Contacts of the strand formed by residues 576 - 584 (chain A) in PDB entry 2QQI
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 LEU 576 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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461A ASN 3.6 4.3 - - - +
462A ILE* 3.5 13.0 - - + +
472A ALA* 3.5 21.6 - - + +
485A LEU* 4.1 15.3 - - + -
498A ILE* 5.6 1.1 - - + -
500A ILE* 3.9 26.7 - - + -
501A GLN 3.5 18.6 - - - +
502A GLY* 5.5 0.2 - - - -
503A GLY* 3.9 3.7 - - - +
515A PHE* 5.6 7.2 - - + -
543A ASN* 4.7 2.2 - - - +
564A ILE* 4.1 25.8 - - + -
574A LEU* 4.0 20.6 - - + -
575A GLY* 1.3 76.8 - - - +
577A ARG* 1.3 74.4 + - - +
578A MET* 4.3 14.6 - - + -
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Residues in contact with ARG 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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364A SER* 5.2 1.8 + - - -
365A ASN* 5.2 4.2 - - - +
368A ASP* 6.0 0.4 + - - -
461A ASN 3.6 19.7 - - - +
462A ILE 3.3 4.3 - - - -
463A ARG 3.6 14.1 - - - +
464A LEU* 3.9 3.1 - - - -
465A VAL* 4.4 2.4 - - - +
466A THR* 3.2 38.8 + - - +
468A ARG 5.1 0.4 - - - -
500A ILE* 3.5 1.4 - - - -
501A GLN* 2.8 78.7 + - + +
502A GLY 2.9 25.8 + - - +
503A GLY* 4.4 2.7 + - - -
504A LYS* 3.5 35.8 - - - +
546A TYR* 3.9 15.4 + - - -
547A ASP* 4.5 4.4 + - - +
576A LEU* 1.3 75.9 - - - +
578A MET* 1.3 63.4 + - - +
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Residues in contact with MET 578 (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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437A MET* 3.1 20.9 - - + +
462A ILE* 2.8 35.9 + - + +
464A LEU* 3.0 21.5 + - - +
485A LEU* 4.7 3.6 - - - -
487A ILE* 4.0 23.1 - - + -
498A ILE* 3.6 26.9 - - + -
499A ILE 3.1 11.2 - - - +
500A ILE* 4.7 1.3 - - + -
562A ILE* 5.3 0.2 - - + -
564A ILE* 4.0 23.6 - - + -
576A LEU* 4.3 15.9 - - + -
577A ARG* 1.3 76.5 - - - +
579A GLU* 1.3 60.9 + - - +
580A LEU* 4.0 25.8 - - + -
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Residues in contact with GLU 579 (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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434A MET* 3.4 34.9 - - + +
435A LEU 3.6 1.6 + - - -
436A GLY* 3.3 16.1 + - - -
437A MET* 2.9 30.1 + - - +
438A VAL* 2.9 24.5 + - + +
439A SER 4.5 0.5 + - - -
442A ILE* 4.5 0.3 - - - +
464A LEU* 3.7 23.3 - - + -
498A ILE* 3.3 6.5 - - - +
499A ILE* 2.8 35.5 + - + -
578A MET* 1.3 74.9 - - - +
580A LEU* 1.3 87.4 + - - +
581A LEU* 4.9 2.5 - - + -
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Residues in contact with LEU 580 (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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434A MET* 3.5 4.7 - - - -
435A LEU* 2.9 43.0 + - + -
437A MET* 4.6 1.8 - - + +
442A ILE* 5.0 2.0 - - + -
487A ILE* 4.1 20.9 - - + -
489A LEU* 4.1 23.1 - - + -
495A VAL* 4.3 11.9 - - + -
497A GLY 3.5 11.9 - - - +
498A ILE* 4.0 18.8 - - + -
517A ILE* 6.3 0.9 - - + -
554A PHE* 5.5 2.0 - - + -
562A ILE* 4.0 31.2 - - + -
564A ILE* 5.6 0.2 - - + -
578A MET* 4.0 17.5 - - + -
579A GLU* 1.3 81.5 + - - +
581A LEU* 1.3 61.4 + - - +
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Residues in contact with LEU 581 (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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335A PHE* 6.0 0.2 - - + -
426A ILE* 4.0 18.2 - - + -
431A CYS 4.6 1.3 - - - +
432A SER* 3.6 30.5 - - - +
433A GLY 3.2 12.1 - - - +
434A MET* 3.9 19.7 - - + -
435A LEU* 4.0 3.1 - - - -
495A VAL* 3.5 5.9 - - - +
496A ARG* 2.9 28.0 + - + -
497A GLY* 2.9 21.2 + - - +
499A ILE* 4.0 19.1 - - + -
551A LEU* 3.8 31.4 - - + -
579A GLU* 4.9 0.9 - - + -
580A LEU* 1.3 77.9 - - - +
582A GLY* 1.3 59.0 + - - +
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Residues in contact with GLY 582 (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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431A CYS* 3.5 19.5 + - - -
433A GLY* 2.9 33.4 + - - +
435A LEU* 3.7 10.7 - - - +
494A ILE 3.2 12.6 - - - -
495A VAL* 4.3 0.7 - - - -
496A ARG 4.5 1.1 - - - -
581A LEU* 1.3 76.7 - - - +
583A CYS* 1.3 63.7 - - - +
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Residues in contact with CYS 583 (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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431A CYS* 2.0 50.9 - - - -
433A GLY 5.4 0.2 - - - +
435A LEU* 3.9 8.3 - - - +
493A LYS* 3.5 7.2 - - - +
494A ILE* 2.9 39.1 + - - +
582A GLY* 1.3 73.0 - - - +
584A GLU* 1.3 75.1 + - - +
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Residues in contact with GLU 584 (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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491A GLU* 4.6 16.3 - - - +
493A LYS* 4.7 15.9 - - + +
494A ILE* 4.4 1.5 - - - +
583A CYS* 1.3 91.5 - - - +
585A VAL* 1.3 70.8 + - - +
586A GLU* 3.6 1.9 + - - +
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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