Contacts of the helix formed by residues 1109 - 1123 (chain 1) in PDB entry 5Z58
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 ARG1109 (chain 1).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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11001 ASN* 6.1 2.5 - - + -
11021 LYS* 2.4 54.2 + - + +
11041 GLN 3.9 2.6 + - - +
11051 GLU* 3.3 31.3 + - - +
11081 ASN* 1.3 79.5 + - - +
11101 VAL* 1.3 54.6 + - - +
11111 CYS 2.8 2.4 + - - -
11121 THR* 2.2 51.3 + - - +
11131 THR* 4.9 4.0 - - - +
11421 ASN* 3.0 52.1 + - - +
11431 VAL* 5.6 1.1 - - - +
11451 ASN* 6.0 0.6 - - - +
11461 GLY* 5.0 10.5 - - - -
141G C 4.1 11.3 + - - -
142G U 3.9 19.1 + - - -
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Residues in contact with VAL1110 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11051 GLU 4.7 0.8 + - - +
11061 ARG* 5.2 9.0 - - + -
11081 ASN* 2.2 38.1 + - - +
11091 ARG* 1.3 73.6 - - - +
11111 CYS* 1.3 55.6 + - - -
11121 THR 3.3 0.4 - - - -
11131 THR* 3.1 23.6 - - + +
11141 VAL* 2.9 27.4 + - + +
11491 LYS* 4.3 20.6 - - + -
11531 PHE* 3.7 24.2 - - + -
143G U 5.8 4.7 - - - +
144G A 4.2 22.0 - - - +
145G U 5.7 0.7 - - - +
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Residues in contact with CYS1111 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10661 LEU* 4.3 21.1 - - + -
10741 ARG* 3.5 35.2 - - - -
10781 VAL* 4.1 10.4 - - + +
11081 ASN* 2.5 41.4 - - + +
11091 ARG 2.8 1.2 + - - -
11101 VAL* 1.3 75.8 - - - +
11121 THR* 1.3 65.8 + - - +
11141 VAL* 2.9 10.8 + - - +
11151 ALA* 2.9 20.8 + - - +
144G A 4.0 20.2 - - - -
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Residues in contact with THR1112 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10631 LEU* 5.9 1.1 - - + -
10661 LEU* 3.6 25.3 - - + +
10971 LEU* 4.1 9.4 - - + +
11001 ASN* 3.6 40.6 + - - +
11081 ASN 4.9 2.9 - - - +
11091 ARG* 2.2 44.8 + - - +
11111 CYS* 1.3 71.6 - - - +
11131 THR* 1.3 58.2 + - - -
11151 ALA* 3.1 12.4 + - - +
11161 ILE* 2.9 34.0 + - - +
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Residues in contact with THR1113 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11091 ARG* 4.2 4.0 + - - +
11101 VAL* 3.1 26.5 + - + +
11111 CYS 3.1 0.2 - - - -
11121 THR* 1.3 82.8 + - - +
11141 VAL* 1.3 59.8 + - - +
11161 ILE* 2.9 25.8 + - - +
11171 ALA* 3.0 11.6 + - - +
11461 GLY* 3.8 15.2 + - - -
11491 LYS* 3.6 15.6 - - + +
11501 SER* 3.3 37.3 - - - +
11531 PHE* 4.1 9.9 - - + -
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Residues in contact with VAL1114 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10781 VAL* 3.7 16.4 - - + -
11101 VAL 2.9 20.7 + - - +
11111 CYS* 2.9 12.1 + - - +
11131 THR* 1.3 74.8 - - - +
11151 ALA* 1.3 59.1 + - - +
11171 ALA* 3.0 5.6 + - - +
11181 ILE* 2.9 36.0 + - + +
11531 PHE* 3.4 29.8 - - + -
11571 TYR* 4.2 11.2 - - + +
144G A 3.6 42.6 - - + +
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Residues in contact with ALA1115 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10661 LEU* 6.3 1.1 - - + -
10781 VAL* 3.9 17.6 - - + +
10811 PHE* 3.8 20.6 - - + -
10821 GLY 6.4 0.2 - - - +
10971 LEU* 3.6 21.1 - - + -
11111 CYS 2.9 12.0 + - - +
11121 THR* 3.1 11.9 + - - +
11141 VAL* 1.3 77.8 - - - +
11161 ILE* 1.3 56.5 + - - +
11181 ILE* 4.6 2.0 - - - +
11191 VAL* 2.9 35.2 + - - +
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Residues in contact with ILE1116 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10941 LEU* 5.3 8.1 - - + +
10971 LEU* 3.6 28.3 - - + +
10981 LEU* 3.9 26.7 - - + -
11121 THR* 2.9 20.2 + - - +
11131 THR* 2.9 19.5 + - - +
11151 ALA* 1.3 75.2 - - - +
11171 ALA* 1.3 58.3 + - - +
11191 VAL* 3.8 3.6 - - - +
11201 ALA* 2.9 30.8 + - + +
11281 VAL* 6.4 1.1 - - + -
11321 LEU* 3.8 26.5 - - + -
11461 GLY 6.0 0.7 - - - +
11471 VAL* 5.7 3.1 - - + -
11501 SER* 4.0 13.9 - - - +
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Residues in contact with ALA1117 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11131 THR 3.0 8.2 + - - +
11141 VAL 3.0 8.9 + - - +
11161 ILE* 1.3 76.9 - - - +
11181 ILE* 1.3 55.7 + - - +
11201 ALA* 2.7 28.8 + - - +
11211 GLU* 2.9 10.8 + - - +
11501 SER 4.8 2.6 + - - +
11531 PHE* 3.9 27.8 - - + -
11541 LEU* 4.1 18.7 - - - +
11571 TYR* 3.9 19.7 - - + +
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Residues in contact with ILE1118 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10781 VAL* 3.6 30.3 - - + +
10791 ASN* 3.9 19.7 - - - +
10821 GLY* 4.0 23.3 - - - +
11141 VAL* 2.9 26.2 + - + +
11151 ALA* 4.3 2.0 - - - +
11171 ALA* 1.3 73.2 - - - +
11191 VAL* 1.3 58.1 + - - +
11211 GLU* 2.9 11.6 + - + +
11221 THR* 2.8 29.3 + - - -
11571 TYR* 4.6 24.9 - - + +
144G A 5.2 2.7 - - - +
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Residues in contact with VAL1119 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10811 PHE* 3.9 27.4 - - + +
10821 GLY* 4.9 2.2 - - - -
10851 ALA* 3.7 23.3 - - + -
10901 PRO* 4.5 13.3 - - + +
10931 VAL* 4.2 18.4 - - + -
10941 LEU* 4.3 20.0 - - + -
10971 LEU* 4.2 2.5 - - + -
11151 ALA* 2.9 26.4 + - - +
11161 ILE* 3.8 5.6 - - - +
11181 ILE* 1.3 75.4 - - + +
11201 ALA* 1.3 63.5 + - - +
11221 THR* 3.1 24.2 + - + +
11231 CYS* 3.6 5.7 + - - +
11281 VAL* 5.0 2.4 - - + +
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Residues in contact with ALA1120 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11161 ILE* 2.9 16.6 + - + +
11171 ALA 2.7 16.9 + - - +
11191 VAL* 1.3 72.7 - - - +
11211 GLU* 1.3 51.9 + - - -
11231 CYS 2.7 18.2 - - - +
11251 PRO* 2.9 23.2 - - + +
11281 VAL* 3.7 31.0 - - + -
11541 LEU* 3.6 25.6 - - + -
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Residues in contact with GLU1121 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11171 ALA 2.9 9.7 + - - +
11181 ILE* 2.9 14.3 + - + +
11201 ALA* 1.3 78.6 - - - +
11221 THR* 1.3 75.0 + - - +
11231 CYS 3.1 9.4 + - - +
11241 SER* 4.0 2.1 + - - -
11251 PRO* 4.8 4.2 - - - +
11541 LEU* 5.3 0.2 - - - +
11571 TYR* 5.2 21.1 - - + +
11581 ILE* 5.5 10.1 - - + -
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Residues in contact with THR1122 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10821 GLY* 3.7 10.0 + - - +
10851 ALA* 3.7 26.5 - - + +
10861 LYS* 3.3 47.9 + - - +
10901 PRO* 5.8 1.3 - - + -
11181 ILE* 2.8 15.4 + - - -
11191 VAL* 3.1 26.5 - - + +
11211 GLU* 1.3 80.6 + - - +
11231 CYS* 1.3 66.9 + - + +
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Residues in contact with CYS1123 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10851 ALA 4.8 2.9 - - - -
10861 LYS* 5.1 9.2 - - - -
10891 GLY* 4.5 8.3 - - - -
10901 PRO* 3.5 36.3 - - + -
11191 VAL 3.6 2.3 - - - +
11201 ALA* 2.7 29.8 - - - +
11211 GLU 3.1 5.3 - - - +
11221 THR* 1.3 87.3 - - - +
11241 SER* 1.3 60.4 + - - +
11271 THR* 5.1 2.9 - - + +
11281 VAL* 4.9 1.0 - - - +
5682 TYR* 6.4 0.2 - - + -
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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