Contacts of the strand formed by residues 193 - 199 (chain A) in PDB entry 1TD2
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 ARG 193 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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183A HIS* 5.0 3.5 + - - -
185A ALA* 5.6 2.6 + - - +
190A SER* 3.6 21.2 + - - +
191A ARG* 3.2 4.3 - - - +
192A ASP* 1.3 87.4 - - + +
194A PHE* 1.3 62.4 + - - +
195A GLU* 3.4 18.3 + - - +
208A SER* 3.1 34.2 + - - -
209A ARG* 3.6 19.4 - - - +
210A PRO* 3.1 36.9 - - + +
211A LEU* 4.0 9.0 - - - +
282A PHE* 5.1 4.0 - - - -
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Residues in contact with PHE 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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182A LYS 3.4 24.0 - - - -
183A HIS* 3.4 38.4 - + + -
193A ARG* 1.3 72.1 - - - +
195A GLU* 1.3 60.7 + - - +
196A MET* 3.7 20.4 - - + -
207A ILE 3.9 0.2 - - - +
208A SER* 3.1 4.9 - - - -
209A ARG* 2.9 79.8 + - + +
210A PRO 4.4 1.6 - - - +
211A LEU* 4.1 19.2 - - + +
222A VAL* 4.3 21.1 - - + -
226A THR* 5.7 1.8 - - - -
248A THR* 5.8 0.8 - - + +
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Residues in contact with GLU 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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183A HIS* 3.3 9.5 - - - -
184A LEU* 3.0 38.7 + - + -
185A ALA 5.5 1.0 - - - +
188A GLY* 3.3 8.2 - - - -
189A TYR* 2.9 26.5 + - - +
190A SER* 3.1 33.9 + - - +
193A ARG* 3.4 12.6 + - - +
194A PHE* 1.3 77.8 - - - +
196A MET* 1.3 71.1 + - - +
206A HIS* 2.6 32.2 + - - +
207A ILE 3.3 3.4 - - - +
208A SER* 3.7 15.2 - - - -
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Residues in contact with MET 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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180A LEU* 4.4 9.0 - - + -
181A VAL 3.3 9.2 - - - +
182A LYS* 3.2 28.3 - - - +
184A LEU* 4.3 4.3 - - - -
194A PHE* 3.7 13.7 - - + -
195A GLU* 1.3 81.7 - - - +
197A LEU* 1.3 70.0 + - - +
206A HIS* 3.7 2.4 - - - -
207A ILE* 3.1 35.8 + - + +
209A ARG* 4.7 6.3 - - - +
226A THR* 3.7 28.9 - - + -
244A LEU* 4.0 12.3 - - + -
247A VAL* 4.6 4.3 - - + -
248A THR* 3.3 38.4 - - + +
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Residues in contact with LEU 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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161A VAL* 4.0 18.8 - - + +
164A ALA* 3.6 30.7 - - + -
165A VAL* 4.0 11.2 - - + +
179A VAL 3.5 1.3 - - - +
180A LEU* 3.1 7.8 - - - +
181A VAL* 2.7 48.3 + - + -
184A LEU* 3.8 13.0 - - + -
196A MET* 1.3 84.5 - - - +
198A LEU* 1.3 60.3 + - - +
199A VAL* 4.0 14.4 - - + -
205A TRP 3.4 14.6 - - - +
206A HIS* 3.6 27.6 - - + -
244A LEU* 5.3 0.4 - - - -
287A LEU* 4.4 4.5 - - + -
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Residues in contact with LEU 198 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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178A ILE* 3.7 27.4 - - + -
179A VAL 3.4 4.9 - - - +
180A LEU* 4.2 7.0 - - + -
197A LEU* 1.3 73.2 - - - +
199A VAL* 1.3 59.3 + - - +
200A THR* 5.8 0.2 - - - -
203A GLU 4.3 0.2 - - - +
204A ALA* 3.4 2.4 - - - -
205A TRP* 2.9 38.2 + - + +
230A LEU* 4.0 32.3 - - + -
234A LEU* 5.4 0.9 - - + -
240A LEU* 3.5 55.9 - - + +
243A ALA* 4.9 0.9 - - + -
244A LEU* 4.2 25.9 - - + +
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Residues in contact with VAL 199 (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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165A VAL* 4.1 14.6 - - + +
168A ALA* 3.8 32.1 - - + -
169A ARG* 3.8 18.6 - - + +
172A ILE* 3.8 3.6 - - + +
178A ILE* 3.5 5.2 - - - +
179A VAL* 2.6 44.1 + - + +
181A VAL* 5.2 0.9 - - + -
197A LEU* 4.1 23.1 - - + -
198A LEU* 1.3 79.6 - - - +
200A THR* 1.3 80.2 + - - +
203A GLU 3.7 5.4 - - - +
204A ALA* 4.0 11.0 - - + -
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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