Contacts of the strand formed by residues 93 - 98 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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61A SER 4.1 10.9 + - - -
62A LEU 2.7 20.0 + - - -
63A LEU* 3.4 19.2 - - - +
64A ILE* 2.7 29.3 + - - +
91A GLY 4.5 0.2 + - - -
92A ALA* 1.3 74.9 - - - +
94A VAL* 1.3 66.3 + - - +
118A ARG* 5.1 1.9 + - - -
113B ASN* 4.1 15.9 + - - -
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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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63A LEU* 4.0 2.5 - - - -
64A ILE* 3.2 11.2 - - + +
66A VAL* 3.6 29.8 - - + -
80A VAL* 5.7 1.1 - - + -
83A ILE* 4.6 8.7 - - + -
84A LYS* 4.5 27.4 + - + +
87A ALA* 3.6 26.0 - - + -
88A ASP* 5.7 0.4 - - - +
93A SER* 1.3 85.3 - - - +
95A VAL* 1.3 65.0 + - - +
96A VAL* 4.3 11.0 + - + +
96B VAL 4.4 4.2 - - - +
97B SER* 4.5 12.3 + - - -
98B MET* 4.9 9.8 + - + +
113B ASN* 5.2 5.7 + - - +
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Residues in contact with VAL 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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63A LEU* 3.4 31.4 - - + -
64A ILE 2.9 9.7 + - - +
65A GLY* 3.4 7.6 - - - -
66A VAL 2.9 24.4 + - - -
94A VAL* 1.3 74.3 - - - +
96A VAL* 1.3 63.0 + - - +
114A LEU* 4.1 8.2 - - + +
117A GLN* 4.1 5.6 - - + -
119A VAL* 4.0 7.6 - - + -
95B VAL* 3.5 36.1 - - + -
96B VAL 3.7 3.1 - - - +
97B SER* 5.4 1.1 - - - +
117B GLN* 3.4 28.7 - - - +
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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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66A VAL* 3.6 10.5 - - + +
68A THR* 3.5 26.9 - - + -
71A LEU* 4.8 8.1 - - + -
80A VAL* 4.2 25.1 - - + -
94A VAL* 4.4 11.4 - - + +
95A VAL* 1.3 76.5 - - - +
97A SER* 1.3 63.5 + - - +
98A MET* 4.7 4.5 - - + -
71B LEU* 5.3 1.3 - - + -
95B VAL* 3.6 8.0 - - - +
96B VAL* 2.9 54.7 + - + +
98B MET* 4.3 19.1 - - + -
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Residues in contact with SER 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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66A VAL 2.8 14.1 + - - +
67A ALA* 3.3 2.4 - - - -
68A THR* 2.8 27.3 + - - +
95A VAL 4.2 0.2 + - - -
96A VAL* 1.3 75.3 - - - +
98A MET* 1.3 67.0 + - - +
99A VAL* 4.5 0.7 - - - +
110A ALA* 4.3 19.8 + - - +
113A ASN* 4.5 11.9 + - - +
114A LEU* 3.9 27.4 - - - -
94B VAL 4.2 13.8 + - - -
95B VAL* 5.8 2.0 - - - +
96B VAL* 5.7 0.2 - - - -
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Residues in contact with MET 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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68A THR* 3.3 18.8 - - + +
69A SER 5.1 1.6 - - - +
70A SER* 4.9 3.6 - - - -
71A LEU* 3.8 32.1 - - + +
96A VAL* 4.7 3.4 - - + -
97A SER* 1.3 81.3 + - - +
99A VAL* 1.3 62.6 + - - +
100A GLU* 3.4 1.7 - - - +
110A ALA* 4.9 2.8 - - - +
80B VAL* 3.3 30.1 - - + +
81B ALA* 3.6 33.2 - - + +
84B LYS* 3.2 45.6 + - + +
94B VAL* 5.1 5.9 + - - -
96B VAL* 4.2 10.3 - - + -
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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