Contacts of the strand formed by residues 754 - 763 (chain D) in PDB entry 4X52
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 PHE 754 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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747D PHE* 4.3 11.5 - - + -
748D LYS* 5.5 5.2 - - - +
751D MET* 3.6 48.1 - - + +
752D LYS 3.1 6.2 + - - +
753D ASN* 1.3 91.0 - - + +
755D LYS* 1.3 60.6 + - - +
756D ILE 4.4 0.5 + - - -
825D ILE* 3.8 18.8 - - + -
828D HIS* 3.4 41.5 - + - -
893D TYR* 3.7 20.0 - + + -
894D THR 3.3 5.4 - - - +
895D GLU* 3.7 31.4 - - + -
896D ASP* 3.5 7.5 + - - +
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Residues in contact with LYS 755 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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754D PHE* 1.3 73.1 - - - +
756D ILE* 1.3 72.3 + - - +
757D GLU* 3.3 33.5 + - - +
893D TYR* 3.2 6.3 - - - -
894D THR* 2.8 41.3 + - - +
895D GLU 5.9 0.2 - - - -
896D ASP* 3.8 14.8 + - - +
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Residues in contact with ILE 756 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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740D TYR* 3.5 25.0 + - - +
744D SER* 3.4 41.1 - - - +
747D PHE* 3.6 36.8 - - + -
748D LYS* 4.4 6.5 - - + -
754D PHE 4.3 0.8 + - - +
755D LYS* 1.3 85.0 - - - +
757D GLU* 1.3 62.7 + - - +
758D LYS 3.7 10.8 - - - +
759D ILE* 3.7 24.5 - - + -
891D ILE* 4.0 8.5 - - + -
892D GLU 3.6 5.2 - - - +
893D TYR* 4.2 1.1 - - - -
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Residues in contact with GLU 757 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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729A LYS* 5.9 1.0 + - - +
732D GLU* 4.8 1.6 - - - +
740D TYR* 5.0 2.7 + - - -
755D LYS* 3.3 33.2 + - - +
756D ILE* 1.3 74.5 - - - +
758D LYS* 1.3 68.7 + - + +
892D GLU* 2.7 22.9 + - + +
893D TYR* 4.1 16.2 - - - +
894D THR* 2.7 35.9 + - + +
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Residues in contact with LYS 758 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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728A TYR 5.5 1.6 + - - -
729A LYS* 3.6 17.4 - - - +
732D GLU* 2.8 40.0 + - - +
740D TYR* 4.7 3.8 - - - -
756D ILE* 3.6 3.5 - - - +
757D GLU* 1.3 87.3 - - + +
759D ILE* 1.3 68.3 + - - +
760D LYS* 3.9 24.7 - - + +
890D VAL 3.9 0.6 - - - +
891D ILE* 3.5 3.1 - - - -
892D GLU* 2.9 57.8 + - + +
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Residues in contact with ILE 759 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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732D GLU* 3.6 5.5 + - - +
733D ILE* 3.0 31.0 + - + +
740D TYR* 3.7 61.4 - - + +
743D VAL* 3.9 25.8 - - + -
744D SER* 3.9 9.0 - - - +
756D ILE* 3.7 17.9 - - + -
758D LYS* 1.3 79.2 - - - +
760D LYS* 1.3 64.5 + - - +
889D TYR* 4.1 26.5 - - + -
890D VAL 3.5 6.7 - - - +
891D ILE* 4.3 7.9 - - + -
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Residues in contact with LYS 760 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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730D LEU* 3.7 42.2 - - + +
731D SER 3.4 6.3 - - - +
732D GLU* 4.0 22.2 - - + +
733D ILE* 4.7 0.2 - - - -
758D LYS* 3.9 31.2 - - + +
759D ILE* 1.3 80.7 - - - +
761D LYS* 1.3 61.1 + - - +
889D TYR* 3.1 10.8 - - - +
890D VAL* 2.9 41.3 + - + +
892D GLU* 4.7 11.0 + - + -
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Residues in contact with LYS 761 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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732A GLU* 4.9 7.7 + - - +
758A LYS* 5.7 3.7 - - - +
729D LYS 3.7 0.5 - - - +
730D LEU* 3.4 6.5 - - - -
731D SER* 2.8 34.6 + - - +
733D ILE* 3.7 29.2 - - + +
737D HIS* 6.4 0.2 - - - +
739D GLU* 3.0 38.2 + - - +
760D LYS* 1.3 71.9 - - - +
762D ILE* 1.3 71.4 + - - +
763D GLU* 3.9 2.3 + - + +
888D GLN* 3.7 11.9 - - - +
889D TYR* 3.9 14.1 - - + -
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Residues in contact with ILE 762 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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728D TYR* 4.9 0.7 - - + -
729D LYS 3.6 6.1 - - - +
730D LEU* 3.6 20.0 - - + -
761D LYS* 1.3 80.6 - - - +
763D GLU* 1.3 70.1 + - - +
764D ASN* 4.5 2.7 - - + +
798D CYS* 3.8 30.7 - - + +
841D PHE* 3.6 32.5 - - + -
886D TYR* 2.9 19.0 + - + +
887D PRO* 3.5 38.6 - - + +
888D GLN* 2.9 13.5 + - - +
889D TYR* 3.8 9.6 - - - +
890D VAL* 3.7 8.7 - - + -
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Residues in contact with GLU 763 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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758A LYS* 4.2 23.4 + - - -
728D TYR* 3.1 6.9 - - - +
729D LYS* 2.8 73.1 + - + +
761D LYS* 3.9 2.2 + - + +
762D ILE* 1.3 74.9 - - - +
764D ASN* 1.3 59.7 + - - +
765D SER* 4.1 5.6 - - - +
768D LEU* 6.5 0.7 - - + -
886D TYR* 3.6 2.2 - - - +
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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