Contacts of the strand formed by residues 538 - 543 (chain B) in PDB entry 4HXG
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 LEU 538 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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472B THR* 4.5 2.7 - - + -
473B ASN* 4.3 3.8 - - - +
476B LEU* 3.9 25.4 - - + -
485B GLY* 3.2 25.8 - - - +
487B SER* 4.0 16.2 - - - +
534B VAL* 5.3 2.7 - - + -
536B ALA 4.3 3.1 - - - +
537B PRO* 1.3 74.7 - - - +
539B LEU* 1.3 69.6 + - - +
540B LEU* 4.1 13.2 - - + -
557B PHE* 3.9 18.2 - - + -
561B LEU* 3.8 26.9 - - + -
567B GLU 3.2 6.6 + - - +
568B VAL* 3.1 17.9 - - + +
569B TYR* 2.8 27.9 + - - -
599B PHE* 3.7 4.0 - - - -
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Residues in contact with LEU 539 (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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485B GLY 3.1 8.0 + - - +
486B ILE* 3.4 16.4 - - + +
487B SER 3.0 25.6 + - - +
538B LEU* 1.3 73.8 - - - +
540B LEU* 1.3 71.8 + - - +
541B ILE* 4.1 21.5 - - + -
569B TYR* 3.5 22.0 - - + +
570B ILE 4.7 0.2 - - - -
571B ALA* 4.4 14.4 - - + +
595B LEU* 4.2 23.1 - - + +
599B PHE* 3.5 46.5 - - + -
611B PHE* 5.9 2.9 - - + -
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Residues in contact with LEU 540 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
473B ASN* 4.0 9.6 - - - +
487B SER* 3.4 34.5 - - - +
538B LEU* 4.1 12.8 - - + -
539B LEU* 1.3 73.9 - - - +
541B ILE* 1.3 58.1 + - - +
554B SER* 3.6 37.0 - - - +
557B PHE* 4.2 9.9 - - + -
558B TYR* 3.8 24.7 - - + +
568B VAL* 4.2 12.3 - - + -
569B TYR 2.6 14.5 + - - +
570B ILE* 3.1 15.0 - - + +
571B ALA 2.7 31.7 + - - -
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Residues in contact with ILE 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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486B ILE* 4.2 11.7 - - + -
487B SER 2.9 7.2 + - - +
488B GLU* 3.4 42.5 - - + +
489B ASN 3.1 23.6 + - - -
539B LEU* 4.1 23.1 - - + -
540B LEU* 1.3 77.0 - - - +
542B HIS* 1.3 68.1 + - - +
554B SER* 3.7 3.1 + - - -
571B ALA* 3.4 12.6 - - + +
573B PHE* 4.3 10.3 - - + -
580B HIS* 4.0 20.0 - - + +
592B ARG* 4.3 17.5 - - + +
595B LEU* 4.6 9.4 - - + -
596B PHE* 5.2 5.8 - - + +
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Residues in contact with HIS 542 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
489B ASN* 3.4 32.5 - - - +
490B GLY 4.3 0.9 - - - -
541B ILE* 1.3 73.8 - - - +
543B SER* 1.3 78.1 + - - +
546B ASP* 3.9 3.2 + - - +
549B CYS* 2.7 31.3 + - + -
550B PRO 3.4 8.2 - - - -
551B LEU* 3.4 37.6 + - + -
553B GLN* 4.8 1.1 - - + -
554B SER* 2.5 38.5 + - - +
570B ILE* 5.3 0.9 - - + -
571B ALA 2.9 10.1 + - - +
572B ILE* 4.3 6.7 - - + -
573B PHE* 2.7 36.2 + - - +
580B HIS* 4.4 3.1 - - - -
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Residues in contact with SER 543 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
489B ASN* 3.1 8.2 + - - +
542B HIS* 1.3 89.4 - - - +
544B LEU* 1.3 65.4 + - - +
545B GLU 3.1 2.2 + - - -
546B ASP* 3.2 15.4 + - - +
551B LEU* 5.5 0.5 + - - +
572B ILE* 5.2 0.2 - - - -
573B PHE* 3.5 5.4 - - - +
575B LYS 3.9 7.2 - - - -
576B GLY 3.2 16.4 + - - -
577B ALA 3.1 19.6 + - - -
580B HIS* 3.1 26.9 - - - -
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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