Contacts of the strand formed by residues 777 - 784 (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 GLN 777 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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748A SER* 3.2 5.7 + - - -
749A SER* 2.7 45.4 + - - -
750A PRO* 3.7 4.4 - - - +
775A VAL* 3.6 15.0 + - + +
776A VAL* 1.3 74.7 - - - +
778A HIS* 1.3 64.8 + - - +
779A ILE* 3.4 28.8 - - + +
898A TYR* 4.6 9.4 - - - +
899A VAL 3.3 17.9 - - - +
900A LYS* 4.6 11.2 - - - +
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Residues in contact with HIS 778 (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 3.3 3.6 - - - +
748A SER* 3.9 2.2 - - - -
776A VAL* 3.6 12.0 - - + +
777A GLN* 1.3 79.4 + - - +
779A ILE* 1.3 66.1 + - - +
780A TYR* 4.3 7.4 - - + -
799A TRP* 3.7 27.8 - + + -
809A LEU* 4.3 6.1 - - + +
899A VAL* 2.9 42.9 + - + +
920A LEU 4.6 2.8 + - - -
922A SER* 3.0 33.5 + - - -
947A VAL* 3.2 36.1 + - + +
949A THR* 3.1 28.8 + - - -
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Residues in contact with ILE 779 (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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745A ARG 4.0 0.2 - - - +
746A GLY* 3.2 5.7 - - - -
747A VAL* 2.8 50.4 + - + +
749A SER* 6.0 1.8 - - - +
777A GLN* 3.4 31.4 - - + +
778A HIS* 1.3 81.3 - - - +
780A TYR* 1.3 65.0 + - - +
781A GLU 4.2 0.2 - - - -
896A ILE* 3.5 25.6 - - + -
897A LEU 3.5 0.9 - - - -
898A TYR* 3.4 28.5 - - + -
947A VAL* 4.8 0.3 - - - +
602B PRO* 3.9 26.0 - - + +
603B THR* 4.3 5.4 - - + +
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Residues in contact with TYR 780 (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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744A ILE* 4.6 5.8 - - + -
745A ARG 3.6 1.8 - - - -
746A GLY* 4.0 6.7 - - - -
778A HIS* 4.3 17.0 - - + -
779A ILE* 1.3 78.1 - - - +
781A GLU* 1.3 61.6 + - - +
795A LEU* 5.5 5.8 - - + -
797A LEU* 3.2 35.0 - - + -
799A TRP* 5.5 0.2 - + - -
820A MET* 6.0 0.2 - - - +
895A ALA 3.8 0.3 - - - +
896A ILE* 3.0 3.9 - - - +
897A LEU* 2.7 51.6 + - + +
899A VAL* 4.6 6.1 - - + -
922A SER* 2.6 42.6 + - - -
923A SER* 3.3 2.9 - - - -
924A ALA* 3.6 23.1 - - + -
945A THR* 3.8 17.7 - - + -
947A VAL* 3.5 26.3 + - + +
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Residues in contact with GLU 781 (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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743A GLU 3.6 1.4 - - - +
744A ILE* 3.2 8.8 - - - +
745A ARG* 2.8 53.9 + - - +
779A ILE 4.2 0.2 - - - -
780A TYR* 1.3 75.8 - - - +
782A LEU* 1.3 62.6 + - - +
783A ARG* 4.0 10.5 - - - +
795A LEU* 5.5 0.7 - - - -
894A SER* 3.2 24.2 + - - -
895A ALA 3.2 9.9 - - - +
896A ILE* 3.7 13.9 - - + +
592B GLY 4.8 2.3 - - - +
594B TYR* 2.9 36.9 + - - -
602B PRO* 3.5 12.3 - - + +
603B THR* 4.1 18.3 + - + -
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Residues in contact with LEU 782 (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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742A VAL* 3.5 24.7 - - + -
743A GLU 3.5 13.5 - - - +
744A ILE* 4.4 3.4 - - + +
780A TYR 4.3 0.4 - - - -
781A GLU* 1.3 72.1 - - - +
783A ARG* 1.3 57.4 + - - +
790A PHE* 4.0 15.3 - - + -
793A ALA* 4.8 4.5 - - + -
794A MET 6.3 0.4 - - - -
795A LEU* 4.0 20.5 - - + +
886A VAL* 4.5 17.0 - - + -
889A LEU* 3.7 23.8 - - + +
894A SER* 3.2 1.9 - - - -
895A ALA* 2.7 43.8 + - + +
926A PHE* 3.6 37.5 - - + -
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Residues in contact with ARG 783 (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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742A VAL* 3.4 5.1 - - - -
743A GLU* 2.9 42.9 + - + +
745A ARG* 6.5 0.2 - - + -
781A GLU* 3.9 12.1 - - - +
782A LEU* 1.3 73.1 - - - +
784A ASN* 1.3 62.9 + - - +
785A ASN* 3.6 27.6 + - - +
889A LEU* 5.0 0.2 - - - -
892A GLY* 2.8 41.5 + - - -
893A LYS* 3.7 8.5 - - - +
894A SER* 2.3 34.8 + - - +
590B GLN* 6.3 2.0 - - - +
594B TYR* 3.2 58.1 - - - +
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Residues in contact with ASN 784 (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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740A ALA* 3.6 12.1 - - - +
742A VAL* 3.3 22.9 - - + +
783A ARG* 1.3 74.0 - - - +
785A ASN* 1.3 58.4 + - - +
786A GLY 3.6 10.4 + - - +
788A SER 3.2 18.9 + - - -
789A SER* 4.0 2.8 - - - +
790A PHE* 3.8 18.6 - - + -
889A LEU* 2.8 33.8 + - + +
890A ASP 3.3 16.7 + - - +
891A ARG 2.5 23.4 - - - +
892A GLY* 3.5 9.2 - - - -
893A LYS 3.1 9.1 + - - +
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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