Contacts of the helix formed by residues 414 - 419 (chain B) in PDB entry 2UZL
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 LYS 414 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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410B ARG* 3.4 31.4 + - - +
411B GLU* 2.9 47.6 + - - +
412B LYS 3.3 0.8 - - - -
413B TYR* 1.3 77.4 - - - +
415B ASN* 1.3 72.3 + - - +
416B SER* 3.7 0.7 + - - -
420B GLY* 3.5 15.7 - - - -
422B SER* 3.6 7.6 - - - +
423B LEU* 3.8 38.9 - - + +
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Residues in contact with ASN 415 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
223B GLU* 4.2 11.5 + - - -
411B GLU 3.7 12.8 + - - +
412B LYS* 3.3 22.2 + - - +
413B TYR 3.4 1.8 - - - -
414B LYS* 1.3 87.2 - - - +
416B SER* 1.3 60.1 + - - +
417B LYS* 3.2 7.9 - - + +
418B TYR* 3.0 24.0 + - + +
420B GLY 3.4 8.3 + - - -
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Residues in contact with SER 416 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
414B LYS 3.7 1.7 + - - -
415B ASN* 1.3 73.1 - - - +
417B LYS* 1.3 62.6 + - - +
418B TYR 3.1 0.2 - - - -
419B HIS* 3.1 21.1 + - - +
420B GLY 4.8 2.5 - - - +
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Residues in contact with LYS 417 (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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223B GLU* 5.9 2.9 - - - -
226B LYS* 6.4 0.2 - - - +
331B SER* 4.1 0.5 + - - -
415B ASN* 3.2 8.4 - - + +
416B SER* 1.3 81.6 + - - +
418B TYR* 1.3 102.2 + - + +
419B HIS* 3.4 15.3 - - - -
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Residues in contact with TYR 418 (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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223B GLU* 4.9 4.1 + - - -
229B ASN* 3.7 25.4 + - - -
331B SER* 3.4 17.4 - - - +
334B MET* 5.2 6.1 - - - -
412B LYS* 3.5 42.5 - - + -
413B TYR* 3.4 49.8 - + + +
415B ASN* 3.0 9.1 + - + +
417B LYS* 1.3 117.3 + - + +
419B HIS* 1.3 65.0 - - - +
420B GLY 3.0 9.7 + - - -
421B VAL* 3.2 19.6 + - - +
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Residues in contact with HIS 419 (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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327B CYS* 3.4 41.6 + - + +
328B LYS* 3.8 38.3 - - + -
331B SER* 3.2 15.6 + - - -
416B SER* 3.1 17.8 + - - +
417B LYS 3.8 15.7 + - - -
418B TYR* 1.3 73.8 - - - +
420B GLY* 1.3 60.4 + - - +
421B VAL* 3.2 4.3 + - + +
424B LEU* 5.9 1.2 - - - +
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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