.8 + - - +
445B LEU* 3.3 5.6 + - - +
446B LYS* 3.0 61.1 + - + +
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Residues in contact with GLU 443 (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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439B LYS* 2.8 39.6 + - + +
440B ASP* 3.6 10.1 - - - +
441B ALA 3.2 0.2 - - - -
442B ARG* 1.3 73.9 - - - +
444B ILE* 1.3 63.9 + - + +
446B LYS* 3.4 13.0 + - - +
447B GLN* 3.1 52.8 + - + +
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Residues in contact with ILE 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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385B MET* 3.4 43.4 - - + +
388B ASP* 3.9 7.6 - - + +
389B ALA* 3.8 23.3 - - + +
392B LYS* 3.7 36.8 - - + +
440B ASP 3.3 12.3 + - - +
441B ALA 3.1 6.6 + - - +
443B GLU* 1.3 78.3 - - + +
445B LEU* 1.3 63.0 + - + +
447B GLN* 3.1 16.9 + - - +
448B ILE* 3.2 12.8 + - - +
454B PHE* 5.8 4.5 - - + -
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Residues in contact with LEU 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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386B ILE* 4.4 7.6 - - + -
389B ALA* 3.5 22.0 - - + -
390B PHE* 5.4 1.1 - - + -
427B PHE* 3.2 63.8 - - + +
430B ILE* 3.6 23.8 - - + -
431B LEU* 3.9 18.6 - - + +
441B ALA 3.3 9.1 + - - +
442B ARG 3.3 7.8 + - - +
444B ILE* 1.3 77.7 - - - +
446B LYS* 1.3 63.4 + - - +
448B ILE* 3.2 20.4 + - + +
449B GLU* 3.2 23.2 + - - +
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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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139A PRO* 6.5 0.4 - - + -
431B LEU* 3.8 24.9 + - + -
442B ARG* 3.0 52.2 + - + +
443B GLU* 3.7 15.3 - - - +
444B ILE 3.2 0.4 - - - -
445B LEU* 1.3 77.3 - - - +
447B GLN* 1.3 70.3 + - - +
449B GLU* 3.1 9.5 + - - +
450B TYR* 3.1 40.6 + - + -
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Residues in contact with GLN 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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385B MET* 4.4 6.7 - - + -
443B GLU* 3.1 51.2 + - + +
444B ILE* 3.1 10.2 + - - +
446B LYS* 1.3 82.2 - - - +
448B ILE* 1.3 61.1 + - - +
450B TYR* 3.4 14.0 + - - +
451B ARG 3.0 3.3 + - - -
452B ASN* 2.9 74.2 + - - +
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Residues in contact with ILE 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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142A GLN* 5.7 0.9 - - - +
155B TYR* 4.6 20.4 - - + -
382B ILE* 4.4 19.5 - - + +
385B MET* 3.9 33.2 - - + +
386B ILE* 3.7 29.6 - - + -
427B PHE* 4.5 8.5 - - + -
444B ILE 3.2 10.3 + - - +
445B LEU* 3.2 25.3 + - + +
447B GLN* 1.3 76.5 - - - +
449B GLU* 1.3 57.6 + - + +
451B ARG* 2.9 28.7 + - - +
453B LEU* 3.9 15.5 - - + -
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Residues in contact with GLU 449 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
137A ASP* 3.5 20.0 - - - +
138A THR 3.8 1.1 + - - -
139A PRO* 3.5 39.6 - - + +
142A GLN* 3.7 35.1 - - + +
143A ARG* 4.6 1.4 + - - -
146A TYR* 4.4 12.0 + - - +
427B PHE* 5.5 6.1 - - + -
431B LEU* 3.6 36.5 - - + +
445B LEU 3.2 12.5 + - - +
446B LYS* 3.1 12.3 + - - +
448B ILE* 1.3 79.7 - - + +
450B TYR* 1.3 61.6 + - + +
451B ARG* 3.1 0.9 + - - -
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Residues in contact with TYR 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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137A ASP* 3.6 23.1 - - - +
138A THR* 5.5 0.2 - - + -
139A PRO* 3.5 31.0 - - + +
247A SER 5.5 1.7 + - - -
248A ASN* 3.4 24.9 + - - -
446B LYS* 3.1 41.9 + - + +
447B GLN* 3.4 19.9 + - - +
449B GLU* 1.3 74.8 - - - +
451B ARG* 1.3 68.6 + - - +
452B ASN* 3.4 5.4 + - + +
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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