Contacts of the strand formed by residues 117 - 124 (chain J) in PDB entry 2DYY
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 ILE 117 (chain J).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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34J PRO* 3.1 27.5 - - - +
47J ILE* 4.0 6.7 - - + -
50J GLN* 3.5 31.6 + - + -
51J THR* 3.5 28.0 - - - +
54J VAL* 3.7 5.5 - - + +
77J VAL* 4.0 4.9 - - + -
78J TYR 3.3 11.2 - - - +
79J LEU* 3.8 10.1 - - + -
88J MET* 3.7 20.4 - - + -
111J LEU* 3.7 4.4 - - - +
115J VAL* 3.5 3.8 - - - +
116J LEU* 1.3 82.1 - - - +
118J GLU* 1.3 65.2 + - - +
119J ILE* 3.6 33.2 - - + -
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Residues in contact with GLU 118 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31J GLY* 3.8 14.6 - - - +
32J GLN 3.4 15.0 - - - +
33J ILE* 3.8 13.2 - - + -
76J THR 3.9 0.2 - - - +
78J TYR* 2.9 46.1 + - + +
111J LEU* 3.7 10.2 - - + +
112J PRO* 3.0 20.0 - - - +
117J ILE* 1.3 74.7 - - - +
119J ILE* 1.3 67.9 + - - +
104L VAL* 3.5 13.6 - - + +
105L ALA 2.5 44.5 + - - +
106L VAL* 3.8 4.2 - - - +
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Residues in contact with ILE 119 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30J ALA 3.8 1.9 - - - +
31J GLY* 4.1 1.8 - - - -
32J GLN* 2.8 38.7 + - - +
51J THR* 5.1 2.2 - - + +
54J VAL* 3.5 18.4 - - + -
55J LEU* 3.3 30.7 - - + -
58J ILE* 3.8 17.6 - - + +
75J VAL* 3.6 28.9 - - + -
76J THR 3.5 5.2 - - - +
77J VAL* 4.3 14.1 - - + -
78J TYR* 5.6 0.2 - - - -
92J TYR* 5.2 4.7 - - + -
96J PHE* 5.6 0.2 - - + -
117J ILE* 3.6 25.6 - - + -
118J GLU* 1.3 82.9 - - - +
120J GLU* 1.3 63.8 + - - +
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Residues in contact with GLU 120 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29J ILE 4.2 6.2 - - - +
30J ALA 4.3 0.7 - - - -
31J GLY* 4.2 5.6 - - - -
74J LYS* 5.4 4.0 - - - -
75J VAL* 3.6 1.4 - - - -
76J THR* 3.0 56.1 + - + +
78J TYR* 4.2 13.3 + - + -
119J ILE* 1.3 77.0 - - - +
121J ALA* 1.3 64.6 + - - +
122J ILE* 4.7 7.6 - - - +
74L LYS* 3.2 29.3 + - - +
76L THR* 4.2 8.1 + - - -
104L VAL* 3.6 43.4 - - + +
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Residues in contact with ALA 121 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29J ILE* 3.0 52.4 + - + +
58J ILE* 4.7 18.4 - - + -
72J VAL* 4.5 9.6 - - + -
74J LYS 3.3 11.2 - - - +
75J VAL* 4.2 13.2 - - + -
96J PHE* 5.3 0.4 - - + -
119J ILE 4.4 0.2 + - - -
120J GLU* 1.3 78.2 - - - +
122J ILE* 1.3 68.3 + - - +
74L LYS* 6.0 0.5 - - - +
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Residues in contact with ILE 122 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26J PHE* 4.1 11.0 - - + -
27J LEU 3.2 8.5 - - - +
28J PHE* 3.8 33.0 - - + -
29J ILE* 5.9 0.7 - - - -
72J VAL* 3.7 4.6 - - - +
73J ILE* 3.0 44.6 + - + +
74J LYS* 2.9 30.7 + - + +
120J GLU* 4.7 4.7 - - - +
121J ALA* 1.3 82.1 - - - +
123J ALA* 1.3 68.5 + - - +
28K PHE* 4.1 20.0 - - + -
122K ILE* 5.8 2.2 - - + -
74L LYS* 3.8 19.3 - - + +
122L ILE* 5.5 1.6 - - + -
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Residues in contact with ALA 123 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26J PHE* 3.2 9.0 - - - -
27J LEU* 2.6 50.7 + - + -
29J ILE* 5.7 0.9 - - + +
62J LEU* 4.2 20.4 - - + -
67J TYR* 3.9 13.9 - - + -
71J ASP* 3.5 17.5 - - + +
72J VAL* 4.2 2.7 - - + -
73J ILE* 4.2 0.9 - - - +
122J ILE* 1.3 77.0 - - - +
124J TYR* 1.3 61.5 + - - +
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Residues in contact with TYR 124 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25J ASN* 3.3 38.3 + - + -
26J PHE* 3.4 42.6 - + + -
67J TYR* 3.8 2.5 - - - -
71J ASP* 3.0 27.7 + - - +
73J ILE* 3.7 18.0 - - + +
123J ALA* 1.3 76.2 - - - +
125J LYS* 1.3 62.7 + - - +
126J GLU* 3.9 35.4 - - + +
2K LYS* 4.3 16.6 - - + +
23K ALA* 3.6 20.2 - - + -
24K GLY* 3.7 20.9 + - - -
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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