Contacts of the strand formed by residues 679 - 684 (chain A) in PDB entry 1L4Z
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 GLU 679 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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560A GLY* 5.7 0.3 - - - -
677A ARG 3.2 16.7 + - - +
678A THR* 1.3 78.8 - - - +
680A CYS* 1.3 63.0 + - - +
681A PHE* 5.2 5.7 - - + -
701A GLN* 2.9 42.2 - - - +
702A LEU 4.1 0.7 - - - -
703A PRO* 3.3 24.1 - - - +
729A HIS* 5.1 3.2 - - - -
747A CYS* 4.1 6.9 - - - +
748A PHE* 4.4 7.3 + - - +
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Residues in contact with CYS 680 (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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678A THR* 3.6 2.5 - - - -
679A GLU* 1.3 75.0 - - - +
681A PHE* 1.3 74.1 + - - +
701A GLN* 3.4 5.5 - - - +
702A LEU* 2.8 35.4 + - - +
704A VAL* 3.5 28.3 - - + -
745A LEU* 3.6 16.8 - - + -
746A VAL 3.1 6.7 - - - +
747A CYS* 2.0 48.7 - - - +
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Residues in contact with PHE 681 (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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557A LYS* 3.7 43.5 - - + -
558A CYS 3.5 11.0 - - - -
573A TRP* 4.0 29.6 - + + -
679A GLU* 5.2 4.3 - - + -
680A CYS* 1.3 81.8 - - - +
682A ILE* 1.3 65.0 + - - +
683A THR* 4.8 1.3 - - + -
699A GLU* 4.1 9.0 - - + -
700A ALA 3.2 21.1 - - - -
701A GLN* 3.1 44.9 - - + -
702A LEU 4.7 0.7 - - - +
744A PRO 4.1 0.2 - - - +
745A LEU* 3.2 6.9 - - - +
746A VAL* 2.8 38.7 + - + +
748A PHE* 6.0 0.9 - - + -
753A TYR* 4.4 13.9 - + - -
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Residues in contact with ILE 682 (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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681A PHE* 1.3 72.9 - - - +
683A THR* 1.3 68.8 + - - +
699A GLU* 3.3 0.7 - - - +
700A ALA* 3.0 38.9 + - + +
702A LEU* 4.0 19.7 - - + -
736A SER* 4.3 13.5 - - - +
738A GLN* 3.8 21.9 - - + +
739A GLY* 4.1 17.9 - - - +
744A PRO 3.7 7.2 - - - +
745A LEU* 3.7 18.8 - - + -
759A THR* 4.5 3.4 - - - +
774A TYR* 3.5 36.1 - - + +
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Residues in contact with THR 683 (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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573A TRP* 3.5 54.7 - - + +
575A TRP* 5.4 0.9 + - - +
576A GLN* 2.7 26.4 + - - +
681A PHE* 4.8 2.9 - - + -
682A ILE* 1.3 82.4 - - - +
684A GLY* 1.3 60.1 + - - +
697A LEU* 4.5 2.7 - - - -
698A LYS 3.2 10.3 - - - -
699A GLU* 3.9 6.3 - - + -
738A GLN 4.2 0.7 - - - -
739A GLY* 3.5 15.3 - - - +
740A ASP 4.3 1.0 + - - -
743A GLY* 4.6 0.2 - - - -
744A PRO* 3.5 28.7 + - - +
746A VAL* 5.7 2.0 - - + -
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Residues in contact with GLY 684 (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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576A GLN* 3.9 5.2 - - - -
683A THR* 1.3 76.8 - - - +
685A TRP* 1.3 63.1 + - - -
697A LEU* 3.6 13.2 - - - +
698A LYS* 3.1 33.5 + - - +
738A GLN 2.9 15.6 + - - +
739A GLY* 4.0 0.9 - - - -
740A ASP* 3.2 12.6 - - - -
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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