Contacts of the strand formed by residues 31 - 38 (chain B) in PDB entry 5T4S
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 31 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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25B GLY* 3.3 1.3 - - - -
26B ILE 2.9 34.1 + - - +
29B PRO 4.3 4.8 - - - +
30B PRO* 1.3 75.2 - - - +
32B THR* 1.3 60.2 + - - +
33B PHE* 3.3 17.8 - - + -
62B LYS* 3.5 17.7 - - - +
63B LEU 3.8 6.5 + - - -
64B PHE* 3.4 23.7 - - - +
65B ASP* 3.0 50.7 - - - +
68B ASP* 3.9 19.2 - - + +
69B SER* 4.7 1.6 - - - -
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Residues in contact with THR 32 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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267A ASP* 3.6 15.5 - - - +
278A THR* 4.2 30.6 + - + -
280A THR* 4.7 3.8 - - + -
23B GLU* 3.7 37.5 - - + +
24B ILE 3.4 6.8 + - - +
25B GLY* 4.5 4.9 - - - -
30B PRO* 4.1 7.0 + - - +
31B GLN* 1.3 70.4 - - - +
33B PHE* 1.3 64.5 + - - +
34B LYS* 6.0 0.4 - - + +
62B LYS* 3.1 31.6 - - - +
125B ASP* 4.7 0.2 - - - +
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Residues in contact with PHE 33 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23B GLU* 3.3 5.7 - - - -
24B ILE* 2.9 34.4 + - + +
26B ILE* 3.7 34.3 - - + -
31B GLN* 3.3 34.8 - - + -
32B THR* 1.3 77.5 - - - +
34B LYS* 1.3 64.1 + - - +
35B VAL* 3.6 6.9 + - + -
46B VAL* 3.9 20.9 - - + -
62B LYS* 3.6 28.7 - - + -
63B LEU 3.6 7.6 - - - -
64B PHE* 3.4 44.2 - + + -
125B ASP* 3.6 14.4 - - + +
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Residues in contact with LYS 34 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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263A PRO* 3.4 15.4 + - - +
265A LEU 4.3 6.7 + - - -
267A ASP* 4.0 11.0 - - - +
280A THR* 3.9 34.9 - - + -
281A SER* 3.4 23.8 + - - +
282A ALA* 5.4 0.6 - - - +
21B TYR* 3.8 31.0 + - + -
22B GLY 3.3 6.3 - - - +
23B GLU* 4.7 3.1 - - + +
32B THR* 4.5 0.4 + - + -
33B PHE* 1.3 72.8 - - - +
35B VAL* 1.3 58.1 + - - +
123B GLU 3.7 17.0 + - - +
124B PHE* 4.0 7.6 - - - -
125B ASP* 2.7 43.1 + - - +
126B GLY 3.1 6.9 + - - -
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Residues in contact with VAL 35 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21B TYR* 3.1 8.2 - - - +
22B GLY 2.6 41.5 + - - +
24B ILE* 3.8 34.5 - - + -
33B PHE* 4.2 8.1 - - + +
34B LYS* 1.3 78.2 - - - +
36B VAL* 1.3 59.7 + - - +
37B PHE* 3.7 27.7 - - + -
46B VAL* 4.5 4.9 - - + -
124B PHE* 4.5 0.2 - - - -
126B GLY* 3.2 21.8 - - - +
127B VAL 4.2 0.7 - - - +
128B VAL* 3.7 22.4 - - + -
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Residues in contact with VAL 36 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20B TYR 3.7 10.3 - - - +
21B TYR* 4.3 0.4 - - + -
35B VAL* 1.3 71.2 - - - +
37B PHE* 1.3 67.9 + - - +
38B ASP* 3.6 6.0 + - + -
124B PHE* 3.5 43.3 - - + -
126B GLY 2.9 10.0 + - - +
127B VAL* 3.5 10.1 - - + +
128B VAL 2.8 26.3 + - - +
228B GLY* 3.8 19.3 - - - +
402B 77O 3.5 38.1 - - + +
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Residues in contact with PHE 37 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10B VAL* 4.0 19.7 - - + -
12B LEU* 3.9 16.2 - - + -
20B TYR 4.5 2.2 + - - -
21B TYR* 5.2 0.4 - - - -
22B GLY* 3.9 15.7 - - - -
23B GLU 4.6 0.4 - - - -
24B ILE* 3.9 11.9 - - + -
35B VAL* 3.7 31.4 - - + -
36B VAL* 1.3 72.8 - - - +
38B ASP* 1.3 53.2 + - - +
99B VAL* 4.0 20.2 - - + -
128B VAL* 3.4 31.4 - - + -
130B MET* 4.1 8.5 - - + -
160B PHE* 3.3 31.4 - - + -
162B TYR* 4.0 2.5 + - - -
176B ILE* 4.0 19.7 - - + -
178B LEU* 6.0 1.1 - - + -
227B THR* 2.7 27.6 + - - -
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Residues in contact with ASP 38 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36B VAL* 4.2 5.4 - - + -
37B PHE* 1.3 71.0 - - - +
39B THR* 1.3 55.9 + - - +
40B GLY* 2.9 20.5 + - - -
41B SER* 2.5 36.1 + - - +
127B VAL* 3.9 23.3 - - + +
128B VAL 3.0 9.3 + - - -
129B GLY* 3.5 0.3 - - - -
130B MET* 2.7 27.3 + - - +
226B ASP* 3.0 15.4 - - - +
227B THR* 3.4 1.3 - - - -
228B GLY* 3.3 18.3 - - - +
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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