Contacts of the strand formed by residues 45 - 51 (chain R) 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 GLY 45 (chain R).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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42R THR* 2.8 34.9 + - - +
43R LYS 3.5 1.2 - - - -
44R GLU* 1.3 82.3 - - - +
46R VAL* 1.3 64.2 + - - -
146R TYR* 3.4 13.4 - - - -
186R LEU* 4.1 9.0 - - - +
215R ILE 3.4 14.8 - - - -
216R THR* 4.2 0.9 - - - -
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Residues in contact with VAL 46 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40R ILE 3.3 16.6 - - - +
41R ALA* 3.8 16.2 - - + -
45R GLY* 1.3 79.1 - - - +
47R VAL* 1.3 70.3 + - - +
48R LEU* 5.6 0.2 - - - +
139R ALA* 3.5 29.2 - - + -
140R GLY 4.3 3.4 - - - +
146R TYR* 3.5 27.8 - - + -
147R GLN 3.9 14.1 - - - +
148R LEU* 4.2 9.6 - - + -
186R LEU* 4.5 0.6 - - - +
214R CYS* 3.0 25.5 - - - +
215R ILE* 3.1 15.8 + - + +
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Residues in contact with VAL 47 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38R ILE 3.8 0.2 - - - +
39R GLY* 3.1 6.8 - - - -
40R ILE 2.8 36.9 + - - +
46R VAL* 1.3 75.2 - - - +
48R LEU* 1.3 67.5 + - - +
49R GLY 4.3 0.2 - - - -
186R LEU* 3.4 29.2 - - + -
189R ALA* 4.0 15.0 - - + -
190R GLU* 3.9 23.1 - - + -
193R VAL* 3.8 25.7 - - + +
212R LEU* 3.9 20.0 - - + -
213R SER 3.4 9.9 - - - +
214R CYS* 4.3 4.7 - - + -
224R TYR* 4.9 0.9 - - + +
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Residues in contact with LEU 48 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38R ILE 3.4 1.8 - - - +
39R GLY* 3.8 7.2 - - - -
46R VAL* 4.2 1.1 + - + +
47R VAL* 1.3 87.0 - - - +
49R GLY* 1.3 58.7 + - - +
67R ILE* 3.7 5.4 - - + +
75R GLY 4.0 2.5 - - - +
76R CYS* 3.7 35.2 - - - +
77R ALA* 3.7 21.5 - - + +
137R LEU* 4.0 9.6 - - + +
139R ALA* 3.7 29.6 - - + -
148R LEU* 3.8 16.8 - - + -
212R LEU* 3.5 1.7 - - - -
213R SER* 2.8 49.3 + - - +
214R CYS* 5.6 0.7 - - - -
215R ILE* 5.9 1.8 - - + -
221R PHE* 4.8 5.4 - - + -
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Residues in contact with GLY 49 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37R ALA* 3.4 0.2 - - - -
38R ILE* 2.8 35.4 + - - +
48R LEU* 1.3 75.2 - - - +
50R VAL* 1.3 67.8 + - - +
67R ILE* 4.3 0.2 - - - -
77R ALA* 5.1 0.5 - - - +
193R VAL* 3.9 19.0 - - - +
197R LEU* 4.1 7.2 - - - +
211R GLN 3.1 11.2 - - - -
212R LEU* 4.0 3.4 - - - -
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Residues in contact with VAL 50 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35R SER* 6.3 0.2 - - - -
36R THR 3.5 6.5 - - - +
37R ALA* 4.0 9.9 - - + -
49R GLY* 1.3 79.3 - - - +
51R GLU* 1.3 64.5 + - - +
52R LYS* 4.8 4.7 - - + +
64R ILE* 6.5 0.2 - - + -
66R LYS* 3.9 25.6 - - + +
67R ILE* 3.5 35.2 - - + -
77R ALA* 3.8 19.3 - - + -
78R MET 4.7 1.8 - - - +
197R LEU* 3.9 10.8 - - - +
210R ALA* 3.4 4.7 - - - -
211R GLN* 2.9 44.8 + - + +
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Residues in contact with GLU 51 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20R ASN 3.8 4.0 - - - -
35R SER* 3.2 15.0 - - - -
36R THR* 2.9 43.0 + - - +
50R VAL* 1.3 72.0 - - - +
52R LYS* 1.3 68.6 + - - +
53R ARG* 3.0 50.2 + - + +
66R LYS* 3.6 5.2 + - - +
167R SER* 4.3 0.5 + - - -
197R LEU* 4.2 4.2 - - + +
200R VAL 5.5 0.5 - - - +
201R MET* 3.8 43.4 - - + +
202R GLU* 4.8 10.4 + - - +
205R GLU* 5.7 2.4 + - - +
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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