Contacts of the strand formed by residues 93 - 98 (chain C) 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 C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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61C SER 3.1 16.3 + - - -
62C LEU 3.0 3.6 + - - -
63C LEU* 4.2 19.7 - - - -
64C ILE* 2.6 38.0 + - - +
84C LYS* 6.3 0.2 - - - +
87C ALA* 4.6 1.1 - - - -
88C ASP* 5.5 2.0 - - - -
92C ALA* 1.3 82.1 + - - +
94C VAL* 1.3 62.3 + - - +
113D ASN* 4.8 16.4 + - - -
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Residues in contact with VAL 94 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63C LEU* 4.5 1.8 - - - -
64C ILE* 3.3 8.5 - - + +
66C VAL* 3.3 32.8 - - + -
80C VAL* 5.6 1.8 - - + -
83C ILE* 3.9 20.4 - - + +
84C LYS* 4.0 23.2 - - + +
87C ALA* 3.5 25.1 - - + -
88C ASP* 5.7 0.4 + - - +
93C SER* 1.3 82.3 - - - +
95C VAL* 1.3 65.0 + - - +
96C VAL* 4.1 13.5 - - + -
97D SER* 4.3 15.8 + - - -
98D MET* 5.3 3.2 + - - -
113D ASN* 5.3 3.6 + - - +
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Residues in contact with VAL 95 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63C LEU* 3.5 18.6 - - + -
64C ILE 2.8 14.5 + - - +
65C GLY* 3.8 8.3 - - - -
66C VAL* 3.0 22.0 + - - +
94C VAL* 1.3 76.3 - - - +
96C VAL* 1.3 61.9 + - - +
97C SER 4.2 0.2 + - - -
114C LEU* 4.2 10.2 - - + +
117C GLN* 4.5 6.5 - - + -
119C VAL* 4.1 8.3 - - + -
95D VAL* 3.7 20.2 - - + -
96D VAL 3.9 7.2 - - - +
97D SER* 5.8 2.7 - - - -
114D LEU* 5.7 1.3 - - + -
117D GLN* 3.2 35.7 - - - +
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Residues in contact with VAL 96 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66C VAL* 3.8 8.5 - - + +
68C THR* 3.5 29.8 - - + -
71C LEU* 4.6 7.0 - - + -
80C VAL* 3.7 29.4 - - + -
94C VAL* 4.1 12.8 - - + -
95C VAL* 1.3 76.0 - - - +
97C SER* 1.3 63.9 + - - +
98C MET* 4.6 6.5 - - + -
114C LEU* 4.8 0.9 - - - -
71D LEU* 5.6 0.7 - - + -
94D VAL 4.5 0.2 - - - +
95D VAL* 3.7 7.0 - - - +
96D VAL* 2.8 53.9 + - + +
98D MET* 4.0 14.6 - - + -
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Residues in contact with SER 97 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66C VAL 2.9 9.6 + - - +
67C ALA* 3.4 3.5 - - - -
68C THR* 3.1 24.3 + - - +
95C VAL 4.2 0.4 + - - -
96C VAL* 1.3 75.1 - - - +
98C MET* 1.3 64.5 + - - +
99C VAL* 3.7 0.5 + - - +
100C GLU* 5.5 0.9 + - - -
110C ALA* 3.8 21.7 + - - +
113C ASN* 4.7 9.1 + - - +
114C LEU* 3.5 31.6 - - - -
84D LYS* 5.6 0.7 + - - -
94D VAL 4.6 10.8 + - - -
95D VAL* 5.3 4.3 - - - -
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Residues in contact with MET 98 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68C THR* 3.5 19.3 - - + +
70C SER* 4.9 5.6 - - - +
71C LEU* 4.0 38.4 - - + +
96C VAL* 4.6 4.3 - - + -
97C SER* 1.3 77.6 + - - +
99C VAL* 1.3 65.8 + - - +
100C GLU* 3.4 4.3 - - - +
80D VAL* 3.6 25.4 - - + -
81D ALA* 4.0 25.8 - - + -
84D LYS* 2.7 56.5 + - + +
94D VAL* 5.0 5.6 + - - -
96D VAL* 4.4 10.8 - - + -
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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
------------------------------------------------------------
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