Contacts of the strand formed by residues 90 - 98 (chain J) in PDB entry 3T30
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 MET 90 (chain J).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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80F ILE 3.5 22.7 - - - +
81F ALA* 3.7 4.0 - - - -
82F SER 3.3 33.4 - - - +
83F LEU* 4.2 1.8 - - - -
88F LEU* 3.8 11.6 - - + +
91F VAL* 3.7 40.4 - - + -
93F MET* 4.2 0.2 - - + -
48J THR* 3.8 16.6 - - + -
49J ILE 3.1 13.7 - - - +
50J CYS* 3.7 16.4 - - + -
83J LEU* 3.7 6.3 - - - -
88J LEU* 3.4 24.1 - - - +
89J PRO* 1.3 81.4 - - - +
91J VAL* 1.3 67.7 + - - +
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Residues in contact with VAL 91 (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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91F VAL* 5.6 1.1 - - - -
90I MET* 3.6 39.7 - - + +
91I VAL* 5.5 0.9 - - - -
92I SER* 4.3 13.0 - - - +
48J THR* 3.3 4.9 - - - -
49J ILE* 2.9 39.3 + - + +
81J ALA* 4.2 6.7 - - + -
83J LEU* 4.1 5.4 - - + -
88J LEU* 4.6 4.5 - - + -
90J MET* 1.3 83.3 - - - +
92J SER* 1.3 74.2 + - - +
93J MET* 3.4 24.3 + - + +
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Residues in contact with SER 92 (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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91F VAL* 4.3 12.3 - - - +
92F SER 3.4 25.8 + - - -
93F MET* 3.9 2.8 - - - -
92I SER* 3.4 22.5 + - - -
47J HIS 3.5 5.2 - - - -
48J THR* 4.1 9.6 - - - -
90J MET* 4.7 0.4 - - - +
91J VAL* 1.3 78.3 - - - +
93J MET* 1.3 61.1 + - - +
94J VAL* 3.5 22.2 + - - +
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Residues in contact with MET 93 (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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48I THR* 3.9 19.5 - - + -
90I MET* 4.2 0.9 - - + -
92I SER* 4.0 14.4 - - - +
94I VAL* 4.1 9.9 - - + -
46J LEU* 3.0 50.4 - - + +
47J HIS 2.6 14.2 + - - +
49J ILE* 4.0 14.4 - - + -
80J ILE* 3.8 24.0 - - - +
81J ALA* 4.4 0.2 - - + -
91J VAL* 3.4 35.2 + - + +
92J SER* 1.3 74.6 - - - +
94J VAL* 1.3 64.9 + - - +
95J GLY 3.2 2.1 + - - -
96J VAL* 3.3 17.8 + - + +
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Residues in contact with VAL 94 (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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93F MET* 3.8 13.9 - - + +
94F VAL 3.6 12.1 - - - +
95F GLY* 3.5 33.2 - - - +
96F VAL* 3.4 27.1 - - + +
94I VAL* 3.7 12.5 - - - +
46J LEU 4.0 5.6 - - - -
47J HIS* 4.0 17.9 - - + +
92J SER* 3.5 17.7 + - - +
93J MET* 1.3 76.9 - - - +
95J GLY* 1.3 61.9 + - - +
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Residues in contact with GLY 95 (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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47I HIS* 5.2 1.4 + - - -
94I VAL* 3.6 16.9 - - - +
45J LEU* 6.3 0.6 - - - +
46J LEU 4.5 0.8 + - - -
47J HIS* 5.0 2.2 - - - -
93J MET 3.2 0.2 + - - -
94J VAL* 1.3 81.5 - - - +
96J VAL* 1.3 64.7 + - - +
97J GLN* 3.4 16.6 + - - +
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Residues in contact with VAL 96 (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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47I HIS* 3.6 46.0 - - + +
94I VAL* 3.6 13.2 - - + -
44J LEU 3.8 0.3 - - - +
45J LEU* 3.5 4.2 - - - +
46J LEU* 2.9 44.3 + - + +
64J ILE* 6.1 0.7 - - + -
93J MET* 3.3 26.8 + - + +
95J GLY* 1.3 76.3 + - - +
97J GLN* 1.3 61.9 + - - +
98J LEU* 4.0 28.5 - - + -
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Residues in contact with GLN 97 (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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16I THR* 5.3 1.7 + - - -
47I HIS* 5.2 0.2 - - - -
118I GLN* 2.6 36.3 + - - +
120I ARG* 5.6 4.9 + - - -
43J ARG* 4.7 22.3 + - - +
44J LEU 3.4 4.5 - - - +
45J LEU* 4.0 32.6 - - + +
95J GLY* 3.4 13.2 + - - +
96J VAL* 1.3 78.2 - - - +
98J LEU* 1.3 56.9 + - - +
99J SER 4.1 0.5 + - - -
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Residues in contact with LEU 98 (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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18I LEU* 5.8 6.7 - - + -
47I HIS* 6.0 0.4 - - + -
118I GLN* 4.0 15.3 - - + +
43J ARG* 3.5 7.7 - - - -
44J LEU* 2.6 48.5 + - + +
46J LEU* 4.4 18.4 - - + -
64J ILE* 4.0 27.8 - - + -
96J VAL* 4.0 15.9 - - + -
97J GLN* 1.3 74.3 - - - +
99J SER* 1.3 62.1 + - - +
100J PRO* 3.6 1.2 - - - +
102J VAL* 4.0 20.4 - - + -
104J PHE* 3.7 30.7 - - + -
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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