Contacts of the strand formed by residues 93 - 98 (chain D) in PDB entry 1TLF
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 SER 93 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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113C ASN* 4.2 19.1 + - - +
61D SER 3.6 16.1 + - - -
62D LEU 2.9 20.9 + - - -
63D LEU* 3.5 17.0 - - - -
64D ILE* 2.8 36.6 + - - +
92D ALA* 1.3 72.8 + - - +
94D VAL* 1.3 61.3 + - - +
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Residues in contact with VAL 94 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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96C VAL 4.5 3.5 - - - +
97C SER* 4.6 12.3 + - - -
98C MET* 5.0 4.1 + - - -
113C ASN* 5.9 1.4 + - - -
63D LEU* 4.6 1.5 - - - +
64D ILE* 3.4 7.6 - - + +
66D VAL* 3.7 28.7 - - + -
80D VAL 5.4 0.7 - - - +
83D ILE* 3.8 14.1 - - + +
84D LYS* 3.9 34.6 + - + +
87D ALA* 3.3 33.9 - - + -
92D ALA 5.3 0.2 - - - +
93D SER* 1.3 77.4 - - - +
95D VAL* 1.3 64.6 + - - +
96D VAL* 4.2 12.8 - - + -
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Residues in contact with VAL 95 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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95C VAL* 3.7 24.9 - - + -
96C VAL 3.7 8.1 - - - +
97C SER* 5.3 6.3 - - - -
113C ASN* 6.5 0.2 - - + -
114C LEU* 5.5 0.9 - - + -
117C GLN* 3.7 22.0 - - + +
63D LEU* 4.1 14.1 - - + -
64D ILE 2.9 10.9 + - - +
65D GLY* 3.3 2.8 - - - -
66D VAL 3.2 21.0 + - - -
94D VAL* 1.3 74.9 - - - +
96D VAL* 1.3 61.3 + - - +
114D LEU* 3.4 22.7 - - + +
117D GLN* 3.7 12.1 - - - +
119D VAL* 4.3 10.1 - - + -
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Residues in contact with VAL 96 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71C LEU* 5.9 0.7 - - + -
95C VAL* 3.8 4.5 - - - +
96C VAL* 2.8 52.3 + - + +
98C MET* 4.4 11.2 - - + -
66D VAL* 3.6 14.6 - - + +
68D THR* 3.7 21.1 - - + -
71D LEU* 4.9 6.1 - - + -
80D VAL* 3.8 27.4 - - + -
94D VAL* 4.2 16.6 - - + -
95D VAL* 1.3 75.8 - - - +
97D SER* 1.3 75.0 + - - +
98D MET* 4.5 5.8 - - + -
114D LEU* 4.7 0.7 - - - -
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Residues in contact with SER 97 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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94C VAL 4.3 12.9 + - - -
95C VAL* 5.4 3.4 - - - +
66D VAL 3.0 17.9 + - - +
67D ALA* 3.6 2.2 - - - -
68D THR 3.2 13.9 + - - -
95D VAL 4.1 0.8 + - - -
96D VAL* 1.3 78.3 - - - +
98D MET* 1.3 66.1 + - - +
110D ALA* 4.0 18.4 - - - +
113D ASN* 4.1 19.9 + - - +
114D LEU* 3.9 27.4 - - - -
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Residues in contact with MET 98 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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80C VAL* 3.4 28.9 - - + -
81C ALA* 4.2 16.8 - - + -
84C LYS* 3.0 51.6 + - + +
94C VAL* 5.3 4.0 + - - -
96C VAL* 4.0 12.1 - - + -
68D THR* 3.7 15.7 - - + +
69D SER 5.0 1.6 - - - +
70D SER* 5.3 2.2 - - - -
71D LEU* 3.5 42.6 - - + +
96D VAL* 4.5 3.6 - - + -
97D SER* 1.3 83.9 + - - +
99D VAL* 1.3 62.3 + - - +
100D GLU* 3.3 2.6 - - - +
110D ALA* 4.7 3.3 - - - +
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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