Contacts of the helix formed by residues 1110 - 1123 (chain 1) in PDB entry 6AH0
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 VAL1110 (chain 1).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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11081 ASN 3.3 3.3 - - - -
11091 ARG* 1.3 79.8 - - - +
11111 CYS* 1.3 60.0 + - - +
11121 THR 3.0 2.2 - - - -
11131 THR* 2.4 31.8 + - - +
11141 VAL 2.9 8.3 + - - -
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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
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11101 VAL* 1.3 73.4 - - - +
11121 THR* 1.3 62.8 + - - +
11141 VAL* 2.8 15.1 + - - +
11151 ALA* 2.9 9.5 + - - -
144G A 6.2 4.0 - - - -
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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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10971 LEU* 6.6 0.2 - - - +
11081 ASN* 5.1 12.2 - - - +
11101 VAL* 2.8 3.6 + - - +
11111 CYS* 1.3 71.9 - - - +
11131 THR* 1.3 66.8 + - - +
11151 ALA* 2.7 14.1 + - - +
11161 ILE* 2.9 9.4 + - - -
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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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11081 ASN 5.6 1.4 + - - -
11101 VAL* 2.4 19.1 + - - +
11121 THR* 1.3 69.8 - - - +
11141 VAL* 1.3 52.2 + - - +
11161 ILE* 2.6 25.0 + - - +
11171 ALA* 2.9 10.0 + - - -
11461 GLY 5.8 2.5 - - - -
11501 SER* 5.0 15.5 - - - +
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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* 6.4 0.4 - - - -
11101 VAL 2.9 6.8 + - - -
11111 CYS* 2.8 11.1 + - - +
11131 THR* 1.3 73.6 - - - +
11151 ALA* 1.3 62.8 + - - +
11171 ALA* 3.2 2.8 + - - +
11181 ILE* 3.0 20.3 + - - -
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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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10781 VAL* 5.9 7.7 - - - +
11111 CYS 2.9 7.4 + - - -
11121 THR* 2.7 16.3 + - - +
11141 VAL* 1.3 67.8 - - - +
11161 ILE* 1.3 65.9 + - - +
11171 ALA 2.8 1.2 + - - -
11181 ILE* 3.0 1.5 + - - +
11191 VAL* 2.9 24.7 + - - +
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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* 6.1 5.4 - - - +
11121 THR 2.9 8.0 + - - -
11131 THR* 2.6 14.5 + - - +
11151 ALA* 1.3 69.2 - - - +
11171 ALA* 1.3 62.7 + - - +
11191 VAL* 4.1 0.8 - - - +
11201 ALA* 2.9 17.3 + - - -
11501 SER* 5.8 2.9 - - - +
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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 2.9 11.2 + - - -
11141 VAL* 3.2 4.0 + - - +
11151 ALA 2.8 1.2 + - - -
11161 ILE* 1.3 74.9 - - - +
11181 ILE* 1.3 54.8 + - - +
11201 ALA* 2.6 25.7 + - - +
11211 GLU 2.9 8.7 + - - -
11501 SER* 5.0 6.2 + - - +
11531 PHE* 5.3 2.7 - - - +
11541 LEU* 4.7 21.0 - - - +
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Residues in contact with ILE1118 (chain 1).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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10821 GLY* 5.5 5.2 - - - -
11141 VAL 3.0 15.7 + - - -
11151 ALA* 3.8 0.7 - - - +
11171 ALA* 1.3 69.1 - - - +
11191 VAL* 1.3 65.5 + - - +
11211 GLU* 2.9 12.9 + - - +
11221 THR* 3.0 9.5 + - - -
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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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10821 GLY* 5.2 11.8 - - - -
10851 ALA* 6.4 1.8 - - - +
11151 ALA* 2.9 14.8 + - - +
11161 ILE* 4.1 0.7 - - - +
11181 ILE* 1.3 72.8 - - - +
11201 ALA* 1.3 54.5 + - - +
11211 GLU 3.1 0.3 - - - -
11221 THR* 2.5 29.3 + - - +
11231 CYS 3.6 5.2 + - - +
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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 13.8 + - - -
11171 ALA* 2.6 14.7 + - - +
11191 VAL* 1.3 67.6 - - - +
11211 GLU* 1.3 56.9 + - - +
11231 CYS 2.7 18.2 - - - +
11251 PRO* 3.2 23.2 - - - +
11281 VAL* 6.4 1.6 - - - +
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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 6.1 + - - -
11181 ILE* 2.9 10.5 + - - +
11191 VAL 2.7 3.6 + - - -
11201 ALA* 1.3 76.4 - - - +
11221 THR* 1.3 52.1 + - - +
11231 CYS* 2.5 27.6 + - - +
11241 SER* 4.3 1.7 - - - -
11251 PRO 4.5 1.0 - - - -
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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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10851 ALA 6.4 0.7 - - - -
10861 LYS* 5.0 12.6 - - - +
11181 ILE 3.0 8.4 + - - -
11191 VAL* 2.5 16.8 + - - +
11211 GLU* 1.3 69.5 - - - +
11231 CYS* 1.3 54.1 + - - -
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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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11191 VAL 3.6 4.9 + - - +
11201 ALA* 2.7 11.3 - - - +
11211 GLU 2.5 18.1 - - - +
11221 THR* 1.3 73.2 - - - +
11241 SER* 1.3 67.7 + - - +
11251 PRO* 3.8 0.3 - - - +
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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