Contacts of the strand formed by residues 3010 - 3018 (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 ALA3010 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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3009B LEU* 1.3 76.0 - - - +
3011B ASN* 1.3 56.1 + - - +
3012B VAL* 3.8 2.0 - - + -
3054B LEU 4.7 1.0 + - - -
3055B ALA* 3.0 8.4 - - + +
3056B ASN* 2.7 32.9 + - - -
3092B ASP* 3.4 22.2 - - + +
3148B SER* 4.0 37.9 - - - +
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Residues in contact with ASN3011 (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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3009B LEU 4.6 2.0 + - - -
3010B ALA* 1.3 71.8 - - - +
3012B VAL* 1.3 62.0 + - - +
3013B VAL* 5.4 2.5 - - + -
3056B ASN* 3.0 37.6 + - - +
3090B ASP* 3.4 31.2 + - - +
3091B VAL* 3.9 2.3 - - - -
3092B ASP* 2.8 45.7 + - - +
3093B GLY 3.2 5.2 + - - +
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Residues in contact with VAL3012 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3010B ALA* 3.7 3.3 + - + +
3011B ASN* 1.3 79.2 - - - +
3013B VAL* 1.3 69.9 + - - +
3014B ILE* 5.0 2.5 - - + -
3055B ALA* 3.9 5.6 - - + -
3056B ASN 3.0 7.2 + - - +
3057B VAL* 3.3 36.6 - - + +
3058B ARG* 3.3 4.5 + - - +
3093B GLY* 3.3 14.6 - - - +
3095B VAL* 3.8 29.6 - - + -
3144B VAL* 4.6 8.5 - - + +
3147B ALA* 3.9 9.0 - - + -
3148B SER* 3.3 39.7 - - - +
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Residues in contact with VAL3013 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3011B ASN* 5.2 2.5 - - + +
3012B VAL* 1.3 78.3 - - - +
3014B ILE* 1.3 66.7 + - - +
3015B LEU* 3.9 25.7 + - + -
3058B ARG* 3.5 31.9 - - + +
3060B GLU* 4.8 8.1 - - + +
3085B LEU* 4.3 17.5 - - + -
3090B ASP 5.8 0.2 - - - +
3091B VAL* 3.9 31.2 - - + -
3093B GLY 3.0 8.6 + - - +
3094B ILE* 3.5 7.4 - - + +
3095B VAL* 2.9 25.8 + - - +
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Residues in contact with ILE3014 (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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3012B VAL* 5.0 2.9 - - + -
3013B VAL* 1.3 75.4 - - - +
3015B LEU* 1.3 65.7 + - - +
3016B ALA 3.7 0.2 + - - -
3041B VAL* 4.0 16.1 - - + +
3045B ILE* 4.3 21.8 - - + -
3051B LEU* 4.6 8.1 - - + -
3057B VAL* 4.8 9.9 - - + -
3058B ARG 3.0 12.3 + - - +
3059B GLY* 3.6 4.2 - - - -
3060B GLU* 2.9 29.6 + - - +
3095B VAL* 3.1 21.1 - - + +
3097B THR* 4.2 23.8 - - + -
3140B LEU* 4.0 22.2 - - + -
3144B VAL* 4.3 15.0 - - + -
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Residues in contact with LEU3015 (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* 4.0 20.9 - - + -
3014B ILE* 1.3 71.4 - - - +
3016B ALA* 1.3 59.5 + - - +
3060B GLU* 3.4 26.5 - - + +
3062B VAL* 3.9 17.7 - - + -
3078B LEU* 4.3 7.0 - - + -
3081B ARG* 4.1 18.4 - - + -
3082B VAL* 3.6 33.7 - - + -
3085B LEU* 4.8 6.7 - - + -
3094B ILE* 4.2 15.3 - - + -
3095B VAL 2.7 13.8 + - - +
3096B ILE* 3.2 18.9 - - + +
3097B THR 3.1 22.0 + - - -
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Residues in contact with ALA3016 (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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3014B ILE* 3.7 1.8 + - + -
3015B LEU* 1.3 71.7 - - - +
3017B THR* 1.3 60.3 + - - +
3018B GLY 4.8 1.3 - - - +
3041B VAL* 3.5 35.7 - - + +
3044B LEU* 5.3 4.0 - - + -
3060B GLU 2.8 10.2 + - - +
3061B GLN* 3.5 16.7 + - - +
3062B VAL* 2.9 27.4 + - - +
3063B MET 3.2 4.7 + - - +
3097B THR* 3.2 15.0 - - - +
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Residues in contact with THR3017 (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 4.2 2.2 - - - +
3016B ALA* 1.3 77.5 - - - +
3018B GLY* 1.3 57.7 + - - +
3062B VAL* 4.7 4.3 - - + -
3063B MET* 3.1 31.2 - - + +
3065B ILE* 3.0 31.1 + - - +
3078B LEU* 3.8 23.1 - - + -
3096B ILE* 3.8 19.1 - - + -
3097B THR* 2.7 24.9 + - - +
3098B HIS* 3.3 20.9 - - + +
3099B GLY 4.4 1.4 + - - -
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Residues in contact with GLY3018 (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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3016B ALA* 3.7 1.6 - - - +
3017B THR* 1.3 80.4 + - - +
3019B GLY* 1.3 64.2 + - - -
3021B ILE* 3.5 19.2 - - - +
3022B ALA* 3.8 9.5 - - - +
3037B ALA* 3.8 3.6 - - - -
3061B GLN* 4.1 2.2 - - - +
3063B MET 3.7 1.6 + - - -
3064B GLN* 3.5 23.4 + - - -
3065B ILE 3.6 4.3 - - - -
3097B THR* 4.4 6.3 + - - +
3099B GLY 4.4 5.4 + - - -
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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