Contacts of the strand formed by residues 103 - 107 (chain J) in PDB entry 3DLL
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 VAL 103 (chain J).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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25J GLY* 4.6 0.2 - - - -
26J ASP 3.1 25.2 + - - +
27J TYR* 3.4 19.1 - - - -
28J VAL* 4.3 3.8 - - - +
29J ALA 6.3 0.2 - - - +
34J GLY* 4.8 2.7 - - - -
35J LEU 3.6 7.9 - - - +
36J ILE* 3.2 28.5 - - + -
68J ARG* 3.1 39.7 - - - +
101J GLY 3.0 0.6 + - - -
102J ARG* 1.3 83.5 + - - +
104J MET* 1.3 61.0 + - - +
105J PHE 3.3 22.7 - - - +
106J GLU* 4.2 5.2 - - + +
133J VAL* 5.7 1.1 - - + -
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Residues in contact with MET 104 (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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35J LEU* 2.9 13.2 + - + +
36J ILE 5.1 0.2 - - - -
37J ALA* 3.7 33.9 - - + +
43J ILE* 4.3 10.3 - - + -
66J TYR 3.6 0.3 - - - +
67J ILE* 4.5 0.2 - - - -
68J ARG* 3.0 19.1 + - - +
69J ILE* 3.3 44.5 - - + +
98J VAL* 4.4 10.5 - - + -
102J ARG* 3.3 3.7 + - + +
103J VAL* 1.3 71.7 - - - +
105J PHE* 1.3 87.2 + - + +
106J GLU* 2.7 17.6 - - - +
126J LEU* 4.0 16.8 - - + -
128J ILE* 4.5 14.4 - - + -
130J THR* 4.9 2.7 - - + -
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Residues in contact with PHE 105 (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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34J GLY* 2.9 4.0 - - - -
35J LEU* 2.6 57.2 + - + -
48J ILE* 5.1 6.5 - - + -
51J CYS* 3.8 25.1 - - + -
55J MET* 3.6 35.7 - - + -
65J ILE* 5.6 0.4 - - + -
66J TYR 4.8 4.9 - - - -
67J ILE* 4.9 14.8 - - + -
69J ILE* 4.6 8.5 - - + -
103J VAL* 3.3 6.8 - - - +
104J MET* 1.3 115.6 - - + +
106J GLU* 1.3 70.0 + - - +
119J PHE* 4.1 9.0 - - + -
122J ALA* 4.5 2.0 - - + -
126J LEU* 3.8 19.7 - - + -
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Residues in contact with GLU 106 (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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28J VAL* 6.1 3.1 - - + -
29J ALA 4.2 19.3 - - - +
30J PHE* 5.3 0.2 - - + -
31J GLY* 5.2 4.0 - - - -
33J TYR 2.6 20.6 - - - +
34J GLY* 3.5 5.4 - - - -
65J ILE* 5.3 0.3 - - - +
66J TYR* 2.1 66.2 + - + +
68J ARG* 2.8 23.6 - - - +
103J VAL* 4.7 3.4 - - + -
104J MET 2.7 19.6 - - - +
105J PHE* 1.3 77.7 - - - +
107J VAL* 1.3 62.4 + - - +
119J PHE* 4.2 4.2 - - - -
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Residues in contact with VAL 107 (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* 4.6 1.1 - - - -
32J ASP* 3.7 5.0 + - - +
33J TYR* 3.0 31.4 + - + +
55J MET* 5.1 8.5 - - + -
59J PHE* 4.0 24.0 - - + -
64J LYS 3.1 17.0 - - - +
65J ILE* 3.5 27.8 - - + -
66J TYR* 4.5 0.2 - - - -
106J GLU* 1.3 76.4 - - - +
108J ALA* 1.3 61.3 + - - +
110J VAL* 4.0 18.2 - - + +
115J ALA* 4.2 10.5 - - + -
118J ALA* 5.7 1.6 - - + -
119J PHE* 4.3 17.3 - - + -
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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