Contacts of the strand formed by residues 742 - 748 (chain A) in PDB entry 1L5G
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 VAL 742 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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740A ALA* 3.0 13.4 + - + +
741A ALA* 1.3 73.1 - - - +
743A GLU* 1.3 67.3 + - - +
782A LEU* 3.5 26.5 - - + -
783A ARG 3.4 14.1 - - - +
784A ASN* 3.3 18.8 - - - +
790A PHE* 3.8 32.8 - - + -
926A PHE* 3.8 23.8 - - + -
928A VAL* 4.0 2.7 - - + -
941A ILE* 3.9 18.6 - - + +
943A ASN* 5.6 2.4 + - - +
1G NAG 5.0 4.2 + - - -
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Residues in contact with GLU 743 (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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741A ALA 5.3 0.2 - - - -
742A VAL* 1.3 77.8 - - - +
744A ILE* 1.3 61.3 + - - +
745A ARG* 4.0 26.6 + - - +
781A GLU 3.6 1.2 - - - +
782A LEU* 3.5 5.9 - - - +
783A ARG* 2.9 40.0 + - + +
785A ASN* 2.8 32.9 + - - +
926A PHE* 4.3 5.6 - - - -
943A ASN* 5.8 2.5 - - - +
590B GLN* 4.0 15.1 - - - +
1G NAG 4.9 10.3 - - - +
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Residues in contact with ILE 744 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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743A GLU* 1.3 76.9 - - - +
745A ARG* 1.3 60.5 + - - +
780A TYR* 4.6 4.7 - - + -
781A GLU 3.2 13.7 - - - +
782A LEU* 4.4 2.9 - - + -
795A LEU* 4.4 15.0 - - + -
924A ALA* 3.5 38.6 - - + +
925A SER 4.2 11.9 - - - +
926A PHE* 3.7 25.3 - - + -
943A ASN* 4.2 3.1 - - + +
944A SER* 3.7 28.3 - - - +
945A THR* 3.4 22.3 + - + +
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Residues in contact with ARG 745 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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743A GLU* 4.0 24.7 + - + +
744A ILE* 1.3 73.8 - - - +
746A GLY* 1.3 65.9 + - - +
780A TYR* 3.6 2.4 - - - -
781A GLU* 2.8 48.9 + - - +
783A ARG* 6.5 0.7 - - + -
945A THR* 4.6 2.2 - - - -
591B PRO 4.9 4.1 + - - -
592B GLY* 3.7 32.4 - - - -
603B THR* 3.7 29.1 + - + +
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Residues in contact with GLY 746 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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744A ILE 4.1 1.6 + - - -
745A ARG* 1.3 85.2 + - - +
747A VAL* 1.3 64.0 + - - +
779A ILE 3.2 9.9 - - - -
780A TYR* 4.0 6.3 - - - -
945A THR* 4.3 6.1 + - - +
946A LEU 5.1 1.6 - - - +
947A VAL* 3.4 22.6 - - - +
603B THR* 4.1 5.0 - - - +
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Residues in contact with VAL 747 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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746A GLY* 1.3 75.7 - - - +
748A SER* 1.3 76.0 + - - +
749A SER* 5.0 1.1 - - - +
751A ASP* 6.1 0.9 - - + -
778A HIS* 3.3 3.3 - - - -
779A ILE* 2.8 49.9 + - + +
947A VAL* 3.4 12.1 - - - +
602B PRO 4.1 3.1 - - - +
603B THR* 3.4 39.5 - - - +
604B CYS 4.4 3.8 - - - +
605B PRO* 4.3 17.5 - - + -
606B ASP 5.5 0.2 - - - +
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Residues in contact with SER 748 (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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747A VAL* 1.3 87.6 - - - +
749A SER* 1.3 69.2 + - - +
750A PRO 3.0 12.8 + - - -
751A ASP* 3.7 15.3 - - - +
776A VAL* 3.7 1.6 - - - +
777A GLN 3.2 9.4 + - - -
778A HIS* 4.1 1.6 - - - -
947A VAL* 3.5 11.9 - - - +
948A THR 3.6 17.0 - - - -
949A THR* 2.5 28.6 + - - -
605B PRO* 5.6 0.2 - - - +
606B ASP* 4.8 4.3 + - - +
1H NAG 5.5 0.2 - - - -
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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