Contacts of the strand formed by residues 74 - 80 (chain J) in PDB entry 6AHU
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 74 (chain J).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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32J VAL* 4.8 5.8 - - + -
33J VAL 3.5 3.9 + - - +
34J ALA* 3.4 11.6 - - + -
35J ILE* 3.0 27.8 + - - +
72J LYS* 3.2 21.9 + - + +
73J ILE* 1.3 80.9 - - - +
75J THR* 1.3 67.7 + - - +
76J ARG* 4.1 5.2 - - + +
101J ASP* 4.6 24.2 - - + +
102J VAL* 5.8 0.9 - - + -
229J LEU* 3.8 35.4 - - + -
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Residues in contact with THR 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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35J ILE* 3.6 7.0 - - + -
37J HIS* 4.3 11.9 - - - +
51J PRO* 5.6 1.6 - - + -
52J VAL* 3.8 31.4 - - + -
54J VAL* 4.3 15.5 - - + -
73J ILE* 5.3 0.9 - - + +
74J LEU* 1.3 78.1 - - - +
76J ARG* 1.3 63.1 + - - +
100J TYR* 3.5 36.2 + - - -
101J ASP* 3.5 10.1 + - - +
102J VAL 4.5 0.3 + - - -
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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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6J ASP* 5.3 10.3 - - - +
7J LEU 4.2 3.4 + - - -
8J ASP* 2.4 44.8 + - - -
32J VAL* 5.8 2.4 - - - +
34J ALA* 3.5 25.0 - - + +
35J ILE 2.6 15.2 + - - +
36J ASN* 3.3 17.3 - - - +
37J HIS* 3.2 28.8 + - - -
74J LEU* 5.1 4.9 - - + +
75J THR* 1.3 78.5 - - - +
77J LEU* 1.3 62.9 + - - +
100J TYR* 4.6 2.0 - - - -
102J VAL* 3.3 45.7 - - + +
104J ALA* 6.2 1.3 - - + -
124J LEU* 4.9 7.9 - - - +
153J GLU* 4.0 6.8 + - - -
186J ILE* 5.8 0.2 - - - +
225J CYS 5.3 1.6 + - - -
228J ALA* 5.5 2.0 - - - +
229J LEU* 3.4 36.6 - - - +
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Residues in contact with LEU 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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36J ASN* 4.6 0.4 - - - +
37J HIS* 3.4 24.0 - - + +
39J VAL* 3.8 20.4 - - + -
46J GLN* 6.5 0.7 - - - -
48J ILE* 6.0 4.3 - - + -
76J ARG* 1.3 77.2 - - - +
78J THR* 1.3 60.2 + - - +
79J ILE* 3.7 26.0 - - + -
100J TYR* 3.6 45.8 - - + -
102J VAL 3.2 7.2 + - - +
103J VAL* 4.6 12.3 - - + -
104J ALA* 2.6 36.8 + - - +
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Residues in contact with THR 78 (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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10J ARG* 3.5 35.6 + - - +
36J ASN* 3.4 28.4 + - - -
37J HIS 2.9 28.0 + - - +
38J ILE* 3.5 7.2 - - + +
39J VAL 3.1 11.6 + - - -
77J LEU* 1.3 73.1 + - - +
79J ILE* 1.3 67.6 + - - +
80J ILE* 3.9 5.4 + - + +
104J ALA* 3.4 12.1 - - - +
106J PHE* 4.7 7.4 - - + -
126J CYS* 3.7 11.7 - - - -
153J GLU* 4.2 0.9 + - - -
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Residues in contact with ILE 79 (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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39J VAL* 3.4 23.6 - - + +
46J GLN* 6.0 1.6 - - - +
77J LEU* 3.7 33.0 - - + -
78J THR* 1.3 73.6 - - - +
80J ILE* 1.3 67.7 + - - +
81J VAL* 3.2 18.8 + - + +
86J HIS* 4.2 9.0 - - + -
90J LEU* 3.8 41.1 - - + -
103J VAL* 3.8 14.1 - - + -
104J ALA 3.3 21.7 + - - +
105J VAL* 5.0 1.3 - - - -
106J PHE* 3.0 26.9 + - - +
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Residues in contact with ILE 80 (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 ILE* 3.8 28.7 - - + -
39J VAL 2.8 15.7 + - - +
40J ASP* 4.2 12.7 - - + -
41J PHE* 3.8 33.2 + - + +
78J THR* 3.9 5.6 + - + +
79J ILE* 1.3 73.7 - - - +
81J VAL* 1.3 60.1 + - - +
86J HIS* 4.8 0.9 + - - -
106J PHE* 3.9 20.4 - - + -
108J LYS* 3.9 31.4 - - - +
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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