Contacts of the helix formed by residues 3071 - 3088 (chain B) in PDB entry 1DJO
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 THR3071 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1231A GLY 5.9 0.2 - - - -
1232A ASN* 3.3 13.0 - - - -
1262A ARG* 3.0 38.4 - - - +
3069B SER 4.1 7.6 - - - +
3070B ILE* 1.3 82.9 - - - +
3072B ASN* 1.3 66.4 + - - +
3073B ASP* 3.4 11.2 + - - +
3074B ASP* 3.1 40.1 + - - +
3075B LEU* 3.3 12.4 + - - +
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Residues in contact with ASN3072 (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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1231A GLY 5.2 0.2 - - - -
1232A ASN* 3.1 30.0 + - - +
3071B THR* 1.3 75.6 - - - +
3073B ASP* 1.3 64.5 + - - +
3075B LEU* 3.3 14.4 + - - +
3076B LEU* 3.1 27.5 + - + +
3221B LEU* 3.8 26.6 + - + +
3222B PRO 4.3 5.9 + - - -
3223B GLN* 5.3 2.8 - - - +
3314B ARG* 3.2 19.3 + - - +
3318B MET* 3.7 28.8 - - - +
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Residues in contact with ASP3073 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1262A ARG* 5.8 1.0 + - - -
3071B THR* 3.2 9.4 + - - +
3072B ASN* 1.3 75.9 - - - +
3074B ASP* 1.3 63.3 + - - +
3076B LEU* 3.7 15.4 - - - +
3077B LYS* 2.9 30.1 + - - +
3219B SER 5.7 0.2 - - - +
3220B SER* 5.7 2.9 - - - -
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Residues in contact with ASP3074 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3063B MET* 3.6 28.8 - - - +
3065B ILE* 4.0 9.8 - - - +
3069B SER 4.4 1.7 - - - +
3070B ILE* 3.6 21.7 - - + +
3071B THR* 3.1 37.2 + - - +
3073B ASP* 1.3 78.1 - - - +
3075B LEU* 1.3 66.0 + - - +
3077B LYS* 3.3 5.5 + - - +
3078B LEU* 2.9 24.9 + - - +
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Residues in contact with LEU3075 (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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3070B ILE* 4.0 14.4 - - + -
3071B THR 3.3 10.9 + - - +
3072B ASN* 3.3 24.3 + - - +
3074B ASP* 1.3 79.5 - - - +
3076B LEU* 1.3 53.0 + - + +
3078B LEU* 3.2 6.7 + - + +
3079B GLY* 2.7 32.6 + - - -
3105B GLU* 6.0 1.1 - - + -
3106B THR* 3.3 44.2 - - + +
3109B PHE* 3.6 38.2 - - + -
3110B LEU* 5.4 0.2 - - - +
3221B LEU* 5.6 1.8 - - + -
3314B ARG* 5.7 1.1 - - - +
3315B ILE* 4.2 20.0 - - + -
3318B MET* 4.5 4.5 - - + -
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Residues in contact with LEU3076 (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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3072B ASN* 3.1 10.1 + - + +
3073B ASP* 3.7 20.2 - - - +
3074B ASP 3.2 0.2 - - - -
3075B LEU* 1.3 77.6 - - - +
3077B LYS* 1.3 60.0 + - - +
3079B GLY* 3.1 0.3 + - - -
3080B LYS* 2.8 44.1 + - - +
3109B PHE* 4.4 4.9 - - + -
3215B ILE* 3.7 25.5 - - + +
3218B ILE* 3.9 21.1 - - + +
3219B SER 4.0 7.4 - - - +
3220B SER* 3.7 20.9 - - - -
3221B LEU* 3.3 36.3 - - + +
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Residues in contact with LYS3077 (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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3062B VAL* 3.4 47.3 + - + +
3063B MET* 4.2 6.7 - - + -
3073B ASP 2.9 19.0 + - - +
3074B ASP* 3.3 6.9 + - - +
3076B LEU* 1.3 75.8 - - - +
3078B LEU* 1.3 61.3 + - - +
3080B LYS* 4.3 4.4 - - - +
3081B ARG* 3.2 29.0 + - - +
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Residues in contact with LEU3078 (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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3015B LEU* 4.3 9.9 - - + -
3017B THR* 3.8 28.3 - - + -
3062B VAL* 4.8 6.3 - - + -
3063B MET* 4.4 9.9 - - + -
3070B ILE* 5.9 3.4 - - + -
3074B ASP 2.9 17.1 + - - +
3075B LEU* 3.5 6.5 - - + +
3077B LYS* 1.3 79.5 - - - +
3079B GLY* 1.3 65.3 + - - +
3081B ARG* 3.3 4.9 + - + +
3082B VAL* 3.0 40.8 + - + +
3096B ILE* 4.1 19.3 - - + -
3098B HIS* 4.6 4.5 - - + -
3106B THR* 4.1 25.6 - - + -
3110B LEU* 4.9 4.9 - - + -
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Residues in contact with GLY3079 (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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3075B LEU 2.7 19.8 + - - -
3076B LEU 3.1 1.5 + - - -
3078B LEU* 1.3 73.3 - - - +
3080B LYS* 1.3 54.8 + - - +
3082B VAL 3.4 0.2 + - - -
3083B ALA* 3.1 18.2 + - - +
3109B PHE* 4.5 4.0 - - - -
3110B LEU* 4.1 10.2 - - - +
3114B GLN* 2.7 32.8 + - - -
3215B ILE* 3.7 11.6 - - - +
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Residues in contact with LYS3080 (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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3076B LEU* 2.8 32.3 + - + +
3077B LYS* 4.3 4.5 - - - +
3079B GLY* 1.3 69.4 - - - +
3081B ARG* 1.3 65.6 + - - +
3083B ALA* 3.3 10.1 + - - +
3084B GLU* 3.1 30.5 + - + +
3215B ILE* 2.9 36.4 + - + +
3216B LYS* 4.0 13.1 + - - +
3218B ILE 3.0 21.7 + - - -
3219B SER* 5.0 5.6 - - - +
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Residues in contact with ARG3081 (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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3015B LEU* 4.1 17.3 - - + -
3060B GLU* 2.7 49.0 + - - +
3062B VAL* 4.4 13.0 - - + -
3077B LYS* 3.2 24.5 + - + +
3078B LEU* 3.3 6.7 + - - +
3080B LYS* 1.3 77.0 - - - +
3082B VAL* 1.3 61.3 - - - +
3084B GLU* 2.8 48.6 + - - +
3085B LEU* 2.8 55.2 - - + +
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Residues in contact with VAL3082 (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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3015B LEU* 3.6 18.4 - - + -
3078B LEU* 3.0 40.7 + - + +
3079B GLY 3.7 4.9 - - - +
3081B ARG* 1.3 75.5 - - - +
3083B ALA* 1.3 58.0 + - - +
3085B LEU* 3.2 6.9 + - - +
3086B ALA* 2.9 28.3 + - + +
3094B ILE* 3.9 19.0 - - + +
3096B ILE* 4.0 12.1 - - + -
3110B LEU* 4.6 5.2 - - + -
3114B GLN* 3.8 19.5 - - + +
3120B ILE* 4.1 18.4 - - + -
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Residues in contact with ALA3083 (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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3079B GLY 3.1 14.8 + - - +
3080B LYS* 3.4 11.2 - - - +
3082B VAL* 1.3 76.9 - - - +
3084B GLU* 1.3 61.2 + - + +
3086B ALA* 3.4 6.2 + - - +
3087B ASP* 3.1 28.9 + - - +
3114B GLN* 3.5 15.0 + - - +
3215B ILE* 3.7 17.7 - - + -
3216B LYS* 4.6 16.5 - - + -
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Residues in contact with GLU3084 (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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3080B LYS* 3.1 16.6 + - + +
3081B ARG* 2.8 50.8 + - - +
3083B ALA* 1.3 75.0 - - + +
3085B LEU* 1.3 63.3 + - - +
3087B ASP* 3.2 19.6 + - - +
3088B SER* 3.3 11.1 + - - -
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Residues in contact with LEU3085 (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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3013B VAL* 4.3 25.4 - - + -
3015B LEU* 4.8 7.9 - - + -
3058B ARG* 6.1 1.6 - - - +
3060B GLU* 4.8 3.1 - - - +
3081B ARG* 2.8 69.3 + - + +
3082B VAL* 3.2 7.6 + - - +
3084B GLU* 1.3 77.7 - - - +
3086B ALA* 1.3 61.5 + - - +
3088B SER* 3.1 14.0 + - - -
3091B VAL* 3.2 43.7 - - + +
3094B ILE* 4.0 14.4 - - + -
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Residues in contact with ALA3086 (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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3082B VAL* 2.9 17.7 + - + +
3083B ALA* 3.8 7.9 - - - +
3084B GLU 3.3 0.2 - - - -
3085B LEU* 1.3 77.1 - - - +
3087B ASP* 1.3 60.8 + - - +
3088B SER 3.2 0.2 - - - -
3094B ILE* 4.0 11.2 - - + +
3114B GLN* 5.4 0.4 - - - +
3116B THR* 3.8 36.3 + - + +
3118B LYS* 2.9 34.2 + - + +
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Residues in contact with ASP3087 (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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3083B ALA 3.1 15.6 + - - +
3084B GLU* 3.4 13.3 - - - +
3085B LEU 3.1 0.6 - - - -
3086B ALA* 1.3 78.7 - - - +
3088B SER* 1.3 60.8 + - - +
3089B ASN* 3.5 11.4 + - - +
3216B LYS* 2.8 36.1 + - - -
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Residues in contact with SER3088 (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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3084B GLU 3.3 8.9 + - - -
3085B LEU* 3.1 15.4 + - - +
3087B ASP* 1.3 76.6 - - - +
3089B ASN* 1.3 58.8 + - - +
3090B ASP* 2.9 31.6 + - - +
3091B VAL* 2.9 18.5 + - - +
3118B LYS* 2.8 21.2 + - - -
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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
------------------------------------------------------------
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