Contacts of the strand formed by residues 540 - 545 (chain B) in PDB entry 2G5T
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 TYR 540 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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531B PRO* 4.0 24.9 - - + -
532B PRO 5.2 0.3 + - - -
533B HIS 3.9 3.3 + - - -
534B PHE* 3.7 22.4 - + - -
535B ASP* 2.7 54.5 + - - +
538B LYS* 3.6 25.7 - - + +
539B LYS* 1.3 73.9 - - - +
541B PRO* 1.3 71.2 - - + +
542B LEU* 3.7 1.0 + - - +
572B ASN* 3.6 29.8 - - + +
574B ILE* 3.7 22.1 - - + +
618B PHE 3.0 9.6 + - - -
619B VAL* 3.5 6.8 - - - +
620B ASP* 2.8 20.8 + - - -
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Residues in contact with PRO 541 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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540B TYR* 1.3 89.8 - - + +
542B LEU* 1.3 59.1 + - - +
571B GLU 5.3 0.7 - - - +
572B ASN 3.8 9.2 - - - +
573B ILE* 3.7 26.1 - - + +
574B ILE* 3.0 25.8 + - - +
620B ASP* 4.5 1.1 - - + -
623B ARG* 3.3 49.1 - - + +
763B PHE* 3.7 22.0 - - + -
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Residues in contact with LEU 542 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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528B MET* 5.1 3.6 - - + -
540B TYR 3.7 0.8 + - - -
541B PRO* 1.3 73.8 - - - +
543B LEU* 1.3 75.2 + - - +
544B LEU* 3.8 12.3 - - + +
574B ILE* 3.3 25.4 - - + +
576B ALA* 4.3 10.5 - - + -
610B ALA* 5.1 2.9 - - + -
613B PHE* 4.0 35.9 - - + -
619B VAL* 3.8 30.2 - - + +
623B ARG 3.0 10.5 + - - -
624B ILE* 3.3 19.2 - - + -
625B ALA 2.8 26.2 + - - -
763B PHE* 3.6 3.9 - - - -
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Residues in contact with LEU 543 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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542B LEU* 1.3 74.5 - - - +
544B LEU* 1.3 69.1 + - - +
545B ASP 3.6 0.7 + - - -
563B TRP* 4.1 8.3 - - + -
567B LEU* 3.4 32.3 - - + -
573B ILE* 4.1 13.6 - - + +
574B ILE 2.7 12.0 + - - +
575B VAL* 3.2 11.4 - - + -
576B ALA 2.8 25.6 + - - -
625B ALA* 3.7 13.0 - - + +
626B ILE* 3.9 4.3 - - - +
627B TRP* 3.4 44.2 - - + +
759B ILE* 4.6 17.3 - - + -
763B PHE* 4.6 4.5 - - + -
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Residues in contact with LEU 544 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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542B LEU* 3.8 8.5 - - + +
543B LEU* 1.3 72.9 - - - +
545B ASP* 1.3 64.4 + - - +
546B VAL* 3.4 1.1 + - + -
576B ALA* 3.3 28.9 - - + +
577B SER* 4.0 6.1 - - - +
578B PHE* 4.4 1.6 - - + +
606B GLN* 3.5 56.5 - - + +
609B ALA* 5.5 0.4 - - + -
610B ALA* 4.4 5.6 - - + +
613B PHE* 4.3 14.1 - - + -
625B ALA 2.9 18.1 + - - +
626B ILE* 3.4 12.7 - - + +
627B TRP 3.1 24.4 + - - +
647B PHE* 4.1 19.5 - - + -
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Residues in contact with ASP 545 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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543B LEU* 3.6 2.2 + - - +
544B LEU* 1.3 70.1 - - - +
546B VAL* 1.3 64.1 + - - +
554B LYS* 2.9 28.6 + - - +
562B ASN* 5.8 1.7 + - - -
564B ALA* 5.0 6.6 - - - +
575B VAL* 3.9 20.7 - - + +
576B ALA 2.6 11.8 + - - +
577B SER* 2.9 34.4 + - - +
578B PHE 4.7 0.5 + - - -
627B TRP* 3.8 35.6 + - - +
628B GLY* 5.5 0.5 - - - -
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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