Contacts of the strand formed by residues 544 - 548 (chain A) in PDB entry 5K7W
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 TRP 544 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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370A PRO 4.5 1.6 - - - +
371A PRO* 4.2 0.9 - - - +
372A GLN* 3.4 24.0 + - - +
391A VAL* 4.3 5.6 - - + -
393A MET* 3.9 28.9 - - + -
518A TYR* 3.8 28.0 + + - +
521A ILE* 3.9 22.4 - - + -
522A GLU* 4.6 6.1 + - - -
530A LYS* 3.2 42.0 - - + +
531A ILE 3.5 36.1 - - - -
532A GLU* 3.7 17.5 - - + +
539A ASN 5.5 0.9 - - - +
541A GLN* 3.5 32.0 + - + +
542A PRO 3.1 24.7 - - - -
543A ASN* 1.3 83.4 - - + +
545A ILE* 1.3 67.4 + - - +
546A THR* 4.2 5.1 + - - +
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Residues in contact with ILE 545 (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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372A GLN* 3.4 44.0 - - + +
373A TRP* 4.7 2.2 - - - +
374A ILE* 4.8 7.4 - - + -
386A LEU* 4.8 9.0 - - + +
389A PHE* 3.9 18.4 - - + -
529A ARG* 3.8 25.4 - - - +
530A LYS 2.9 10.5 + - - +
531A ILE* 3.3 10.0 - - + +
532A GLU* 2.9 25.1 + - - +
544A TRP* 1.3 73.7 - - - +
546A THR* 1.3 63.5 + - - +
547A LEU* 4.2 20.9 - - + -
556A LEU* 4.9 3.1 - - + -
561A VAL* 4.6 16.2 - - + -
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Residues in contact with THR 546 (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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372A GLN 3.0 13.0 + - - -
373A TRP* 3.1 9.4 - - - -
374A ILE 2.9 26.5 + - - -
532A GLU* 3.6 12.0 - - + +
535A GLY* 3.8 33.4 - - - -
536A ARG 4.4 8.7 - - - +
539A ASN* 4.1 9.8 + - + -
540A VAL* 3.6 23.3 - - + -
541A GLN 4.6 1.7 + - - -
544A TRP* 4.6 5.4 - - - +
545A ILE* 1.3 75.2 - - - +
547A LEU* 1.3 65.3 + - - +
551A LEU* 3.3 9.5 - - + +
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Residues in contact with LEU 547 (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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374A ILE* 3.6 35.7 - - + +
376A CYS* 4.2 6.5 - - - -
378A ILE* 3.9 22.0 - - + -
381A LEU* 4.3 5.8 - - + -
383A VAL* 4.2 14.8 - - + -
386A LEU* 4.0 13.0 - - + -
531A ILE* 3.9 16.2 - - + -
532A GLU 2.9 11.6 + - - +
533A LEU* 3.5 25.8 - - + -
534A PHE 2.9 25.8 + - - -
535A GLY 3.0 7.3 + - - -
545A ILE* 4.2 10.5 - - + -
546A THR* 1.3 81.1 - - - +
548A GLY* 1.3 56.9 + - - +
551A LEU* 3.6 3.1 - - - -
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Residues in contact with GLY 548 (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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374A ILE 3.4 2.6 + - - -
375A CYS* 3.2 10.9 - - - -
376A CYS* 3.1 21.7 + - - -
378A ILE* 4.1 1.2 - - - +
534A PHE* 4.5 0.4 - - - -
535A GLY 3.6 15.7 - - - -
547A LEU* 1.3 76.6 - - - +
549A ASN* 1.3 61.7 + - - -
550A GLN 3.3 3.4 + - - -
551A LEU* 3.3 8.8 - - - +
601A SAH 3.7 15.3 - - - -
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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