Contacts of the strand formed by residues 621 - 624 (chain E) in PDB entry 4P6X
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 LEU 621 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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608E LEU* 4.5 6.7 - - + -
612E SER* 3.4 16.4 - - - +
616E SER* 5.9 0.4 - - - -
620E LEU* 1.3 91.1 - - - +
622E TYR* 1.3 61.3 + - - +
623E PHE* 3.6 14.6 + - + -
628E ILE* 3.7 6.5 - - - +
629E ILE* 3.1 37.3 + - + +
634E MET* 4.7 4.5 - - - -
643E CYS* 3.5 48.9 - - + +
646E MET* 3.9 17.5 - - + +
647E LEU* 3.6 31.6 - - + +
650E SER* 4.9 0.7 - - - -
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Residues in contact with TYR 622 (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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543E VAL* 5.9 1.1 - - + -
608E LEU* 3.5 4.9 - - - +
611E ARG* 2.7 62.6 + - + +
612E SER* 3.0 11.2 + - - +
615E GLN* 3.0 47.7 - - + +
616E SER* 4.6 12.8 - - - -
621E LEU* 1.3 71.3 - - - +
623E PHE* 1.3 52.8 + - - +
624E ALA* 3.3 20.2 - - - +
625E PRO* 3.9 24.1 + - + +
627E LEU 4.6 1.6 - - - -
628E ILE* 3.3 33.5 - - + +
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Residues in contact with PHE 623 (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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543E VAL* 5.0 1.0 - - - +
544E LEU 4.5 1.7 - - - +
563E LEU* 3.3 43.1 - - + -
566E LEU* 3.5 22.8 - - + +
570E GLN* 3.5 12.1 + - - -
608E LEU* 3.7 22.7 - - + -
611E ARG* 3.5 11.8 + - - +
621E LEU* 3.6 14.2 + - + -
622E TYR* 1.3 72.7 - - - +
624E ALA* 1.3 63.0 + - - +
627E LEU* 3.5 13.9 + - + +
629E ILE* 3.3 37.0 - - + -
639E MET* 4.6 2.0 - - + -
643E CYS* 4.7 2.5 - - - -
646E MET* 3.8 23.1 - - - -
900E HCY 3.3 33.7 - + + -
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Residues in contact with ALA 624 (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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543E VAL* 4.5 3.6 - - - -
544E LEU 3.1 23.8 - - - +
546E ALA* 3.6 17.7 - - + +
566E LEU* 4.2 3.1 - - + -
622E TYR* 3.3 10.6 - - - -
623E PHE* 1.3 77.2 - - - +
625E PRO* 1.3 71.8 - - + +
626E ASP* 3.1 14.8 - - - +
627E LEU* 2.9 18.4 + - + +
628E ILE* 3.2 10.2 - - - +
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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