Contacts of the strand formed by residues 26 - 35 (chain D) in PDB entry 3RT0
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 GLN 26 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25D SER* 1.3 91.5 + - - +
27D CYS* 1.3 60.0 + - - +
115D ASN* 5.7 1.2 - - - +
140D VAL* 3.8 22.8 - - + +
141D VAL 3.1 19.3 - - - +
142D ASP* 3.9 13.2 - - - +
143D VAL* 4.3 1.8 - - - +
149D LYS* 5.7 0.2 - - - -
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Residues in contact with CYS 27 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26D GLN* 1.3 74.8 - - - +
28D SER* 1.3 63.5 + - - +
139D PHE* 4.1 3.3 - - - -
140D VAL* 3.3 2.5 - - - +
141D VAL* 2.8 43.2 + - - +
143D VAL* 4.1 5.7 - - + +
149D LYS* 3.3 32.5 - - + +
152D THR* 3.7 34.8 - - - -
153D CYS* 3.7 19.1 - - - -
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Residues in contact with SER 28 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27D CYS* 1.3 80.0 - - - +
29D SER* 1.3 67.2 + - - +
30D THR* 5.4 0.9 + - - -
138D SER* 5.4 1.7 - - - -
139D PHE* 2.6 28.6 + - - -
140D VAL* 4.2 8.9 - - - +
149D LYS* 5.3 4.1 - - - +
153D CYS* 3.9 7.0 - - - -
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Residues in contact with SER 29 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28D SER* 1.3 80.2 + - - +
30D THR* 1.3 76.4 + - - +
31D LEU* 4.8 0.2 - - - -
138D SER* 3.5 2.9 - - - -
139D PHE* 3.3 53.7 + - - +
153D CYS* 4.3 4.9 - - - -
157D GLU* 2.6 32.4 + - - +
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Residues in contact with THR 30 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28D SER* 5.4 0.7 + - - -
29D SER* 1.3 83.6 + - - +
31D LEU* 1.3 72.6 + - - +
32D VAL* 4.6 5.8 - - + +
136D ILE* 3.6 29.2 - - + -
137D GLU 3.5 8.3 - - - +
138D SER* 3.7 12.9 - - - +
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Residues in contact with LEU 31 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30D THR* 1.3 84.8 - - - +
32D VAL* 1.3 66.0 + - - +
135D ALA 3.9 0.3 - - - +
136D ILE* 3.4 4.3 - - - +
137D GLU 2.8 38.6 + - - +
139D PHE* 4.4 4.7 - - + -
157D GLU* 3.4 50.0 - - + +
160D ILE* 3.9 24.7 - - + -
161D GLN* 3.5 33.2 - - + +
164D LEU* 4.0 16.5 - - + +
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Residues in contact with VAL 32 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30D THR* 4.6 5.4 - - + -
31D LEU* 1.3 82.5 - - - +
33D LYS* 1.3 62.5 + - - +
34D HIS* 4.1 15.3 - - + +
134D LEU* 3.1 35.7 - - + -
135D ALA 3.3 3.4 - - - +
136D ILE* 4.0 21.8 - - + -
161D GLN* 4.0 11.9 + - - +
164D LEU* 4.4 2.2 - - - -
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Residues in contact with LYS 33 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32D VAL* 1.3 79.2 - - - +
34D HIS* 1.3 76.6 + - - +
35D ILE* 3.7 11.7 + - + +
134D LEU* 3.7 1.7 - - - -
135D ALA* 2.8 42.4 + - + +
161D GLN* 5.1 3.1 - - - +
164D LEU* 3.7 36.8 - - + +
165D ASN* 3.5 28.9 + - - +
168D ALA* 3.5 25.1 - - - +
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Residues in contact with HIS 34 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32D VAL* 4.1 16.0 - - + +
33D LYS* 1.3 92.9 + - - +
35D ILE* 1.3 61.7 + - - +
36D LYS* 4.3 1.7 + - - +
125D GLU* 2.7 37.1 + - - +
127D ILE* 4.0 12.3 - - + +
133D THR 3.7 4.3 - - - -
134D LEU* 3.9 12.9 - - + +
172D GLU* 4.5 2.6 - - - +
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Residues in contact with ILE 35 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33D LYS* 4.0 13.2 - - + +
34D HIS* 1.3 79.2 - - - +
36D LYS* 1.3 64.4 + - - +
37D ALA* 3.1 14.6 + - + +
42D VAL* 4.0 16.6 - - + -
125D GLU* 5.2 1.2 - - - +
132D GLY* 3.7 3.8 - - - -
133D THR* 2.7 46.0 + - + +
135D ALA* 4.4 9.2 - - + -
167D LEU* 3.8 35.4 - - + -
168D ALA* 3.8 18.2 - - + +
171D THR* 3.1 22.4 - - - +
172D GLU* 3.6 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