Contacts of the strand formed by residues 14 - 18 (chain J) in PDB entry 6LTJ
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 LEU 14 (chain J).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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12J GLY 5.0 0.2 - - - -
13J ALA* 1.3 81.6 - - - +
15J VAL* 1.3 62.3 + - - +
16J PHE* 3.8 24.1 + - + -
26J GLY* 3.6 22.0 - - - +
27J TYR* 3.6 32.1 - - + -
107J TYR* 5.0 5.2 - - + +
111J VAL* 4.1 23.1 - - + -
118J HIS* 3.6 36.1 - - + +
119J PRO 3.0 10.6 + - - +
120J VAL* 3.4 8.6 - - + +
121J LEU* 2.8 26.5 + - - +
113K LYS* 6.2 0.2 - - - -
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Residues in contact with VAL 15 (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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14J LEU* 1.3 76.7 - - - +
16J PHE* 1.3 63.8 + - - +
25J ALA* 3.3 2.1 - - - -
26J GLY 2.9 23.9 + - - +
27J TYR 4.5 0.2 - - - +
28J ALA* 4.3 14.6 - - + -
121J LEU* 3.6 13.7 - - + +
157J LEU* 5.6 2.2 - - + -
394J TRP* 2.8 62.6 + - + +
397J GLY* 3.6 34.1 - - - +
398J SER* 3.7 10.3 - - - +
401J ALA* 4.9 2.5 - - + -
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Residues in contact with PHE 16 (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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14J LEU* 3.8 28.9 - - + -
15J VAL* 1.3 79.5 - - - +
17J ASP* 1.3 59.5 + - - +
18J ILE* 4.6 15.7 - - + -
24J ARG 3.7 2.5 - - - -
25J ALA* 3.6 26.2 - - + -
103J LEU* 4.3 13.7 - - + -
106J THR* 3.8 22.4 - - + -
107J TYR* 3.6 35.0 - + - -
111J VAL* 5.2 5.2 - - + -
120J VAL* 3.8 20.6 - - + -
121J LEU 3.0 16.2 + - - +
122J MET* 3.4 37.2 - - + +
123J SER* 3.8 3.6 + - - -
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Residues in contact with ASP 17 (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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16J PHE* 1.3 74.6 - - - +
18J ILE* 1.3 90.1 + - - +
19J GLY* 3.8 2.4 - - - -
24J ARG* 2.5 84.3 + - + +
123J SER* 4.2 15.8 - - - +
124J GLU* 5.6 0.3 - - - -
154J THR* 5.0 7.6 - - - +
157J LEU* 6.5 0.9 - - + -
393J SER* 4.7 14.3 + - - +
394J TRP* 4.2 12.4 - - + -
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Residues in contact with ILE 18 (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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16J PHE* 4.6 18.2 - - + -
17J ASP* 1.3 87.9 + - - +
19J GLY* 1.3 61.9 + - - +
22J THR 4.5 0.9 - - - -
23J VAL* 3.7 25.1 - - + +
39J THR* 4.7 10.5 - - - +
87J PRO* 6.3 0.2 - - + -
88J LEU* 3.7 29.3 - - + +
91J GLY 5.3 2.8 - - - +
93J VAL* 5.7 2.2 - - + -
99J PHE* 3.6 42.4 - - + -
102J ILE* 5.1 6.5 - - + -
103J LEU* 5.0 6.1 - - + -
122J MET* 4.7 10.5 - - + -
123J SER 5.0 4.4 + - - +
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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