Contacts of the helix formed by residues 3185 - 3189 (chain I) in PDB entry 2ZLE
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 ASN3185 (chain I).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3183I THR 3.8 1.2 + - - -
3184I ASN* 1.3 72.9 - - - +
3186I HIS* 1.3 61.4 + - - +
3187I VAL 3.0 0.4 - - - -
3188I VAL* 4.5 1.1 - - - -
3189I ASP* 3.0 33.2 + - - +
3211I LYS* 3.1 49.3 - - - +
3212I ASP 4.6 2.9 - - - +
3213I PRO* 3.9 23.3 - - - +
3216I ASP* 3.2 28.9 + - - +
3217I ILE 4.0 10.8 - - - +
3218I ALA* 3.9 10.9 - - + +
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Residues in contact with HIS3186 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3167I ALA* 5.2 2.9 - - - +
3184I ASN* 3.1 30.1 - - + +
3185I ASN* 1.3 81.0 - - - +
3187I VAL* 1.3 70.2 + - + +
3189I ASP* 4.6 6.6 - - - +
3216I ASP* 3.0 33.0 + - - +
3282I ASN* 5.5 4.0 - - - +
3283I SER* 3.9 17.1 + - - -
3300I ALA* 3.8 23.8 - - + +
3304I PRO* 6.3 2.9 - - + -
3305I ASP 5.6 1.1 - - - +
3306I GLY* 4.5 17.5 - - - +
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Residues in contact with VAL3187 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3137I ILE* 4.4 7.4 - - + -
3139I VAL* 3.5 26.8 - - + +
3165I PHE* 5.1 0.9 - - - -
3167I ALA* 3.6 15.0 - - + +
3168I LEU 3.8 12.6 - - - +
3169I GLY* 3.7 37.2 - - - +
3183I THR* 4.3 6.5 - - - +
3184I ASN* 3.6 30.7 - - + +
3185I ASN 3.0 0.8 - - - -
3186I HIS* 1.3 93.8 - - + +
3188I VAL* 1.3 66.2 + - + +
3189I ASP 3.4 3.6 + - - +
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Residues in contact with VAL3188 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3137I ILE* 4.8 7.2 - - + -
3139I VAL* 4.0 17.5 - - + -
3183I THR* 3.9 25.1 - - + -
3184I ASN 3.6 2.9 + - - +
3185I ASN* 4.4 2.7 - - - +
3187I VAL* 1.3 78.9 - - + +
3189I ASP* 1.3 71.1 + - - +
3190I ASN 3.3 0.2 + - - -
3191I ALA* 2.9 25.8 + - + +
3194I ILE* 5.1 6.1 - - + -
3208I MET* 3.5 33.0 - - + +
3211I LYS* 5.1 2.2 - - + -
3218I ALA* 3.7 22.4 - - + -
3220I ILE* 4.3 11.0 - - + -
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Residues in contact with ASP3189 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3165I PHE* 3.9 10.6 - - - -
3185I ASN* 3.0 31.3 + - - +
3186I HIS* 4.7 7.5 - - - +
3187I VAL 3.4 4.5 - - - +
3188I VAL* 1.3 77.8 - - - +
3190I ASN* 1.3 94.6 + - - +
3191I ALA 3.2 0.5 + - - -
3211I LYS* 2.5 33.6 + - - +
3213I PRO* 5.3 2.6 - - - +
3434I GLN* 5.7 0.7 + - - -
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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