Contacts of the helix formed by residues 70 - 77 (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 ILE 70 (chain J).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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37J PHE* 3.9 13.7 - - + -
38J PRO 5.9 0.4 - - - +
41J ILE* 4.1 19.1 - - + +
68J TYR* 4.4 9.2 - - + +
69J TYR* 1.3 89.8 - - + +
71J ASP* 1.3 88.8 + - - +
73J ASN* 3.7 5.9 + - - +
74J ALA* 3.4 12.7 + - - -
101J ALA* 4.6 20.2 - - + +
102J ILE* 3.4 37.5 - - + -
105J HIS* 4.1 31.4 - - + +
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Residues in contact with ASP 71 (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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37J PHE* 4.6 23.6 - - + -
38J PRO* 5.7 8.4 + - - +
70J ILE* 1.3 80.5 - - + +
72J THR* 1.3 81.9 + - + +
73J ASN* 3.0 32.1 + - - +
74J ALA* 3.3 12.9 + - - +
75J LEU* 3.3 9.1 + - - +
105J HIS* 3.3 32.2 + - + +
109J MET* 5.7 2.1 - - - +
110J HIS* 5.0 7.1 + - - +
176K LEU* 6.5 0.4 - - + -
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Residues in contact with THR 72 (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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37J PHE* 6.6 0.2 - - + -
71J ASP* 1.3 82.0 + - + +
73J ASN* 1.3 65.9 + - - -
75J LEU* 3.1 16.9 - - + +
76J ARG* 2.8 34.0 + - - +
176K LEU* 4.0 37.9 - - + -
271K SER* 4.4 1.4 + - - -
272K CYS* 4.3 15.7 - - - +
277K THR* 6.0 1.8 - - + +
280K ASN* 4.7 20.0 - - + -
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Residues in contact with ASN 73 (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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69J TYR* 3.0 47.3 + - + +
70J ILE 3.7 3.6 + - - +
71J ASP* 3.0 19.9 + - - +
72J THR* 1.3 79.2 + - - +
74J ALA* 1.3 66.3 - - - +
75J LEU 2.9 1.1 - - - -
76J ARG 2.9 11.4 + - - -
77J VAL* 2.9 27.1 + - - +
270K GLU 4.5 0.9 - - - +
271K SER* 2.6 39.0 + - - -
272K CYS* 4.0 2.6 + - - +
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Residues in contact with ALA 74 (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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40J ALA 4.6 10.8 - - - +
42J GLY* 4.3 12.1 - - - +
69J TYR* 3.9 31.2 - - + +
70J ILE* 3.4 8.2 + - - +
71J ASP 3.3 10.8 + - - +
73J ASN* 1.3 77.0 - - - +
75J LEU* 1.3 64.6 + - - +
77J VAL* 4.3 4.9 + - - +
78J PRO 5.7 0.2 - - - -
82J MET* 4.6 12.5 - - + +
253J TYR* 5.9 0.2 - - - -
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Residues in contact with LEU 75 (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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38J PRO* 5.5 7.4 - - + -
71J ASP 3.3 4.7 + - - +
72J THR* 3.1 25.5 + - + +
73J ASN 2.9 0.4 - - - -
74J ALA* 1.3 81.9 - - - +
76J ARG* 1.3 83.9 + - + +
77J VAL 4.2 0.3 + - - -
78J PRO* 5.2 2.4 - - - +
253J TYR* 3.6 42.0 - - + +
257J CYS* 5.3 7.9 - - + -
280K ASN* 3.5 24.7 - - + +
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Residues in contact with ARG 76 (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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72J THR 2.8 16.8 + - - +
73J ASN 2.9 1.4 + - - -
75J LEU* 1.3 97.9 - - + +
77J VAL* 1.3 66.3 + - - +
78J PRO* 3.5 10.3 - - - +
257J CYS* 5.3 8.7 - - - +
272K CYS* 4.5 7.9 - - + +
276K GLU* 3.9 39.3 + - - +
279K PHE* 3.5 30.1 - - - -
280K ASN* 2.9 43.8 + - - +
283K MET* 5.7 0.6 - - - +
320K LEU* 5.2 6.5 - - - +
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Residues in contact with VAL 77 (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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69J TYR* 3.8 24.2 - - + -
73J ASN* 2.9 29.8 + - - +
74J ALA* 4.3 5.5 + - - +
75J LEU 3.9 1.0 - - - -
76J ARG* 1.3 79.8 - - - +
78J PRO* 1.4 60.6 - - - +
79J ARG* 2.9 16.2 + - + +
82J MET* 5.7 5.2 - - + -
270K GLU* 3.2 33.0 - - - +
271K SER 4.5 9.4 - - - +
272K CYS* 4.8 2.0 - - - +
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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