Contacts of the strand formed by residues 752 - 757 (chain A) in PDB entry 3L4U
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 752 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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635A PRO* 4.7 6.7 - - + -
736A PRO* 6.4 0.2 - - + -
737A THR 3.3 15.0 - - - +
738A GLN* 3.6 32.8 - - + +
739A GLN 5.6 0.2 - - - -
750A ASN 4.3 1.6 - - - +
751A PRO* 1.3 74.4 - - - +
753A GLY* 1.3 59.5 + - - +
768A LEU* 4.9 5.6 - - + -
770A TRP* 5.0 8.1 - - + -
811A LEU* 3.9 24.2 - - + -
812A ALA 2.9 19.4 + - - +
813A PHE* 3.5 24.0 - - + -
814A ASN* 2.9 32.8 + - - +
860A LEU* 3.9 29.6 - - + -
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Residues in contact with GLY 753 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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736A PRO* 3.6 4.9 - - - +
737A THR* 2.9 40.9 + - - +
752A LEU* 1.3 76.1 - - - +
754A LEU* 1.3 61.8 + - - -
813A PHE* 3.6 11.1 - - - -
815A GLU* 3.3 16.6 - - - -
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Residues in contact with LEU 754 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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734A ILE* 4.1 16.4 - - + -
735A PHE 3.5 2.0 - - - -
736A PRO* 4.1 9.2 - - + -
737A THR* 5.1 0.2 - - - -
753A GLY* 1.3 82.6 - - - +
755A ILE* 1.3 66.0 + - - +
756A ILE* 4.0 3.4 - - + -
789A PHE* 3.7 42.8 - - + -
796A LEU* 4.1 25.6 - - + -
798A VAL* 4.9 3.6 - - + -
813A PHE* 3.7 26.9 - - + -
815A GLU 3.1 6.5 + - - -
816A ILE* 3.5 20.3 - - + -
817A LYS* 2.9 26.9 + - - +
858A LEU* 5.6 1.1 - - + -
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Residues in contact with ILE 755 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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633A LEU* 4.9 3.4 - - + -
703A TYR* 3.8 32.1 - - + +
729A LEU* 3.6 26.7 - - + -
734A ILE* 3.2 4.4 - - - -
735A PHE* 2.8 44.3 + - + +
737A THR* 3.9 25.4 - - + +
754A LEU* 1.3 77.0 - - - +
756A ILE* 1.3 62.2 + - - +
757A ALA 4.8 0.2 - - - +
817A LYS* 3.4 28.3 - - + +
819A LEU* 3.8 19.5 - - + -
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Residues in contact with ILE 756 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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733A TYR 4.1 2.5 - - - -
734A ILE* 4.0 19.1 - - + -
754A LEU* 4.6 3.6 - - + -
755A ILE* 1.3 73.9 - - - +
757A ALA* 1.3 58.1 + - - +
758A LEU* 3.6 28.3 + - + -
764A ALA* 4.0 8.7 - - + -
791A VAL* 3.8 30.3 - - + -
796A LEU* 4.2 17.7 - - + -
816A ILE* 3.5 29.4 - - + -
817A LYS 2.8 11.3 + - - +
818A ILE* 4.2 16.2 - - + -
819A LEU* 2.8 29.7 + - - +
868A TRP* 5.5 1.3 - - + -
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Residues in contact with ALA 757 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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701A TYR* 3.7 25.1 - - + -
729A LEU* 4.4 2.7 - - + -
730A ARG 3.4 22.2 - - - +
732A GLY* 2.7 24.9 + - - -
733A TYR 2.9 19.2 + - - +
735A PHE* 4.3 10.8 - - + -
755A ILE 3.8 1.4 + - - -
756A ILE* 1.3 70.2 - - - +
758A LEU* 1.3 60.4 + - - +
764A ALA* 3.6 3.3 - - - +
819A LEU* 4.2 11.9 - - + -
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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