Contacts of the strand formed by residues 3055 - 3065 (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 ALA3055 (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* 4.1 12.8 - - - -
3010B ALA 3.0 16.4 - - - +
3012B VAL* 3.9 11.4 - - + -
3051B LEU 3.4 10.9 + - - +
3052B ALA* 3.9 11.7 + - - +
3053B ASP 3.8 0.8 - - - -
3054B LEU* 1.3 75.3 - - - +
3056B ASN* 1.3 63.8 + - - +
3057B VAL* 3.2 17.2 + - + +
3144B VAL* 4.3 2.2 - - + +
3148B SER* 2.9 29.2 - - - +
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Residues in contact with ASN3056 (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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3008B LYS* 5.8 0.6 - - - +
3009B LEU* 3.3 39.7 + - - +
3010B ALA 2.7 7.7 + - - -
3011B ASN* 3.0 29.8 + - - +
3012B VAL 3.0 22.0 + - - +
3055B ALA* 1.3 70.3 - - - +
3057B VAL* 1.3 60.1 + - - +
3058B ARG* 4.2 0.3 + - - +
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Residues in contact with VAL3057 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3012B VAL* 3.3 17.0 - - + +
3014B ILE* 4.8 10.1 - - + -
3045B ILE* 4.4 16.6 - - + +
3051B LEU* 4.3 28.9 - - + +
3052B ALA* 5.4 1.8 - - - +
3055B ALA 3.2 14.5 + - - +
3056B ASN* 1.3 78.3 - - - +
3058B ARG* 1.3 61.8 + - - +
3144B VAL* 3.9 32.5 - - + -
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Residues in contact with ARG3058 (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 3.3 4.2 + - - +
3013B VAL* 3.5 27.6 - - + +
3014B ILE* 3.0 23.6 + - - -
3045B ILE* 4.4 4.0 - - - -
3057B VAL* 1.3 77.3 - - - +
3059B GLY* 1.3 82.4 + - - +
3060B GLU* 4.0 20.7 + - - +
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Residues in contact with GLY3059 (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* 3.5 8.1 - - - -
3041B VAL* 3.8 14.8 - - - +
3042B ASP* 4.9 6.0 + - - +
3045B ILE* 3.7 23.7 - - - +
3058B ARG* 1.3 92.6 + - - +
3060B GLU* 1.3 61.9 + - - +
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Residues in contact with GLU3060 (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* 4.8 7.4 - - + +
3014B ILE 2.9 7.2 + - - +
3015B LEU* 3.4 28.1 - - + +
3016B ALA 2.8 25.5 + - - -
3041B VAL* 3.8 6.0 - - - +
3058B ARG* 4.0 17.2 + - - +
3059B GLY* 1.3 74.1 - - - +
3061B GLN* 1.3 67.2 + - - +
3062B VAL* 3.3 7.5 + - + +
3081B ARG* 2.7 43.9 + - - -
3085B LEU* 4.8 3.6 - - - +
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Residues in contact with GLN3061 (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* 3.5 18.7 + - - +
3018B GLY 4.1 2.2 - - - +
3039B VAL 4.8 1.0 + - - -
3040B GLY* 3.3 6.5 - - - -
3041B VAL* 2.7 42.0 + - + +
3060B GLU* 1.3 74.4 - - - +
3062B VAL* 1.3 63.5 + - - +
3063B MET* 2.7 28.9 + - - +
3064B GLN* 3.3 31.1 + - + +
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Residues in contact with VAL3062 (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* 3.9 39.7 - - + -
3016B ALA 2.9 11.4 + - - +
3017B THR* 4.7 4.0 - - + -
3060B GLU* 4.0 9.0 - - + +
3061B GLN* 1.3 74.6 - - - +
3063B MET* 1.3 76.8 + - + +
3077B LYS* 3.4 46.8 + - + +
3078B LEU* 4.8 11.2 - - + -
3081B ARG* 4.4 14.1 - - + -
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Residues in contact with MET3063 (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 3.4 0.2 + - - -
3017B THR* 3.1 35.7 - - - +
3061B GLN* 2.7 27.5 + - - -
3062B VAL* 1.3 100.1 - - + +
3064B GLN* 1.3 58.4 + - - +
3065B ILE* 4.2 22.4 - - + -
3070B ILE* 5.5 2.9 - - + -
3074B ASP* 3.6 50.9 - - + +
3077B LYS* 4.2 9.6 - - + -
3078B LEU* 4.4 13.5 - - + -
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Residues in contact with GLN3064 (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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3017B THR 3.8 0.7 - - - -
3018B GLY* 3.5 10.0 - - - -
3037B ALA* 3.4 42.0 + - + +
3038B LYS 4.0 3.4 + - - -
3039B VAL 3.2 31.8 + - - +
3040B GLY* 3.9 5.5 - - - +
3061B GLN* 3.3 28.6 + - + +
3063B MET* 1.3 72.9 - - - +
3065B ILE* 1.3 64.3 + - - +
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Residues in contact with ILE3065 (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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3017B THR* 3.0 16.5 + - - +
3019B GLY 3.0 24.6 + - - -
3037B ALA* 3.6 9.1 - - - +
3063B MET* 4.2 19.1 - - + -
3064B GLN* 1.3 84.3 - - - +
3066B ALA* 1.3 74.5 + - - +
3067B SER* 3.7 5.0 + - - +
3069B SER* 4.5 5.2 - - - +
3070B ILE* 3.8 40.4 - - + +
3074B ASP* 4.0 10.8 - - - +
3098B HIS* 6.4 0.2 - - + -
3099B GLY 5.5 0.2 + - - -
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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
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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