Contacts of the strand formed by residues 21 - 31 (chain 6) in PDB entry 4UOW
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 VAL 21 (chain 6).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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32 ILE* 6.5 0.2 - - + -
42 PRO* 5.9 7.0 - - + -
166 ILE* 3.3 3.6 - - - +
196 GLY 5.5 1.1 - - - +
206 LYS* 1.3 74.9 - - - +
226 LEU* 1.3 64.1 + - - +
236 THR* 5.2 3.1 - - - +
656 ILE* 4.0 20.2 - - + -
666 ILE 3.5 10.3 - - - +
676 MET* 3.9 33.0 - - + +
686 ASP 4.9 2.0 - - - +
97 ALA* 4.2 15.8 - - + +
887 ILE* 3.2 28.0 + - + +
897 GLY* 3.3 0.2 - - - -
907 GLU 2.9 28.3 + - - +
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Residues in contact with LEU 22 (chain 6).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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146 ILE* 3.7 12.6 - - + -
166 ILE* 3.7 28.3 - - + -
206 LYS 4.0 0.4 + - - -
216 VAL* 1.3 73.1 - - - +
236 THR* 1.3 68.0 + - - +
246 VAL* 4.3 5.4 - - + -
646 LEU 3.4 1.0 - - - +
656 ILE* 3.3 9.7 - - - +
666 ILE* 2.8 51.5 + - + +
696 VAL* 4.0 7.6 - - + -
946 ILE* 3.6 46.2 - - + -
907 GLU 3.6 1.3 - - - +
927 PHE* 3.6 31.6 - - + -
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Residues in contact with THR 23 (chain 6).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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216 VAL* 5.2 3.1 - - - +
226 LEU* 1.3 74.9 + - - +
246 VAL* 1.3 63.7 + - - +
256 ALA* 4.6 4.5 - - + +
636 THR* 4.0 16.8 - - + -
646 LEU 3.3 2.9 - - - -
656 ILE* 3.5 18.8 - - + +
107 PRO 4.6 7.7 + - - +
117 ARG* 5.3 5.9 - - + +
127 PHE* 5.2 4.3 - - + +
907 GLU 3.0 15.2 + - - -
917 ALA* 3.6 19.8 - - + -
927 PHE* 2.8 38.7 + - - +
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Residues in contact with VAL 24 (chain 6).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
106 LEU* 4.2 24.9 - - + -
116 PRO* 4.3 19.3 - - + -
146 ILE* 3.5 29.2 - - + -
226 LEU* 4.3 10.8 - - + -
236 THR* 1.3 77.4 - - - +
256 ALA* 1.3 62.5 + - - +
266 CYS 3.9 0.3 + - - -
386 TRP* 4.4 8.1 - - + -
626 THR 3.6 1.4 - - - +
636 THR* 3.3 3.8 - - - -
646 LEU* 2.9 50.3 + - + +
926 VAL* 4.9 8.5 - - + -
946 ILE* 4.7 6.7 - - + -
927 PHE* 3.7 5.4 - - + +
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Residues in contact with ALA 25 (chain 6).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96 ALA 4.4 2.4 - - - +
116 PRO* 5.3 2.3 - - - +
236 THR* 4.0 4.2 - - + -
246 VAL* 1.3 75.4 - - - +
266 CYS* 1.3 60.7 + - - +
616 LEU* 4.5 13.7 - - + -
626 THR 3.5 4.0 - - - -
636 THR* 4.0 18.4 - - + +
127 PHE* 5.3 7.6 - - + -
157 ARG* 6.1 1.8 - - + -
927 PHE 2.9 17.7 + - - +
937 ALA* 3.7 26.8 - - + +
947 ALA 4.2 4.5 + - - -
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Residues in contact with CYS 26 (chain 6).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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76 ILE* 3.7 25.4 - - - -
96 ALA 3.5 20.4 - - - +
106 LEU* 3.8 22.2 - - + -
246 VAL 3.9 0.4 + - - +
256 ALA* 1.3 75.9 - - - +
276 ALA* 1.3 73.3 + - - +
386 TRP* 5.0 2.2 - - + -
616 LEU* 3.4 4.9 - - - +
626 THR* 2.8 52.9 + - + +
796 LEU* 3.7 11.2 - - + -
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Residues in contact with ALA 27 (chain 6).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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86 GLU* 3.0 44.9 + - + +
96 ALA 4.8 1.8 + - - -
266 CYS* 1.3 84.1 - - - +
286 PHE* 1.3 62.9 + - - +
606 ASP 3.4 12.3 - - - +
616 LEU* 4.0 3.0 - - + +
157 ARG* 3.9 34.8 - - - +
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Residues in contact with PHE 28 (chain 6).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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66 LYS 3.3 13.9 - - - +
76 ILE* 4.7 0.9 - - + -
86 GLU* 3.8 3.0 - - - +
266 CYS* 5.9 0.4 - - - -
276 ALA* 1.3 76.0 - - - +
296 THR* 1.3 75.4 + - - +
336 THR* 4.2 4.3 - - + -
346 PRO* 3.9 26.2 - - + -
366 VAL* 3.8 21.1 - - + -
576 ASN* 5.4 0.7 - - + -
586 THR 3.4 22.2 - - - -
596 ASP 3.3 19.8 - - - +
606 ASP* 3.0 24.1 + - - +
616 LEU* 3.3 35.7 - - - -
626 THR* 3.6 11.2 - - + -
816 LEU* 3.6 26.5 - - + -
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Residues in contact with THR 29 (chain 6).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36 ILE* 4.9 5.8 - - - +
46 PRO 4.2 3.8 + - - -
56 PRO* 3.3 20.4 - - - +
66 LYS* 3.1 30.2 + - + +
86 GLU* 3.7 27.1 - - + +
286 PHE* 1.3 89.6 - - - +
306 GLY* 1.3 60.3 + - - +
346 PRO* 3.9 1.4 - - - +
596 ASP 6.0 0.2 - - - -
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Residues in contact with GLY 30 (chain 6).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36 ILE* 3.6 17.3 - - - +
46 PRO 3.8 8.3 - - - -
56 PRO* 4.1 0.9 - - - -
296 THR* 1.3 78.6 + - - +
316 GLU* 1.3 73.2 + - - +
326 PRO 3.5 12.1 - - - +
336 THR* 3.8 8.1 + - - +
346 PRO* 3.9 4.5 - - - +
596 ASP 5.2 3.1 - - - +
836 ASN* 4.0 5.4 - - - -
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Residues in contact with GLU 31 (chain 6).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26 GLY* 3.8 3.0 - - - -
36 ILE* 2.9 60.5 + - + +
306 GLY* 1.3 81.8 - - - +
326 PRO* 1.4 65.0 - - + +
336 THR* 3.9 15.9 + - - -
836 ASN* 3.6 1.5 + - - -
856 PHE* 3.7 3.8 - - - -
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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