Contacts of the strand formed by residues 90 - 98 (chain F) 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 F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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48F THR* 3.8 20.9 - - + -
49F ILE 3.2 12.1 - - - +
50F CYS* 3.8 13.0 - - + -
83F LEU* 3.6 6.7 - - - -
88F LEU* 3.3 25.5 + - - +
89F PRO* 1.3 80.7 - - - +
91F VAL* 1.3 69.0 + - - +
80G ILE 3.5 20.6 - - - +
81G ALA* 3.7 4.3 - - - -
82G SER 3.4 33.9 - - - +
83G LEU* 4.0 2.2 - - - -
88G LEU* 3.6 15.6 - - + +
91G VAL* 3.7 39.5 - - + -
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Residues in contact with VAL 91 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48F THR* 3.3 5.5 - - - -
49F ILE* 2.9 46.0 + - + +
81F ALA* 4.2 2.0 - - + -
83F LEU* 4.0 5.4 - - + -
88F LEU* 4.7 2.9 - - + -
90F MET* 1.3 83.1 - - - +
92F SER* 1.3 74.9 + - - +
93F MET* 3.5 24.0 + - + -
91G VAL* 5.6 0.7 - - - -
90J MET* 3.7 41.1 - - + -
91J VAL* 5.6 0.7 - - - -
92J SER* 4.3 11.4 - - - +
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Residues in contact with SER 92 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47F HIS 3.5 5.4 - - - -
48F THR* 4.1 9.6 - - - -
90F MET* 4.6 0.8 - - - +
91F VAL* 1.3 79.1 - - - +
93F MET* 1.3 61.0 + - - +
94F VAL* 3.6 21.5 + - - +
91G VAL* 4.2 12.0 - - - +
92G SER 3.4 26.3 + - - -
93G MET* 3.9 2.2 - - - -
92J SER* 3.4 22.0 + - - -
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Residues in contact with MET 93 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46F LEU* 3.1 47.9 - - + +
47F HIS 2.8 17.3 + - - +
48F THR* 5.2 0.2 - - - -
49F ILE* 3.7 13.5 - - + -
80F ILE* 3.6 24.9 - - - +
91F VAL* 3.5 33.0 - - + -
92F SER* 1.3 73.0 - - - +
94F VAL* 1.3 66.2 + - - +
96F VAL* 3.2 20.9 + - + +
48J THR* 4.0 17.3 - - + -
90J MET* 4.2 1.3 - - + -
92J SER* 3.9 15.5 - - - +
94J VAL* 4.1 8.7 - - + -
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Residues in contact with VAL 94 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46F LEU 3.9 6.3 - - - -
47F HIS* 3.9 22.7 - - + +
92F SER* 3.6 17.3 + - - +
93F MET* 1.3 77.7 - - - +
95F GLY* 1.3 61.2 + - - +
93G MET* 3.9 12.6 - - + +
94G VAL 3.5 21.7 - - - +
95G GLY* 3.6 24.5 - - - +
96G VAL* 3.5 24.0 - - + +
94J VAL* 3.6 12.5 - - - +
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Residues in contact with GLY 95 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45F LEU* 6.1 1.0 - - - +
46F LEU 4.4 1.4 + - - -
47F HIS* 4.9 2.2 - - - -
94F VAL* 1.3 80.6 - - - +
96F VAL* 1.3 64.3 + - - +
97F GLN* 3.4 17.9 + - - +
47J HIS* 5.2 1.2 + - - -
94J VAL* 3.5 16.0 - - - +
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Residues in contact with VAL 96 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45F LEU* 3.5 4.7 - - - +
46F LEU* 2.9 44.7 + - + +
93F MET* 3.2 23.8 + - + +
95F GLY* 1.3 76.6 + - - +
97F GLN* 1.3 61.1 + - - +
98F LEU* 4.0 27.4 - - + -
47J HIS* 3.6 36.1 - - + +
94J VAL* 3.4 28.3 - - + -
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Residues in contact with GLN 97 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43F ARG* 3.1 27.3 + - - +
44F LEU 3.4 4.3 - - - -
45F LEU* 3.3 30.6 - - + +
95F GLY* 3.4 14.8 + - - +
96F VAL* 1.3 76.3 - - - +
98F LEU* 1.3 57.2 + - - +
120F ARG* 3.4 33.7 + - - +
47J HIS* 5.2 0.2 - - - -
118J GLN* 2.6 33.6 + - - +
120J ARG* 5.3 7.3 - - - +
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Residues in contact with LEU 98 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43F ARG* 3.4 9.2 - - - +
44F LEU* 2.8 47.8 + - + +
46F LEU* 4.6 13.7 - - + -
64F ILE* 3.7 25.6 - - + -
96F VAL* 4.0 17.5 - - + -
97F GLN* 1.3 76.4 - - - +
99F SER* 1.3 60.8 + - - +
100F PRO* 3.6 0.7 - - - +
102F VAL* 3.9 29.2 - - + -
104F PHE* 3.9 14.6 - - + -
18J LEU* 4.1 21.5 - - + -
47J HIS* 5.8 0.2 - - + -
118J GLN* 3.7 16.6 - - - +
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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