Contacts of the strand formed by residues 591 - 596 (chain D) in PDB entry 2QY0
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 ARG 591 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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447D ILE* 3.7 23.1 + - + +
450D GLY* 3.1 26.7 + - - +
451D GLN* 3.0 19.0 - - - +
452D LYS* 3.6 30.1 - - + +
453D ALA* 3.9 1.6 - - - +
577D SER* 3.1 4.5 - - - -
578D GLY 2.8 32.6 + - - +
580D GLY 5.5 0.4 - - - -
582D MET* 3.4 53.3 - - - +
587D ALA* 4.1 9.9 - - + -
589D ASP* 3.6 8.9 - - - +
590D LEU* 1.3 80.7 - - - +
592D PHE* 1.3 64.4 + - - +
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Residues in contact with PHE 592 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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441C VAL* 4.3 19.5 - - + -
447D ILE* 4.0 4.5 - - - -
450D GLY* 3.1 3.8 - - - -
451D GLN* 2.9 68.4 + - + +
452D LYS 3.9 17.7 - - - -
453D ALA* 4.0 10.8 - - - -
457D ASN* 4.9 1.8 - - - -
458D PHE* 3.8 25.4 - + + -
575D TYR* 3.8 33.4 - + + -
576D VAL 3.2 12.1 - - - +
577D SER* 3.9 8.5 - - - -
591D ARG* 1.3 78.0 - - - +
593D VAL* 1.3 70.3 + - - +
594D ARG* 5.4 2.0 - - + -
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Residues in contact with VAL 593 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
447D ILE* 3.5 10.8 - - + -
448D ILE 3.4 17.7 - - - +
449D GLY 3.7 0.2 - - - +
450D GLY* 3.2 30.3 - - - -
575D TYR* 3.4 7.1 - - - +
576D VAL* 2.9 38.8 + - + +
592D PHE* 1.3 79.1 - - - +
594D ARG* 1.3 61.0 + - - +
595D LEU* 4.0 24.5 - - + -
630D GLN* 3.5 23.8 - - + -
631D ASP 4.4 8.5 - - - +
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Residues in contact with ARG 594 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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442C GLU* 4.0 11.5 + - - -
573D MET* 3.3 53.7 - - + +
574D GLY 3.2 10.5 - - - +
575D TYR* 3.2 40.5 + - + -
592D PHE* 5.5 2.5 - - + -
593D VAL* 1.3 75.8 - - - +
595D LEU* 1.3 65.1 + - - +
596D PRO* 4.6 0.9 - - - +
628D LEU* 5.5 1.6 - - - +
630D GLN* 4.5 14.2 + - - +
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Residues in contact with LEU 595 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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573D MET* 3.4 6.2 - - - +
574D GLY 2.8 32.3 + - - -
576D VAL* 3.6 22.4 - - + -
593D VAL* 4.0 12.3 - - + -
594D ARG* 1.3 75.6 - - - +
596D PRO* 1.3 70.8 - - + +
623D ALA* 4.8 2.7 - - + -
624D GLY* 4.1 20.6 - - - +
628D LEU* 4.9 2.7 - - + -
630D GLN* 3.3 44.4 - - + +
631D ASP* 4.6 7.0 - - - +
632D ALA 5.4 0.4 - - - +
641D PHE* 3.6 15.2 - - + -
670D TYR* 3.4 25.6 - - - +
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Residues in contact with PRO 596 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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571D GLY* 4.6 9.0 - - - -
572D LEU 3.5 7.2 - - - +
573D MET* 3.7 22.4 - - + -
594D ARG 4.6 0.4 - - - +
595D LEU* 1.3 85.1 - - + +
597D VAL* 1.3 70.9 + - - +
598D ALA* 3.5 0.4 + - - -
623D ALA* 3.3 3.7 - - - +
624D GLY* 2.9 36.8 + - - +
625D HIS* 5.3 2.2 - - + -
628D LEU* 3.6 30.3 - - + -
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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