Contacts of the strand formed by residues 190 - 197 (chain A) in PDB entry 1TAD
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 LEU 190 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28A ARG* 3.5 46.4 - - + +
30A VAL* 4.2 9.2 - - + -
186A SER* 3.1 6.1 - - - -
187A PHE 2.8 31.9 + - - +
188A LYS 3.1 9.2 + - - +
189A ASP* 1.3 80.1 - - - +
191A ASN* 1.3 60.7 + - - +
192A PHE* 3.7 19.4 + - + -
336A THR* 3.8 19.5 - - + -
339A ILE* 4.2 15.9 - - + -
340A ILE* 3.7 27.6 - - + -
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Residues in contact with ASN 191 (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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27A ALA* 2.8 33.5 + - - +
28A ARG 2.7 13.1 + - - +
29A THR* 3.3 11.8 + - - +
30A VAL* 2.7 32.6 + - - -
185A PHE 3.8 2.5 - - - -
186A SER* 2.8 31.7 + - - -
189A ASP 4.7 1.2 + - - -
190A LEU* 1.3 71.2 + - - +
192A PHE* 1.3 57.7 + - - +
193A ARG* 3.5 23.0 + - - +
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Residues in contact with PHE 192 (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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30A VAL* 3.5 18.6 - - + -
32A LEU* 3.8 25.6 - - + -
184A GLN* 3.1 17.0 - - - -
185A PHE* 2.8 47.4 + + + +
187A PHE* 3.8 22.4 - + + -
190A LEU* 3.8 32.8 - - + -
191A ASN* 1.3 68.4 - - - +
193A ARG* 1.3 77.7 + - - +
194A MET* 3.7 3.1 - - + +
332A PHE* 3.5 21.5 - + - -
336A THR* 3.5 27.8 - - + -
339A ILE* 4.1 9.6 - - + -
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Residues in contact with ARG 193 (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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29A THR* 3.3 26.3 + - + +
30A VAL 2.9 10.8 + - - +
31A LYS* 3.5 6.6 - - + -
32A LEU* 2.8 26.1 + - - +
182A GLU* 3.3 23.6 - - - +
183A THR 3.8 2.5 - - - -
184A GLN* 2.9 33.3 - - + +
185A PHE 3.9 6.1 + - - +
186A SER* 5.2 0.4 + - - -
191A ASN* 3.5 34.5 + - - +
192A PHE* 1.3 99.4 + - - +
194A MET* 1.3 60.0 + - - +
195A PHE* 3.6 22.7 - - + -
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Residues in contact with MET 194 (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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32A LEU* 3.3 28.5 - - + -
34A LEU* 4.0 35.0 - - + -
45A ILE* 5.0 2.5 - - + -
46A VAL* 4.5 8.1 - - + -
49A MET* 3.7 30.3 - - + -
181A ILE 3.6 0.7 - - - +
182A GLU* 3.3 2.6 - - - -
183A THR* 2.7 54.4 + - - +
185A PHE* 4.2 10.3 - - + -
192A PHE* 5.2 1.3 - - + -
193A ARG* 1.3 73.7 - - - +
195A PHE* 1.3 63.8 + - - +
196A ASP* 4.3 0.5 + - - +
218A ILE* 4.9 0.7 - - + -
332A PHE* 3.6 33.4 - - + -
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Residues in contact with PHE 195 (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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31A LYS* 3.9 24.5 - - + -
32A LEU 2.8 15.1 + - - +
33A LEU* 3.5 7.1 - - + -
34A LEU* 2.8 27.2 + - - +
180A ILE* 4.1 10.1 - - + -
181A ILE 3.3 4.3 - - - +
182A GLU* 3.4 50.0 - - + -
193A ARG* 3.6 26.5 - - + -
194A MET* 1.3 73.7 - - - +
196A ASP* 1.3 60.8 + - - +
354A CAC 3.9 20.4 - - + +
59C LEU* 3.6 30.7 - - + -
60C GLU* 5.0 1.6 - - - -
63C LEU* 4.0 17.9 - - + -
164C VAL* 4.8 0.4 - - + -
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Residues in contact with ASP 196 (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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34A LEU* 3.9 19.5 - - + +
42A LYS* 4.7 7.9 - - + +
43A SER* 3.9 16.3 + - - -
46A VAL* 3.4 34.2 - - + +
177A THR* 4.4 4.7 + - - -
179A GLY 3.7 0.3 - - - +
180A ILE* 3.3 7.1 - - - +
181A ILE* 3.2 62.3 + - - +
183A THR* 4.6 1.0 + - - -
194A MET 4.3 0.5 - - - +
195A PHE* 1.3 74.1 - - - +
197A VAL* 1.3 65.8 + - - +
354A CAC 3.9 0.9 - - - -
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Residues in contact with VAL 197 (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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34A LEU 4.0 3.9 + - - +
35A LEU* 3.9 12.6 - - + -
42A LYS* 3.0 25.9 - - + +
177A THR* 4.8 1.8 - - - -
178A THR 3.8 5.4 - - - +
179A GLY 3.3 15.3 - - - +
196A ASP* 1.3 79.6 - - - +
198A GLY* 1.3 76.1 + - - +
203A GLU* 4.7 5.2 - - + +
206A LYS* 5.3 3.1 - - - -
207A TRP* 3.4 30.3 - - + +
354A CAC 3.2 48.7 - - + +
355A ALF 3.5 3.4 - - - -
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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