Contacts of the strand formed by residues 850 - 855 (chain A) in PDB entry 5ID6
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 ILE 850 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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842A VAL* 3.8 11.4 - - + -
843A VAL 3.4 7.6 - - - +
844A VAL* 4.1 0.4 - - - -
848A GLY 3.5 0.6 + - - -
849A ASN* 1.3 73.4 - - - +
851A VAL* 1.3 64.2 + - - +
852A GLU 3.8 24.0 - - - +
853A GLN* 3.8 12.8 - - + +
1172A ASN 4.6 2.7 - - - +
1173A ALA 3.7 19.7 - - - +
1174A ILE* 3.5 23.5 + - - +
1175A LEU* 3.4 35.0 - - - +
1176A PRO* 3.5 8.7 - - + -
1185A TYR* 3.5 37.2 - - + -
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Residues in contact with VAL 851 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
827A TYR* 3.6 28.5 - - + +
843A VAL* 2.7 16.6 + - + +
845A ASP* 4.1 13.7 - - + +
849A ASN* 3.9 9.9 - - + +
850A ILE* 1.3 78.5 - - - +
852A GLU* 1.3 57.7 + - - +
918A TYR* 3.6 36.3 - - + +
1172A ASN* 3.3 21.3 + - - +
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Residues in contact with GLU 852 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
841A ILE 3.9 0.6 - - - +
842A VAL* 3.3 3.5 - - - -
843A VAL* 2.7 47.5 + - + +
850A ILE* 3.8 3.7 - - - +
851A VAL* 1.3 82.8 - - - +
853A GLN* 1.3 59.9 + - - +
854A TYR* 3.2 31.0 + - + -
914A LEU* 4.1 5.5 - - - +
917A LYS* 2.8 22.6 + - - -
918A TYR* 2.4 34.7 + - - +
1172A ASN* 3.2 24.7 + - - +
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Residues in contact with GLN 853 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
840A TYR* 4.1 7.4 - - + -
841A ILE 3.4 9.4 - - - +
842A VAL* 4.3 7.0 - - + -
850A ILE* 3.8 12.7 - - + +
852A GLU* 1.3 74.4 - - - +
854A TYR* 1.3 67.4 + - - +
1171A GLU 4.4 0.2 - - - +
1172A ASN* 3.3 23.0 + - - +
1173A ALA* 3.4 28.5 + - - +
1175A LEU 2.8 26.2 + - - -
1176A PRO* 3.4 6.7 - - - +
1177A LYS* 2.9 51.6 + - - +
1181A ALA* 3.5 9.2 - - - +
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Residues in contact with TYR 854 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
840A TYR* 3.4 14.2 - - - -
841A ILE* 3.1 39.4 + - + +
843A VAL* 6.1 0.2 - - + -
852A GLU* 3.2 32.6 + - + -
853A GLN* 1.3 83.7 - - - +
855A SER* 1.3 75.7 + - - +
856A LEU* 3.7 24.7 + - + +
910A LYS* 5.4 2.6 + - - +
914A LEU* 3.4 33.6 - - + +
1172A ASN* 4.8 2.7 - - - -
1177A LYS* 4.7 3.8 - - - +
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Residues in contact with SER 855 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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837A ASN* 2.7 30.8 + - - +
839A LEU 3.9 0.4 - - - -
840A TYR* 3.3 20.0 + - - -
854A TYR* 1.3 89.1 - - - +
856A LEU* 1.3 60.1 + - - +
857A ASN* 2.9 27.7 + - - +
858A GLU* 4.7 8.1 + - - +
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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