Contacts of the strand formed by residues 540 - 544 (chain B) in PDB entry 3HIH
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 LYS 540 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5B SO4 2.8 43.0 + - - -
410B TRP* 6.4 0.2 - - + -
411B VAL 5.5 0.2 - - - -
414B TRP* 6.0 0.7 - - - +
493B ALA* 3.9 22.9 - - + +
531B GLN* 4.3 9.0 - - + +
532B ILE 3.3 4.9 - - - -
533B ASN* 3.4 36.5 - - - +
534B PHE* 4.5 1.3 - - - -
538B HIS* 3.2 19.2 + - - +
539B THR* 1.3 79.8 - - - +
541B LEU* 1.3 65.4 + - - +
542B ILE* 5.5 1.3 - - + -
551B THR 3.8 0.6 - - - +
552B TYR* 3.4 8.7 - - - -
553B ILE* 2.9 58.7 + - + +
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Residues in contact with LEU 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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530B VAL 4.4 0.2 - - - -
531B GLN* 3.2 7.4 - - - +
532B ILE* 2.9 40.2 + - + +
534B PHE* 4.2 14.6 - - + -
540B LYS* 1.3 73.7 - - - +
542B ILE* 1.3 61.9 + - - +
543B LEU* 4.0 8.5 - - + -
550B VAL* 3.8 15.7 - - + -
551B THR 3.3 2.9 - - - +
552B TYR* 3.7 16.8 - - + -
576B LEU* 3.7 29.2 - - + -
579B ARG* 3.6 35.9 - - + +
580B LEU* 4.2 7.6 - - + +
583B ALA* 3.8 18.4 - - + -
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Residues in contact with ILE 542 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
407B PRO* 4.2 22.2 - - + +
409B PHE 4.3 4.0 - - - +
410B TRP* 3.6 42.2 - - + -
525B LEU* 6.5 0.2 - - + -
529B SER* 4.8 11.0 - - - +
530B VAL 3.6 5.2 - - - +
531B GLN* 4.1 17.0 - - + +
540B LYS* 5.5 1.6 - - + -
541B LEU* 1.3 77.0 - - - +
543B LEU* 1.3 65.9 + - - +
544B CYS* 4.0 2.2 + - + -
549B ALA 4.1 0.3 - - - +
550B VAL* 3.4 2.4 - - - -
551B THR* 2.8 59.7 + - + +
553B ILE* 4.3 11.9 - - + -
559B PHE* 4.3 8.7 - - + -
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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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377B MET* 3.6 32.0 - - + +
381B LEU* 3.9 27.1 - - + -
529B SER* 3.2 8.5 - - - -
530B VAL* 2.8 44.0 + - + +
532B ILE* 4.4 11.0 - - + -
541B LEU* 4.7 6.7 - - + -
542B ILE* 1.3 73.0 - - - +
544B CYS* 1.3 59.3 + - - +
549B ALA 3.6 4.9 - - - +
550B VAL* 3.5 30.7 - - + -
564B LEU* 4.6 6.3 - - + -
580B LEU* 4.4 1.8 - - + -
583B ALA* 3.8 27.1 - - + -
587B VAL* 5.0 1.1 - - + -
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Residues in contact with CYS 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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377B MET* 4.8 0.4 - - - -
380B GLN* 4.3 1.3 - - - +
405B CYS 5.6 2.5 - - - +
407B PRO* 5.8 9.0 - - + -
527B ASN 5.4 1.8 - - - -
529B SER* 4.0 14.1 - - - +
542B ILE* 4.0 2.8 + - + +
543B LEU* 1.3 73.0 - - - +
545B PRO* 1.3 62.7 - - - +
546B LEU* 3.5 28.3 - - - -
547B MET* 3.5 25.5 + - + -
548B ALA* 2.9 22.2 + - - -
549B ALA* 3.0 23.3 + - + +
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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