Contacts of the strand formed by residues 537 - 544 (chain B) in PDB entry 1KT8
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 HIS 537 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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513B GLU 3.3 21.8 - - - -
514B MET* 3.3 16.6 - - + -
515B THR* 3.2 30.6 + - + -
535B THR* 3.6 15.8 + - - +
536B ASP* 1.3 95.9 - - + +
538B MET* 1.3 63.9 + - - +
553B ILE* 4.0 18.6 - - + -
554B GLN 3.3 12.3 - - - +
555B PRO 4.5 0.7 - - - -
556B PHE* 3.9 8.4 - - - +
624B LEU* 4.0 13.8 - - + +
627B VAL* 3.9 19.5 - - + +
628B ASP* 3.2 23.2 + - - +
665B VAL 4.8 0.5 - - - +
667B LEU* 4.8 5.0 + - - +
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Residues in contact with MET 538 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63A PRO* 3.8 28.5 - - + -
537B HIS* 1.3 76.3 - - - +
539B LEU* 1.3 61.7 + - - +
540B MET* 4.7 2.7 - - - -
553B ILE* 3.2 4.5 - - - -
554B GLN* 2.9 58.5 + - + +
555B PRO 3.7 3.8 - - - +
556B PHE* 3.9 4.3 - - + -
557B GLN 3.5 35.0 - - - +
559B LEU* 4.4 10.5 - - + -
624B LEU* 3.5 10.2 - - - +
664B PHE* 4.3 21.3 - - + -
665B VAL 3.3 15.9 - - - +
666B ILE* 4.0 13.2 - - + -
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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
----------------------------------------------------------
510B LEU* 4.1 5.8 - - + -
538B MET* 1.3 77.0 - - - +
540B MET* 1.3 68.5 + - - +
541B VAL* 4.4 11.4 - - + -
551B PRO* 4.3 4.7 - - + -
552B ARG 4.0 21.5 - - - +
553B ILE* 4.1 12.3 - - + +
617B LEU* 3.9 15.5 - - + -
620B CYS* 3.8 38.1 - - + +
621B ILE* 4.7 1.6 - - + -
624B LEU* 3.9 9.6 - - + +
663B LEU* 4.8 1.8 - - + -
664B PHE* 3.0 9.6 - - - +
665B VAL* 2.9 57.3 + - + +
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Residues in contact with MET 540 (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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538B MET* 4.4 4.7 + - + -
539B LEU* 1.3 78.8 - - - +
541B VAL* 1.3 69.0 + - - +
542B GLU* 4.8 6.5 - - + +
550B GLN 4.0 2.6 - - - +
551B PRO* 3.8 17.7 - - - +
552B ARG* 3.8 30.0 + - - +
553B ILE 4.9 0.2 - - - +
554B GLN* 3.2 26.7 - - - +
557B GLN* 5.1 4.5 - - + +
558B ASN 5.4 2.5 - - - +
559B LEU* 4.2 16.8 - - + -
662B LEU* 3.3 33.9 - - + -
663B LEU 3.3 5.2 - - - -
664B PHE* 4.3 8.1 - - - -
1001B ACY 3.5 29.4 - - - +
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Residues in contact with VAL 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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505B PHE* 3.8 37.2 - - + -
539B LEU* 4.4 12.1 - - + -
540B MET* 1.3 80.1 - - - +
542B GLU* 1.3 66.1 + - - +
548B TRP* 3.5 28.3 - - + -
549B GLY 3.7 21.1 - - - +
550B GLN 4.6 2.5 - - - -
551B PRO* 4.0 13.5 - - + -
662B LEU* 3.4 3.9 - - - +
663B LEU* 2.8 45.8 + - + +
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Residues in contact with GLU 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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540B MET* 4.8 5.5 - - + +
541B VAL* 1.3 78.2 - - - +
543B TRP* 1.3 60.0 + - - +
544B ASN* 5.9 3.4 - - - +
547B GLY 3.7 0.6 - - - +
548B TRP* 3.5 5.1 - - - -
549B GLY* 2.7 37.7 + - - +
550B GLN 5.2 1.0 + - - -
649B ASN* 5.1 1.7 + - - -
660B ARG* 3.3 31.0 + - - +
661B ALA 3.8 6.4 - - - +
662B LEU* 3.7 16.7 - - + +
1001B ACY 2.8 25.8 + - - +
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Residues in contact with TRP 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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503B SER* 4.7 6.4 + - - -
542B GLU* 1.3 77.0 - - - +
544B ASN* 1.3 73.6 + - - +
547B GLY* 3.3 33.0 - - - -
548B TRP* 3.5 40.2 - + + +
610B PRO* 3.5 36.7 - - + +
657B GLN* 5.7 6.1 - - + -
658B PRO* 3.5 17.5 - - + -
659B ARG* 3.4 27.1 - - - -
660B ARG* 3.2 11.3 - - - +
661B ALA* 3.0 42.7 + - + +
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Residues in contact with ASN 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 GLU* 5.9 3.4 - - - +
543B TRP* 1.3 91.8 - - - +
545B ASP* 1.3 62.2 + - + +
546B LYS* 2.4 69.1 + - - +
547B GLY* 2.8 24.6 + - - +
659B ARG 3.3 19.7 - - - +
660B ARG* 4.1 14.0 - - + +
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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