Contacts of the strand formed by residues 90 - 98 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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48A THR* 3.8 22.4 - - + -
49A ILE 3.2 13.7 - - - +
50A CYS* 3.8 9.0 - - + -
83A LEU* 3.7 7.0 - - - -
88A LEU* 3.2 26.8 + - - +
89A PRO* 1.3 81.9 - - - +
91A VAL* 1.3 67.0 + - - +
80E ILE 3.5 22.2 - - - +
81E ALA* 3.6 6.1 - - - -
82E SER 3.4 32.8 - - - +
83E LEU* 4.1 1.3 - - - -
88E LEU* 3.7 13.4 - - + +
91E VAL* 3.6 40.8 - - + -
93E MET* 4.1 0.2 - - + -
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Residues in contact with VAL 91 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48A THR* 3.2 5.9 - - - -
49A ILE* 2.9 44.3 + - + +
81A ALA* 4.2 3.6 - - + -
83A LEU* 4.1 13.2 - - + -
88A LEU* 5.0 5.6 - - + -
90A MET* 1.3 82.2 - - - +
92A SER* 1.3 70.6 + - - +
93A MET* 3.8 23.7 + - + +
90B MET* 3.7 28.7 - - + +
91B VAL* 5.3 1.3 - - - -
92B SER* 4.3 15.9 - - - +
91E VAL* 5.4 1.3 - - - -
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Residues in contact with SER 92 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47A HIS 3.5 4.7 - - - -
48A THR* 3.9 15.0 - - - -
91A VAL* 1.3 78.4 - - - +
93A MET* 1.3 58.7 + - - +
94A VAL* 3.7 8.0 + - - +
92B SER* 4.1 10.7 + - - -
91E VAL* 3.8 15.4 - - - +
92E SER 2.8 27.6 + - - +
93E MET* 3.4 14.8 - - - +
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Residues in contact with MET 93 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46A LEU* 3.2 41.8 - - + +
47A HIS 2.9 13.2 + - - +
48A THR* 5.4 0.2 - - - -
49A ILE* 3.5 28.7 - - + -
80A ILE* 3.8 24.5 - - - +
91A VAL* 3.8 22.4 - - + +
92A SER* 1.3 71.6 - - - +
94A VAL* 1.3 65.5 + - - +
95A GLY 3.2 1.7 + - - -
96A VAL* 3.3 20.2 + - + +
47B HIS* 6.1 0.2 - - - -
48B THR* 4.3 13.2 - - + -
90B MET* 4.8 0.2 - - + -
92B SER* 4.0 15.9 - - - +
94B VAL* 3.9 16.2 - - + -
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Residues in contact with VAL 94 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46A LEU 4.2 5.6 - - - -
47A HIS* 4.1 20.2 - - + +
92A SER* 3.5 9.6 + - - +
93A MET* 1.3 75.4 - - - +
95A GLY* 1.3 62.1 + - - +
94B VAL* 3.6 12.5 - - - +
93E MET* 3.6 22.0 - - + +
94E VAL 3.5 21.7 - - - +
95E GLY* 3.6 24.0 - - - +
96E VAL* 3.5 25.4 - - + +
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Residues in contact with GLY 95 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45A LEU* 6.3 0.4 - - - +
46A LEU 4.4 2.0 + - - -
47A HIS* 4.9 2.6 + - - -
93A MET 3.2 0.2 + - - -
94A VAL* 1.3 80.4 - - - +
96A VAL* 1.3 66.2 + - - +
97A GLN* 3.4 19.3 + - - +
47B HIS* 5.2 1.7 + - - -
94B VAL* 3.6 14.9 - - - +
118B GLN* 5.9 0.2 + - - -
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Residues in contact with VAL 96 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45A LEU* 3.5 5.2 - - - +
46A LEU* 3.1 44.6 + - + +
64A ILE* 6.1 0.2 - - + -
93A MET* 3.3 23.1 + - + +
94A VAL 3.6 0.2 - - - -
95A GLY* 1.3 78.8 + - - +
97A GLN* 1.3 61.8 + - - +
98A LEU* 3.8 29.6 - - + -
47B HIS* 3.7 35.2 - - + +
94B VAL* 3.5 27.4 - - + -
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Residues in contact with GLN 97 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43A ARG* 3.9 30.9 + - + +
44A LEU 3.5 5.2 - - - -
45A LEU* 3.7 30.1 - - + +
95A GLY* 3.4 17.5 + - - +
96A VAL* 1.3 81.2 - - - +
98A LEU* 1.3 56.3 + - - +
120A ARG* 4.6 14.1 + - - +
16B THR* 5.0 1.0 + - - -
118B GLN* 2.7 32.5 + - - +
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Residues in contact with LEU 98 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43A ARG* 2.8 18.5 - - - -
44A LEU* 2.8 37.4 + - + +
46A LEU* 4.0 14.6 - - + -
64A ILE* 3.8 22.4 - - + -
96A VAL* 3.8 20.6 - - + -
97A GLN* 1.3 75.0 - - - +
99A SER* 1.3 61.7 + - - +
102A VAL* 3.8 26.9 - - + -
104A PHE* 3.9 15.3 - - + -
18B LEU* 3.7 29.4 - - + -
47B HIS* 5.6 0.2 - - + -
118B GLN* 4.0 9.2 - - - +
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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