Contacts of the strand formed by residues 90 - 98 (chain G) 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 G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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48G THR* 3.8 19.7 - - + -
49G ILE 3.1 13.9 - - - +
50G CYS* 3.7 12.8 - - + -
83G LEU* 3.6 7.9 - - - -
88G LEU* 3.4 25.2 + - - +
89G PRO* 1.3 78.7 - - - +
91G VAL* 1.3 68.5 + - - +
80H ILE 3.6 21.1 - - - +
81H ALA* 3.6 10.5 - - - -
82H SER 3.2 34.8 - - - +
83H LEU* 4.1 2.0 - - - -
88H LEU* 3.6 14.3 - - + +
91H VAL* 3.7 37.0 - - + -
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Residues in contact with VAL 91 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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90F MET* 3.7 41.3 - - + +
91F VAL* 5.6 0.4 - - - -
92F SER* 4.2 12.1 - - - +
48G THR* 3.3 5.9 - - - -
49G ILE* 2.9 43.2 + - + +
81G ALA* 4.3 1.8 - - + -
83G LEU* 4.2 4.7 - - + -
88G LEU* 4.8 2.7 - - + -
90G MET* 1.3 83.8 - - - +
92G SER* 1.3 72.4 + - - +
93G MET* 3.6 23.6 - - + -
91H VAL* 5.5 1.3 - - - -
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Residues in contact with SER 92 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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92F SER* 3.4 21.7 + - - -
47G HIS 3.4 9.4 - - - -
48G THR* 3.9 13.2 - - - -
90G MET* 4.6 1.0 - - - +
91G VAL* 1.3 77.7 - - - +
93G MET* 1.3 60.3 + - - +
94G VAL* 3.6 13.0 + - - +
91H VAL* 4.2 8.7 - - - +
92H SER 2.7 29.0 + - - -
93H MET* 4.3 1.9 - - - -
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Residues in contact with MET 93 (chain G).
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* 6.2 0.2 - - - -
48F THR* 3.7 16.2 - - + -
90F MET* 4.2 0.9 - - + -
92F SER* 3.9 11.4 - - - +
94F VAL* 4.1 14.1 - - + -
46G LEU* 3.1 47.3 - - + +
47G HIS 2.8 16.7 + - - +
48G THR* 5.1 0.7 - - - +
49G ILE* 4.3 13.9 - - + -
80G ILE* 3.7 27.6 - - - +
91G VAL* 3.6 30.7 - - + -
92G SER* 1.3 71.0 - - - +
94G VAL* 1.3 69.4 + - - +
96G VAL* 3.2 20.4 + - + +
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Residues in contact with VAL 94 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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94F VAL* 3.5 13.2 - - - +
46G LEU 4.0 5.2 - - - -
47G HIS* 4.0 26.5 - - + +
92G SER* 3.6 5.9 - - - +
93G MET* 1.3 79.5 - - - +
95G GLY* 1.3 61.6 + - - +
93H MET* 3.9 21.3 - - + +
94H VAL 3.5 22.4 - - - +
95H GLY* 3.8 22.4 - - - +
96H VAL* 3.7 21.1 - - + +
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Residues in contact with GLY 95 (chain G).
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* 5.1 1.7 + - - -
94F VAL* 3.6 14.7 - - - +
45G LEU* 6.2 0.4 - - - +
46G LEU 4.4 2.0 + - - -
47G HIS* 4.9 2.8 - - - -
94G VAL* 1.3 81.1 - - - +
96G VAL* 1.3 64.5 + - - +
97G GLN* 3.3 19.1 + - - +
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Residues in contact with VAL 96 (chain G).
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* 3.7 31.9 - - + +
94F VAL* 3.5 21.5 - - + -
45G LEU* 3.4 5.5 - - - +
46G LEU* 3.0 47.5 + - + +
93G MET* 3.2 29.2 + - + +
95G GLY* 1.3 79.3 + - - +
97G GLN* 1.3 60.9 + - - +
98G LEU* 3.9 29.4 - - + -
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Residues in contact with GLN 97 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16F THR* 5.2 1.6 - - - +
118F GLN* 2.7 34.6 + - - +
43G ARG* 3.9 23.3 - - + +
44G LEU 3.5 4.0 - - - -
45G LEU* 3.5 21.3 - - + +
95G GLY* 3.3 16.8 + - - +
96G VAL* 1.3 79.8 - - - +
98G LEU* 1.3 55.9 + - - +
99G SER 4.3 0.2 + - - -
120G ARG* 3.1 27.7 + - - +
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Residues in contact with LEU 98 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18F LEU* 4.0 22.2 - - + -
47F HIS* 5.7 0.7 - - + +
118F GLN* 3.8 17.7 - - - +
43G ARG* 3.1 10.1 - - - +
44G LEU* 2.8 47.3 + - + +
46G LEU* 4.3 13.5 - - + -
64G ILE* 4.0 15.9 - - + -
96G VAL* 3.9 18.4 - - + -
97G GLN* 1.3 73.3 - - - +
99G SER* 1.3 61.2 + - - +
100G PRO* 3.7 0.7 - - - +
102G VAL* 3.9 22.9 - - + -
104G PHE* 3.8 30.5 - - + -
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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