Contacts of the strand formed by residues 102 - 106 (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 VAL 102 (chain J).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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74J LEU* 5.8 1.1 - - + -
75J THR 4.5 2.2 + - - -
76J ARG* 3.3 37.9 - - + +
77J LEU 3.2 21.7 + - - -
100J TYR 3.2 5.7 - - - +
101J ASP* 1.3 84.8 - - + +
103J VAL* 1.3 64.2 + - - +
104J ALA* 4.0 1.5 + - + +
123J ASP* 3.3 9.4 - - + -
124J LEU* 3.8 28.9 - - + -
153J GLU* 5.5 1.6 - - - +
228J ALA 4.6 0.4 - - - +
229J LEU* 3.9 33.2 - - + +
232J GLY* 4.0 14.6 - - - +
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Residues in contact with VAL 103 (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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77J LEU* 3.8 15.9 - - + +
79J ILE* 3.8 25.4 - - + -
90J LEU* 5.9 0.7 - - + -
99J LEU 4.6 5.8 - - - +
100J TYR* 3.3 20.4 - - + +
101J ASP 5.1 0.4 - - - -
102J VAL* 1.3 73.4 - - - +
104J ALA* 1.3 62.3 + - - +
122J VAL* 4.1 14.1 - - + +
123J ASP* 3.0 37.9 + - - +
124J LEU 3.5 0.9 + - - +
235J ARG* 3.5 33.7 - - - +
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Residues in contact with ALA 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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36J ASN* 5.4 0.9 - - - +
76J ARG* 6.2 1.1 - - + -
77J LEU 2.6 24.7 + - - +
78J THR* 3.9 12.8 - - - +
79J ILE* 3.3 23.2 + - - +
102J VAL* 4.0 3.2 + - + -
103J VAL* 1.3 75.7 - - - +
105J VAL* 1.3 60.2 + - - +
124J LEU* 3.3 13.2 - - + +
126J CYS* 3.9 11.9 - - - -
153J GLU* 3.8 24.5 - - - +
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Residues in contact with VAL 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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79J ILE* 4.0 2.7 - - + -
81J VAL* 3.8 27.4 - - + -
87J CYS* 6.0 0.2 - - - -
90J LEU* 4.4 12.1 - - + -
104J ALA* 1.3 74.4 - - - +
106J PHE* 1.3 60.9 + - - +
107J PRO* 3.6 6.1 - - + +
112J LEU* 5.5 2.9 - - + -
116J ALA* 4.3 14.1 - - + -
120J LEU* 4.5 13.2 - - + -
122J VAL* 3.9 22.0 - - + +
124J LEU 3.1 12.6 + - - +
125J VAL* 3.9 17.9 - - + -
126J CYS* 2.6 36.5 + - - +
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Residues in contact with PHE 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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10J ARG* 5.5 3.4 - - - -
78J THR* 4.7 7.0 - - + -
79J ILE 3.0 19.0 + - - +
80J ILE* 3.9 27.6 - - + -
81J VAL* 2.9 27.2 + - - +
105J VAL* 1.3 77.2 - - - +
107J PRO* 1.3 67.7 - - - +
108J LYS* 3.6 28.9 - - + -
126J CYS* 3.3 28.3 - - + -
127J ILE* 4.8 0.2 - - - -
128J THR* 3.2 46.2 - - - -
133J LEU* 5.3 9.0 - - + -
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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