Contacts of the strand formed by residues 898 - 902 (chain E) in PDB entry 6C3P
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 TRP 898 (chain E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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702E ARG* 3.2 35.8 + - + +
704E PRO* 4.4 25.6 - - + -
707E GLN* 5.2 3.4 - - + +
708E LEU 3.2 3.5 + - - +
709E THR* 2.8 48.5 + - + +
710E MET 3.0 4.5 + - - -
896E ALA* 3.8 2.1 - - - +
897E ASP* 1.3 80.6 - - + +
899E ILE* 1.3 83.9 + - - +
900E ILE* 3.5 17.4 - - + +
910E GLU* 3.4 21.0 - - + +
911E GLY* 3.8 24.5 - - - -
912E THR 4.9 1.6 - - - +
915E ASP* 4.9 4.3 - - - -
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Residues in contact with ILE 899 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
710E MET* 3.4 11.7 - - + +
712E VAL* 4.8 8.1 - - + -
893E LEU* 3.5 48.5 - - + +
896E ALA* 4.0 8.5 - - + +
897E ASP 5.0 0.4 - - - +
898E TRP* 1.3 89.2 + - - +
900E ILE* 1.3 74.8 + - - +
901E ALA* 4.7 3.8 - - + +
909E ARG 6.3 0.2 - - - -
910E GLU* 3.1 30.4 - - - +
911E GLY 4.3 11.3 - - - +
912E THR* 4.1 30.3 - - - +
916E PHE* 6.1 1.1 - - + -
926E HIS* 6.2 2.5 - - + -
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Residues in contact with ILE 900 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
701E ILE* 4.8 16.8 - - + -
702E ARG 4.9 2.0 - - - +
703E ILE* 4.8 9.2 - - + -
709E THR* 3.1 30.5 - - + +
710E MET 2.7 13.6 + - - +
711E ILE* 3.2 24.1 - - + +
712E VAL* 3.1 28.2 + - - +
722E LEU* 5.2 0.4 - - + -
898E TRP* 3.5 18.4 - - + +
899E ILE* 1.3 78.7 - - - +
901E ALA* 1.3 63.2 + - - +
902E MET* 3.7 26.9 - - + -
907E ILE* 4.1 15.3 - - + -
909E ARG 3.7 5.2 - - - +
910E GLU* 4.9 2.9 - - + -
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Residues in contact with ALA 901 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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712E VAL* 3.8 14.6 - - + +
899E ILE* 4.7 4.0 - - + +
900E ILE* 1.3 74.4 - - - +
902E MET* 1.3 54.5 + - - +
907E ILE* 3.3 4.9 - - - +
908E GLN* 2.4 37.4 + - + -
909E ARG* 3.0 32.6 + - + +
922E GLN* 4.8 8.1 - - - +
926E HIS* 5.9 5.4 - - + +
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Residues in contact with MET 902 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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696E LEU* 5.6 2.9 - - - -
699E ILE* 6.4 0.7 - - - -
711E ILE* 3.6 22.4 - - + -
712E VAL 3.3 8.5 + - - +
713E GLY* 3.2 26.4 - - - -
717E CYS* 3.8 15.1 - - + +
718E GLY 3.2 28.5 - - - +
719E LYS* 3.6 9.6 - - - +
722E LEU* 3.6 31.4 - - + -
900E ILE* 3.7 15.3 - - + -
901E ALA* 1.3 73.2 - - - +
903E LYS* 1.3 62.7 + - - +
906E THR 3.2 22.0 - - - +
907E ILE* 3.6 10.3 - - + -
908E GLN* 3.8 5.6 - - - +
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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
------------------------------------------------------------
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