Contacts of the strand formed by residues 1016 - 1020 (chain B) in PDB entry 6AHU
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 ARG1016 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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20A A 2.4 53.7 + - - -
21A U 4.2 7.1 + - - -
863B LEU* 4.6 11.4 - - + -
866B LYS* 2.4 55.4 + - - +
867B GLY* 3.8 13.0 - - - -
868B SER 4.7 2.9 - - - +
893B CYS* 5.0 5.7 - - - +
894B GLY 5.5 0.9 - - - +
1006B LEU* 3.5 3.8 - - - -
1007B LEU* 2.5 57.9 + - + +
1009B PRO* 5.6 7.7 - - - +
1014B GLN* 3.9 20.5 + - + +
1015B TYR* 1.3 78.8 - - - +
1017B PHE* 1.3 59.4 + - - +
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Residues in contact with PHE1017 (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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863B LEU* 3.4 12.6 - - - +
864B LEU* 3.7 54.1 + - + -
865B SER* 5.0 12.9 + - - +
886B LEU* 3.7 30.5 - - + -
891B HIS* 6.1 2.0 - - - -
892B TYR 3.5 27.4 - - - -
893B CYS* 5.3 0.9 - - - -
894B GLY* 5.2 6.1 - - - -
1004B LEU* 4.0 28.5 - - + -
1005B VAL 3.7 6.7 - - - +
1006B LEU* 3.5 20.4 - - + +
1016B ARG* 1.3 75.3 - - - +
1018B ALA* 1.3 63.1 + - - +
1019B ARG* 5.8 1.8 - - - -
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Residues in contact with ALA1018 (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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861B LEU* 3.7 29.4 - - + -
862B SER 3.3 21.1 - - - +
863B LEU* 3.7 14.4 - - + +
864B LEU 4.8 0.7 - - - +
1003B GLY 2.9 14.6 - - - +
1004B LEU* 3.3 8.0 - - - +
1005B VAL 3.1 17.0 + - - +
1007B LEU* 4.0 3.8 - - + -
1017B PHE* 1.3 76.6 - - - +
1019B ARG* 1.3 66.0 + - - +
1020B ILE* 4.0 1.3 - - + -
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Residues in contact with ARG1019 (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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820B GLY 5.2 3.2 + - - -
822B SER* 2.8 30.5 + - - -
860B SER 4.1 0.2 - - - +
861B LEU* 3.4 5.1 - - - -
862B SER* 2.7 42.3 + - - +
864B LEU* 5.4 20.9 - - + +
1001B GLN* 4.7 11.1 - - - +
1003B GLY* 3.4 4.5 - - - +
1004B LEU* 4.4 25.5 - - - +
1017B PHE* 5.8 1.6 - - + -
1018B ALA* 1.3 80.6 - - - +
1020B ILE* 1.3 65.6 + - - +
1021B ALA* 3.4 5.6 + - + +
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Residues in contact with ILE1020 (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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819B CYS* 3.2 32.1 - - + +
859B VAL* 3.7 28.5 - - + -
860B SER 4.1 3.6 - - - -
861B LEU* 4.4 12.6 - - + -
875B ILE* 5.0 8.1 - - + -
964B LEU* 6.2 2.7 - - + -
985B VAL* 5.7 3.8 - - + -
990B LEU* 4.6 16.2 - - + -
1003B GLY* 2.9 26.3 + - - +
1005B VAL* 3.7 36.1 - - + +
1018B ALA* 5.6 0.9 - - + +
1019B ARG* 1.3 72.1 + - - +
1021B ALA* 1.3 62.7 + - - +
1022B ILE* 4.0 17.5 - - + -
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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