Contacts of the strand formed by residues 573 - 577 (chain A) in PDB entry 1QFM
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 CYS 573 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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548A LEU 3.1 4.6 + - - +
549A THR* 3.1 27.9 - - - +
550A ILE* 3.0 24.7 + - - +
571A PHE* 3.5 1.4 - - - +
572A GLY* 1.3 82.2 - - - +
574A VAL* 1.3 69.1 + - - +
575A ILE* 4.4 2.5 - - - -
632A SER* 3.3 9.0 - - - -
699A PHE* 3.5 36.3 - - - -
700A ILE* 4.0 19.1 - - - -
703A CYS* 4.8 1.8 - - - -
704A LEU* 4.3 11.7 - - + -
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Residues in contact with VAL 574 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
550A ILE* 3.5 20.2 - - + -
560A VAL* 3.7 40.2 - - + +
564A ALA* 4.1 7.6 - - + -
571A PHE* 4.3 3.8 - - + -
573A CYS* 1.3 80.0 - - - +
575A ILE* 1.3 67.7 + - - +
576A ALA* 4.0 2.9 - - + +
631A PRO* 3.6 27.4 - - + -
632A SER 2.8 11.0 + - - +
633A MET* 3.3 20.8 - - + +
634A LEU 2.9 26.3 + - - +
635A LEU* 6.0 0.4 - - + +
699A PHE* 4.3 0.7 - - - -
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Residues in contact with ILE 575 (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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469A PHE* 4.9 1.3 - - + -
549A THR* 4.5 4.0 - - + -
550A ILE 3.0 10.1 + - - +
551A ASN* 2.9 42.2 + - + +
552A GLY 3.5 2.1 + - - -
560A VAL* 3.8 2.6 - - - +
573A CYS* 4.4 4.0 - - - -
574A VAL* 1.3 77.9 - - - +
576A ALA* 1.3 60.4 + - - +
577A GLN* 4.3 3.4 - - + -
634A LEU* 3.3 13.0 - - + +
636A LEU* 4.2 15.5 - - + -
696A MET* 3.5 56.3 - - + +
699A PHE* 4.4 15.7 - - + -
700A ILE* 3.8 22.0 - - + -
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Residues in contact with ALA 576 (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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552A GLY 3.7 4.7 - - - -
557A GLY* 3.9 13.0 - - - +
560A VAL* 3.6 19.3 - - + -
561A ALA* 4.9 2.7 - - + +
574A VAL* 4.0 5.2 - - + -
575A ILE* 1.3 71.7 - - - +
577A GLN* 1.3 63.6 + - - +
579A GLY 4.9 1.5 + - - -
581A MET* 3.9 11.5 - - + +
634A LEU 3.0 8.5 + - - -
635A LEU* 3.3 25.1 - - + +
636A LEU 3.0 23.0 + - - +
649A SER* 5.3 0.7 + - - -
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Residues in contact with GLN 577 (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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471A TYR* 5.6 1.0 - - - -
551A ASN* 3.0 31.9 + - - +
552A GLY 3.0 13.2 + - - +
553A GLY* 3.1 9.3 + - - -
554A SER 2.8 19.6 + - - -
557A GLY* 4.0 0.5 - - - -
575A ILE* 4.3 2.0 - - + -
576A ALA* 1.3 74.4 - - - +
578A VAL* 1.3 75.4 + - + +
579A GLY* 2.8 5.0 + - - -
636A LEU* 3.6 22.2 - - + +
692A GLU* 3.3 32.5 + - - -
696A MET* 3.7 17.6 - - - +
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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