Contacts of the strand formed by residues 730 - 737 (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 730 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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608A VAL* 3.3 31.2 - - + +
609A SER* 5.3 0.2 - - - -
610A VAL* 4.5 19.7 - - + +
714A ASP* 4.4 1.3 - - - -
715A LEU* 2.5 52.2 + - + +
728A PRO* 4.0 20.6 - - + +
729A VAL* 1.3 76.8 - - - +
731A SER* 1.3 65.4 + - - +
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Residues in contact with SER 731 (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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610A VAL* 5.5 0.2 - - - +
712A LYS* 3.9 18.7 - - - +
713A PHE 3.2 8.6 + - - -
714A ASP* 3.0 21.0 + - - -
729A VAL* 4.1 2.2 + - - +
730A VAL* 1.3 78.1 - - - +
732A HIS* 1.3 60.2 + - - +
733A LYS* 4.2 1.1 + - - +
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Residues in contact with HIS 732 (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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610A VAL* 3.6 42.5 - - + +
611A ASP 3.3 19.2 + - - -
612A SER* 4.4 19.2 - - - -
627A LEU* 3.9 23.5 - - + +
712A LYS* 3.6 1.9 - - - -
713A PHE* 2.6 47.8 + + + +
715A LEU* 4.5 7.4 - - + -
730A VAL 3.9 0.8 + - - -
731A SER* 1.3 73.2 - - - +
733A LYS* 1.3 79.5 + - - +
734A VAL* 4.0 14.0 - - + +
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Residues in contact with LYS 733 (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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709A THR* 4.8 7.1 - - - +
710A SER* 3.3 27.3 + - - +
711A VAL 3.4 7.9 - - - +
712A LYS* 3.5 20.2 - - + -
731A SER* 4.2 1.5 - - - +
732A HIS* 1.3 90.6 + - - +
734A VAL* 1.3 65.0 + - - +
735A ASP* 3.7 20.4 + - - +
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Residues in contact with VAL 734 (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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614A GLN 4.3 4.9 - - - +
615A LYS* 3.4 26.2 - - - +
616A LYS* 3.9 8.1 - - - +
617A ILE* 4.3 11.9 - - + -
625A LEU* 4.3 22.2 - - + -
627A LEU* 5.4 0.4 - - + -
710A SER* 3.0 18.4 - - - -
711A VAL* 2.9 25.8 + - + +
713A PHE* 5.4 6.5 - - + -
732A HIS* 4.0 21.3 - - + +
733A LYS* 1.3 81.7 - - - +
735A ASP* 1.3 71.7 + - - +
736A LEU* 3.7 3.0 - - - +
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Residues in contact with ASP 735 (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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615A LYS 3.7 11.1 + - - +
616A LYS* 3.4 9.2 - - + +
617A ILE* 3.1 27.0 + - - +
709A THR* 3.1 29.6 + - - +
710A SER* 3.8 2.9 - - - -
733A LYS* 3.7 23.6 + - - -
734A VAL* 1.3 76.2 - - - +
736A LEU* 1.3 65.1 + - - +
937A PRO* 6.0 1.7 - - - +
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Residues in contact with LEU 736 (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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617A ILE* 3.4 17.3 - - + +
619A ILE* 4.4 17.7 - - + -
701A VAL* 6.3 0.7 - - + -
703A GLN* 5.6 5.4 - - + -
704A GLN 5.5 4.7 - - - +
705A SER 4.6 13.0 - - - +
706A GLU 5.2 0.2 - - - +
707A MET* 3.9 22.4 - - + +
708A ASP 4.2 6.3 - - - +
709A THR 2.9 13.8 + - - +
710A SER* 3.6 2.9 - - - +
711A VAL* 3.4 49.6 - - + +
734A VAL 3.7 4.7 - - - +
735A ASP* 1.3 78.4 - - - +
737A ALA* 1.3 58.9 + - - +
936A LEU* 3.1 26.8 - - + +
937A PRO* 4.8 2.9 - - - +
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Residues in contact with ALA 737 (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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616A LYS* 4.1 19.1 - - + -
617A ILE 2.9 8.6 + - - +
618A TYR* 3.2 32.5 - - + -
619A ILE* 3.0 32.3 + - - +
735A ASP* 3.7 0.4 + - + -
736A LEU* 1.3 74.3 - - - +
738A VAL* 1.3 65.8 + - - +
937A PRO* 5.9 2.7 - - - -
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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