Contacts of the helix formed by residues 3102 - 3114 (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 THR3102 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1230A TYR 4.8 0.4 - - - -
1231A GLY* 4.3 8.7 - - - +
1254A THR* 4.1 12.8 - - + -
3067B SER* 2.9 43.3 + - - +
3068B GLU* 4.1 5.2 - - - -
3070B ILE* 3.8 11.7 - - + +
3098B HIS* 3.3 6.0 - - - -
3101B ASP* 1.3 78.8 - - - +
3103B LEU* 1.3 60.3 + - - +
3104B GLU* 3.2 3.4 - - - +
3105B GLU* 2.8 50.7 + - - +
3106B THR* 3.1 12.4 + - - -
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Residues in contact with LEU3103 (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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3098B HIS* 3.7 28.0 - - - +
3099B GLY 3.4 16.0 + - - +
3100B THR* 3.5 13.0 + - - +
3102B THR* 1.3 76.9 - - - +
3104B GLU* 1.3 62.5 + - - +
3106B THR* 3.2 1.2 + - - -
3107B ALA* 2.9 35.5 + - + +
3122B VAL* 3.6 29.2 - - + -
3123B VAL* 4.1 15.3 - - - -
3124B GLY 4.1 3.1 - - - +
3159B VAL* 4.1 16.8 - - + -
3161B MET* 4.4 8.3 - - - -
3171B VAL* 5.2 2.0 - - + -
3182B PHE* 3.8 24.9 - - + -
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Residues in contact with GLU3104 (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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1282A HIS* 4.8 4.8 - - - -
3100B THR 4.8 0.4 + - - +
3101B ASP 4.5 7.2 - - - +
3102B THR* 4.7 3.1 - - - -
3103B LEU* 1.3 85.4 - - - +
3105B GLU* 1.3 75.3 + - + +
3107B ALA* 4.6 2.5 - - - -
3108B TYR* 3.4 13.2 + - - +
3168B GLY 4.0 0.2 - - - +
3171B VAL* 3.4 21.1 - - - +
3172B SER* 2.8 27.2 + - - -
3173B LYS* 3.0 32.5 + - - +
3182B PHE* 4.5 5.2 - - + -
3309B ASN* 3.5 6.4 + - - -
3311B GLU* 2.9 28.1 - - + +
3312B LYS* 2.9 27.3 + - - +
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Residues in contact with GLU3105 (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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1230A TYR* 3.9 6.4 - - - +
1231A GLY* 3.0 33.6 + - - -
1254A THR* 4.2 5.9 - - - +
1282A HIS* 5.1 1.0 + - - -
3070B ILE* 5.5 0.2 - - - +
3075B LEU* 5.2 1.6 - - + -
3101B ASP 4.5 1.0 - - - +
3102B THR* 2.8 34.2 + - - +
3104B GLU* 1.3 87.8 - - + +
3106B THR* 1.3 65.0 + - - +
3108B TYR* 3.4 2.5 + - - +
3109B PHE* 3.1 22.0 + - - +
3311B GLU* 3.9 33.3 - - + +
3312B LYS* 5.5 1.6 - - - -
3314B ARG* 4.5 7.8 + - - -
3315B ILE* 3.8 26.4 - - + +
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Residues in contact with THR3106 (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* 3.8 3.6 - - - +
3075B LEU* 3.3 31.2 - - + +
3078B LEU* 4.1 14.4 - - + -
3096B ILE* 5.9 1.1 - - + -
3098B HIS* 2.7 41.9 + - + -
3102B THR* 3.1 4.5 + - - -
3103B LEU 3.9 3.6 - - - -
3105B GLU* 1.3 76.3 - - - +
3107B ALA* 1.3 66.1 + - - +
3109B PHE* 3.1 2.5 + - + +
3110B LEU* 3.0 41.7 + - + +
3122B VAL* 5.5 3.6 - - + -
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Residues in contact with ALA3107 (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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3103B LEU* 2.9 28.0 + - + +
3104B GLU* 4.3 2.7 - - - +
3106B THR* 1.3 76.3 - - - +
3108B TYR* 1.3 63.0 + - - +
3110B LEU* 3.6 1.9 + - - +
3111B ASN* 3.1 21.1 + - - +
3122B VAL* 4.1 22.4 - - + +
3157B VAL* 3.6 16.5 - - + +
3159B VAL* 5.5 2.0 - - + -
3168B GLY* 3.9 24.0 - - - +
3171B VAL* 5.4 1.1 - - + -
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Residues in contact with TYR3108 (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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3104B GLU 3.4 16.4 + - - +
3105B GLU* 3.4 4.8 + - - +
3106B THR 3.2 0.2 - - - -
3107B ALA* 1.3 76.9 - - - +
3109B PHE* 1.3 69.6 + - - +
3111B ASN* 3.1 15.4 + - + +
3112B LEU* 3.2 28.5 + - + +
3168B GLY 3.6 8.6 + - - +
3169B ARG* 3.7 26.5 - - + -
3308B LEU* 3.5 29.6 - - + +
3312B LYS* 3.5 39.0 - - + +
3315B ILE* 4.0 11.2 - - + -
3316B LEU* 3.7 19.9 - - + +
3337B TYR 2.8 30.5 + - - -
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Residues in contact with PHE3109 (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* 3.6 54.1 - - + -
3076B LEU* 4.4 11.9 - - + -
3079B GLY* 4.5 4.3 - - - -
3105B GLU 3.1 14.3 + - - +
3106B THR* 3.1 11.6 + - + +
3108B TYR* 1.3 75.3 - - - +
3110B LEU* 1.3 74.0 + - + +
3112B LEU* 3.0 16.1 + - - +
3113B VAL* 3.3 29.7 + - + +
3215B ILE* 4.0 24.0 - - + -
3218B ILE* 5.5 0.9 - - + -
3221B LEU* 4.6 16.2 - - + -
3315B ILE* 3.7 14.7 - - + +
3318B MET* 5.2 2.5 - - + -
3319B VAL* 4.0 26.2 - - + -
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Residues in contact with LEU3110 (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 5.4 0.2 - - - +
3078B LEU* 4.9 3.8 - - + -
3079B GLY* 4.1 15.3 - - - +
3082B VAL* 4.6 7.6 - - + -
3096B ILE* 3.6 30.5 - - + -
3106B THR* 3.0 29.7 + - + +
3107B ALA 3.8 1.3 - - - +
3109B PHE* 1.3 89.7 - - + +
3111B ASN* 1.3 61.6 + - - +
3113B VAL* 4.3 1.8 - - - -
3114B GLN* 3.1 60.0 + - + +
3120B ILE* 4.3 6.7 - - + -
3122B VAL* 4.3 13.9 - - + -
3157B VAL* 3.8 15.3 - - + +
3208B THR* 4.7 0.2 - - - +
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Residues in contact with ASN3111 (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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3107B ALA 3.1 13.8 + - - +
3108B TYR* 3.1 22.3 + - + +
3110B LEU* 1.3 77.0 - - - +
3112B LEU* 1.3 59.1 + - - +
3156B GLY* 3.5 2.3 - - - -
3157B VAL* 2.9 36.7 + - + +
3167B SER* 5.4 0.6 + - - -
3169B ARG* 4.0 29.4 - - - +
3206B ARG 4.3 4.9 + - - -
3207B HIS* 3.4 33.3 - - - +
3208B THR* 2.9 29.8 + - - +
3337B TYR 5.5 0.4 + - - -
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Residues in contact with LEU3112 (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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3108B TYR* 3.4 37.5 - - + +
3109B PHE 3.0 8.0 + - - +
3111B ASN* 1.3 82.6 - - - +
3113B VAL* 1.3 64.3 + - + +
3114B GLN 3.8 0.7 - - - -
3206B ARG 4.8 3.4 - - - +
3208B THR 5.2 0.2 - - - -
3211B SER* 2.7 29.7 + - - -
3213B PHE* 3.6 10.1 - - + +
3315B ILE* 4.3 4.7 - - + -
3316B LEU* 3.5 36.6 - - + -
3319B VAL* 4.2 20.0 - - + -
3337B TYR* 3.4 38.6 - - + +
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Residues in contact with VAL3113 (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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3109B PHE* 3.3 39.0 + - + +
3110B LEU* 4.3 2.5 - - - -
3112B LEU* 1.3 82.9 - - - +
3114B GLN* 1.3 71.5 + - - +
3115B LYS* 3.4 5.5 + - - -
3213B PHE* 4.3 9.6 - - + -
3214B ASP* 3.8 4.0 - - - +
3215B ILE* 3.1 47.6 + - + +
3218B ILE* 4.2 16.2 - - + -
3319B VAL* 3.9 29.8 - - + -
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Residues in contact with GLN3114 (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* 2.7 39.9 + - - -
3082B VAL* 3.8 10.6 - - + +
3083B ALA* 3.5 26.5 + - - +
3086B ALA* 5.4 0.2 - - - +
3110B LEU* 3.1 35.4 + - + +
3112B LEU 3.8 0.8 - - - -
3113B VAL* 1.3 82.4 - - - +
3115B LYS* 1.3 59.1 + - - +
3116B THR* 2.9 13.7 + - + +
3120B ILE* 3.7 28.3 - - + -
3208B THR* 3.0 27.1 - - + +
3215B ILE* 4.0 7.8 - - - +
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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