Contacts of the strand formed by residues 734 - 740 (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 LEU 734 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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693D LEU* 4.0 5.8 - - + -
696D ALA* 3.6 38.6 - - + +
697D ILE* 3.7 20.2 - - + +
700D GLN* 2.5 22.9 + - - +
701D PHE* 3.9 22.2 - - + -
726D LEU* 4.0 8.5 - - + -
727D ALA 3.3 3.6 - - - +
728D SER* 4.0 3.8 - - - -
732D GLY 4.0 4.0 - - - +
733D LYS* 1.3 79.6 - - - +
735D SER* 1.3 64.8 + - - +
753D LEU* 3.8 22.4 - - + -
791D TYR* 3.7 28.0 - - + -
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Residues in contact with SER 735 (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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701D PHE* 4.8 2.7 - - - -
725D TRP 3.4 1.2 - - - +
726D LEU* 3.4 6.5 - - - +
727D ALA* 2.9 37.3 + - - +
733D LYS* 5.1 4.1 + - - -
734D LEU* 1.3 78.1 - - - +
736D ILE* 1.3 63.8 + - - +
737D GLU* 2.7 29.5 + - - +
750D LEU* 4.0 11.8 - - - +
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Residues in contact with ILE 736 (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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701D PHE* 3.7 26.6 - - + -
707D PHE* 4.0 14.1 - - + -
710D GLU* 3.7 32.5 - - + +
711D PHE* 3.8 21.1 - - + +
714D ALA* 3.7 29.4 - - + -
724D VAL* 3.9 13.2 - - + -
725D TRP 3.2 3.6 - - - +
726D LEU* 4.8 0.7 - - + -
735D SER* 1.3 77.0 - - - +
737D GLU* 1.3 67.0 + - - +
738D LYS* 4.3 1.2 + - + +
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Residues in contact with GLU 737 (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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723D TRP 3.7 0.2 - - - +
724D VAL* 3.5 2.8 - - - +
725D TRP* 2.7 50.7 + - + +
727D ALA* 4.6 7.6 - - + -
735D SER* 2.7 32.0 + - - +
736D ILE* 1.3 78.8 - - - +
738D LYS* 1.3 62.1 + - - +
739D GLU* 3.7 21.4 + - - +
745D PRO* 4.9 2.7 - - + -
748D LYS* 3.5 27.2 + - - -
750D LEU* 3.6 21.3 - - + +
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Residues in contact with LYS 738 (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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714D ALA* 3.3 49.4 - - + +
717D THR* 3.8 21.7 - - - +
718D LEU* 4.2 20.2 - - + +
723D TRP 3.7 4.3 - - - -
724D VAL* 4.7 0.7 - - + +
736D ILE* 4.3 1.5 + - + -
737D GLU* 1.3 72.5 - - - +
739D GLU* 1.3 65.4 + - - +
740D PRO* 3.6 9.9 - - + +
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Residues in contact with GLU 739 (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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718D LEU* 3.8 3.5 - - - +
722D GLY* 3.1 0.3 - - - -
723D TRP* 2.7 44.8 + - + +
725D TRP* 3.7 25.1 - - + -
737D GLU* 3.8 22.0 - - + +
738D LYS* 1.3 79.5 - - - +
740D PRO* 1.3 70.7 - - - +
743D GLY* 3.4 30.4 - - - +
744D ASN 3.5 25.0 + - - +
745D PRO* 3.7 5.5 - - - +
748D LYS* 5.4 7.3 + - - +
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Residues in contact with PRO 740 (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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541C ASN* 6.1 2.2 - - - +
718D LEU* 4.5 10.8 - - + -
719D PHE 5.6 2.5 - - - +
721D SER 3.5 9.6 - - - +
722D GLY* 4.0 0.4 - - - -
738D LYS* 3.6 10.5 - - + +
739D GLU* 1.3 88.1 - - - +
741D ASN* 1.3 72.9 + - - +
742D ALA 3.1 1.0 + - - -
743D GLY* 3.0 15.6 + - - -
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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
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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