Contacts of the helix formed by residues 3079 - 3087 (chain C) in PDB entry 1D1Z
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 LYS3079 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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3064C TRP* 4.2 2.9 - - - -
3077C PHE* 3.5 5.5 - - - +
3078C ARG* 1.3 102.4 - - + +
3080C ILE* 1.3 61.3 + - - +
3081C LYS* 4.2 11.2 - - + +
3082C ASN* 2.9 51.9 + - - +
3083C LEU 3.1 8.7 + - - -
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Residues in contact with ILE3080 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3004C VAL* 3.3 26.0 - - + -
3031C LEU* 4.3 22.2 - - + -
3041C TYR* 6.4 0.2 - - + -
3056C VAL* 3.6 32.3 - - + -
3064C TRP* 3.7 36.3 - - + +
3079C LYS* 1.3 72.7 - - - +
3081C LYS* 1.3 66.9 + - + +
3083C LEU* 3.1 20.2 + - + +
3084C ILE* 3.1 26.7 + - + +
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Residues in contact with LYS3081 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3004C VAL* 3.3 44.4 - - + +
3005C ALA 5.4 0.2 - - - +
3079C LYS* 3.2 8.4 - - + +
3080C ILE* 1.3 79.7 - - + +
3082C ASN* 1.3 61.5 + - - +
3084C ILE* 3.5 9.3 + - - +
3085C SER* 3.0 29.3 + - - -
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Residues in contact with ASN3082 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3077C PHE* 3.6 22.4 - - + -
3078C ARG* 5.7 1.4 - - - +
3079C LYS* 2.9 49.9 + - - +
3081C LYS* 1.3 79.3 - - - +
3083C LEU* 1.3 66.4 + - - +
3085C SER* 3.4 7.8 + - - -
3086C ALA* 3.0 18.2 + - - +
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Residues in contact with LEU3083 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3043C LEU* 4.8 4.7 - - + -
3056C VAL* 4.1 16.4 - - + -
3064C TRP* 3.9 9.0 - - + -
3065C SER* 3.7 41.1 - - - +
3066C ALA* 3.9 2.7 - - + +
3077C PHE* 3.6 30.8 - - + -
3079C LYS 3.1 6.3 + - - +
3080C ILE* 3.1 23.3 + - + +
3082C ASN* 1.3 78.4 - - - +
3084C ILE* 1.3 77.9 + - + +
3086C ALA* 3.2 2.6 + - - +
3087C PHE* 3.2 48.3 + - + -
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Residues in contact with ILE3084 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3004C VAL* 4.8 11.9 - - + -
3006C VAL* 4.5 10.5 - - + -
3029C TYR* 3.7 24.0 - - + +
3031C LEU* 5.0 10.3 - - + -
3043C LEU* 4.0 27.4 - - + -
3080C ILE* 3.1 23.4 + - + +
3081C LYS* 3.8 10.1 - - - +
3082C ASN 3.2 0.2 - - - -
3083C LEU* 1.3 86.7 - - + +
3085C SER* 1.3 65.7 + - - +
3087C PHE* 3.2 11.1 + - - -
3088C GLN* 3.4 28.4 + - - +
3098C LEU* 3.8 9.8 - - + +
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Residues in contact with SER3085 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3081C LYS 3.0 18.2 + - - -
3082C ASN* 3.8 9.9 + - - -
3083C LEU 3.3 0.2 - - - -
3084C ILE* 1.3 77.2 - - - +
3086C ALA* 1.3 59.0 + - - +
3088C GLN* 3.1 24.5 + - - +
3089C LYS* 2.5 34.9 + - - +
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Residues in contact with ALA3086 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3075C ARG* 3.8 20.5 + - - +
3077C PHE* 3.5 35.2 - - + -
3082C ASN 3.0 10.5 + - - +
3083C LEU 3.2 2.4 + - - +
3085C SER* 1.3 76.7 - - - +
3087C PHE* 1.3 60.3 - - + +
3088C GLN 3.1 0.2 - - - -
3089C LYS* 3.1 27.6 + - - +
3092C GLN* 3.4 17.5 - - - +
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Residues in contact with PHE3087 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3043C LEU* 4.8 4.5 - - + -
3066C ALA* 4.0 22.7 - - + -
3068C THR* 3.8 25.6 - - + -
3075C ARG* 6.0 5.2 - - + -
3077C PHE* 4.5 13.2 - + - -
3083C LEU* 3.2 42.9 + - + +
3084C ILE 3.2 1.9 + - - -
3086C ALA* 1.3 75.7 - - + +
3088C GLN* 1.3 56.8 + - - +
3089C LYS 3.2 6.3 + - - +
3092C GLN* 3.4 39.9 - - + -
3094C ILE* 3.8 29.0 - - + +
3097C PRO* 3.6 6.2 - - - +
3098C LEU* 3.0 45.7 + - + +
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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