Contacts of the strand formed by residues 722 - 728 (chain D) in PDB entry 1UES
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 GLY 722 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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718D LEU* 3.9 7.0 - - - -
721D SER* 1.3 78.7 - - - +
723D TRP* 1.3 67.6 + - - -
739D GLU 3.1 13.0 - - - -
741D ASN 3.5 9.2 - - - -
758D VAL* 2.9 33.6 + - - +
759D TRP* 3.3 13.1 - - - -
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Residues in contact with TRP 723 (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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670D GLN* 2.9 24.0 + - - -
673D ASN* 3.3 36.5 - - + +
674D HIS* 3.3 39.0 - + - -
677D TYR* 4.0 19.7 - - + -
718D LEU* 3.4 8.5 - - - +
722D GLY* 1.3 73.6 - - - -
724D VAL* 1.3 60.9 + - - +
725D TRP* 3.9 11.9 - - + -
739D GLU* 2.7 45.0 + - + +
741D ASN 3.0 21.4 + - - -
743D GLY 4.0 2.9 - - - -
755D THR* 3.3 25.8 - - + +
756D PHE 3.4 6.5 - - - -
757D ASP* 3.3 47.1 - - + -
758D VAL* 4.4 1.1 - - - -
759D TRP* 3.5 4.2 - - - +
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Residues in contact with VAL 724 (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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711D PHE* 3.5 37.7 - - + +
714D ALA* 3.7 26.7 - - + +
715D GLY* 3.9 26.5 - - - +
718D LEU* 4.7 0.4 - - + +
723D TRP* 1.3 74.6 - - - +
725D TRP* 1.3 62.1 + - - +
736D ILE* 3.9 5.4 - - + -
737D GLU 3.5 5.2 - - - +
738D LYS* 4.7 1.6 - - + +
755D THR* 2.9 18.1 + - - -
756D PHE* 3.0 43.8 + - + +
758D VAL* 4.7 2.8 - - + +
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Residues in contact with TRP 725 (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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673D ASN* 3.0 32.9 + - - -
676D LEU* 3.6 30.7 - - + -
711D PHE* 3.5 6.6 - - - -
723D TRP* 3.9 7.9 - - + +
724D VAL* 1.3 74.1 - - - +
726D LEU* 1.3 68.6 + - - +
735D SER 3.4 0.9 - - - +
736D ILE* 3.2 5.9 - - - -
737D GLU* 2.7 46.7 + - + +
739D GLU* 3.7 19.1 - - + -
743D GLY 3.8 2.6 + - - -
744D ASN* 3.6 7.9 - - - -
745D PRO* 3.4 32.2 - - + +
752D PRO* 3.3 28.9 - - + -
753D LEU 4.1 1.8 - - - -
754D LEU* 3.2 27.6 - - - -
755D THR* 3.3 40.6 + - + -
790D ARG* 5.0 0.2 - - - -
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Residues in contact with LEU 726 (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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693D LEU* 4.8 6.5 - - + -
697D ILE* 4.7 14.8 - - + -
701D PHE* 4.7 3.1 - - + -
707D PHE* 3.9 30.1 - - + -
711D PHE* 3.5 16.1 - - + -
725D TRP* 1.3 76.6 - - - +
727D ALA* 1.3 64.4 + - - +
734D LEU* 4.0 25.4 - - + -
735D SER 3.4 12.3 - - - +
736D ILE* 4.8 0.4 - - + -
753D LEU* 2.9 47.5 + - + +
754D LEU* 2.9 27.1 + - + +
784D TRP* 4.9 5.8 - - + -
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Residues in contact with ALA 727 (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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726D LEU* 1.3 75.3 - - - +
728D SER* 1.3 61.1 + - - +
734D LEU* 3.3 6.6 - - - +
735D SER* 2.9 37.4 + - - +
737D GLU* 4.6 3.8 - - + -
745D PRO* 3.6 30.7 - - + -
750D LEU* 3.9 16.6 - - + -
751D ASN 3.1 15.0 - - - +
753D LEU* 4.1 5.2 - - - -
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Residues in contact with SER 728 (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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727D ALA* 1.3 75.4 - - - +
729D ASP* 1.3 68.1 + - - +
732D GLY* 4.3 1.3 - - - -
733D LYS 3.1 9.6 - - - -
734D LEU* 4.0 1.6 - - - -
750D LEU* 3.6 7.0 - - - -
751D ASN* 2.9 50.5 + - - +
753D LEU* 4.0 6.1 - - - +
791D TYR* 3.7 36.8 + - - -
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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