Contacts of the strand formed by residues 210 - 216 (chain U) in PDB entry 3TDD
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 210 (chain U).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49U ILE* 4.4 16.2 - - + -
50U SER 3.6 12.3 - - - +
51U GLN* 4.4 4.7 - - + +
52U LYS* 3.5 18.1 - - - +
194U ILE* 3.5 48.9 - - + -
197U MET* 4.8 0.9 - - + -
205U PHE* 3.9 41.1 - - + -
206U SER 4.2 2.6 + - - +
207U LYS 4.3 3.8 - - - +
208U ASN* 4.3 1.5 - - - +
209U ASP* 1.3 89.6 - - - +
211U GLU* 1.3 63.3 + - - +
212U VAL* 4.8 2.9 - - + -
229U ILE* 3.8 26.6 - - + +
233U LEU* 4.5 5.8 - - + -
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Residues in contact with GLU 211 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48U VAL 3.8 0.5 - - - +
49U ILE* 3.6 3.5 - - - +
50U SER* 2.9 40.9 + - - +
51U GLN 4.6 4.3 - - - +
52U LYS* 4.4 14.8 + - + +
64U VAL 3.5 6.2 - - - +
65U SER* 2.5 42.4 + - - +
66U TYR* 3.1 23.0 + - - +
67U ILE* 3.4 26.4 - - + +
210U LEU* 1.3 76.6 - - - +
212U VAL* 1.3 65.7 + - - +
223U THR* 6.2 1.8 - - - -
229U ILE* 4.4 2.7 - - - -
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Residues in contact with VAL 212 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47U VAL* 4.2 2.9 - - + -
48U VAL 3.5 6.5 - - - +
49U ILE* 4.1 18.2 - - + -
67U ILE* 3.9 4.3 - - - +
190U VAL* 3.8 19.5 - - + -
194U ILE* 4.6 9.2 - - + -
210U LEU* 4.8 2.9 - - + -
211U GLU* 1.3 84.3 - - - +
213U GLY* 1.3 70.1 + - - +
214U VAL* 4.2 2.0 - - + -
223U THR* 3.2 9.5 - - - -
224U LEU* 3.0 57.0 + - + +
229U ILE* 4.1 25.3 - - + +
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Residues in contact with GLY 213 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47U VAL* 3.5 4.9 - - - +
48U VAL* 3.0 48.9 + - - +
67U ILE* 4.4 3.4 - - - -
212U VAL* 1.3 75.0 - - - +
214U VAL* 1.3 65.7 + - - +
221U PHE* 4.0 13.5 - - - -
222U PHE 3.5 6.3 - - - -
223U THR* 4.1 2.0 - - - -
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Residues in contact with VAL 214 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45U CYS* 4.7 0.4 - - + -
46U THR 3.5 8.1 - - - +
47U VAL* 4.4 3.8 - - + -
186U TRP* 3.8 48.7 - - + -
190U VAL* 3.9 13.7 - - + -
212U VAL* 4.2 7.4 - - + -
213U GLY* 1.3 80.0 - - - +
215U ALA* 1.3 68.7 + - - +
216U THR* 4.2 2.5 - - + -
221U PHE* 3.2 5.6 - - - -
222U PHE* 2.6 71.0 + - + -
224U LEU* 4.2 4.7 - - + -
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Residues in contact with ALA 215 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45U CYS* 3.1 9.5 - - - +
46U THR* 2.8 38.4 + - - +
73U THR 4.5 1.1 - - - +
139U VAL* 4.4 1.3 - - + -
140U SER* 3.6 36.1 - - - +
141U VAL* 3.2 2.6 - - - +
214U VAL* 1.3 74.0 - - - +
216U THR* 1.3 62.0 + - - +
220U LYS 3.5 4.0 - - - -
221U PHE* 3.6 20.2 - - + -
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Residues in contact with THR 216 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44U ASP 4.3 5.2 - - - +
45U CYS* 4.2 9.9 - - + -
73U THR* 5.3 2.6 - - - +
141U VAL* 3.3 20.0 + - - +
186U TRP* 4.4 13.0 - - + -
214U VAL* 4.2 9.4 - - + -
215U ALA* 1.3 78.9 - - - +
217U LYS* 1.3 73.1 + - - +
218U ASP 3.0 3.8 + - - -
220U LYS* 2.6 33.1 + - - +
222U PHE* 4.1 20.9 - - + -
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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