Contacts of the strand formed by residues 550 - 566 (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 GLU 550 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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400A ILE* 4.4 1.3 - - - -
498A ILE 3.7 0.2 - - - +
499A ILE* 3.4 4.5 - - - -
500A ILE* 2.8 35.6 + - + +
543A ASN* 3.5 17.9 + - - +
544A ASN* 3.1 50.0 + - - +
545A ASN* 4.3 1.0 + - - -
548A THR* 4.0 8.8 - - + +
549A PRO* 1.3 79.0 - - - +
551A LEU* 1.3 62.0 + - - +
552A ARG* 2.9 41.8 + - - +
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Residues in contact with LEU 551 (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* 4.1 25.6 - - + -
400A ILE* 4.0 17.5 - - + +
497A GLY* 4.4 3.4 - - - -
498A ILE 3.6 14.4 - - - +
499A ILE* 4.0 7.9 - - + +
550A GLU* 1.3 72.7 - - - +
552A ARG* 1.3 93.6 + - - +
553A THR* 4.4 16.6 + - + +
581A LEU* 3.8 28.7 - - + -
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Residues in contact with ARG 552 (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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497A GLY* 3.3 2.3 - - - -
498A ILE* 2.8 51.8 + - + +
500A ILE* 4.0 15.7 - - + +
515A PHE* 4.5 6.3 - - + -
540A PHE* 3.9 27.6 - - + -
541A GLU* 2.8 30.5 + - - +
542A GLY 2.8 29.5 + - - -
544A ASN* 5.4 0.6 - - - +
550A GLU* 2.9 38.3 + - - +
551A LEU* 1.3 90.2 + - - +
553A THR* 1.3 62.7 + - - +
554A PHE* 4.0 1.4 - - - -
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Residues in contact with THR 553 (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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496A ARG* 2.6 32.9 + - - -
497A GLY* 4.4 1.8 - - - -
538A LYS* 4.7 7.4 + - - -
540A PHE* 3.9 10.0 - - - -
551A LEU* 4.7 18.4 - - + +
552A ARG* 1.3 76.8 - - - +
554A PHE* 1.3 74.4 + - - +
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Residues in contact with PHE 554 (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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495A VAL* 3.5 32.3 - - + -
496A ARG* 3.4 16.7 + - - +
497A GLY* 3.5 31.9 - - - -
498A ILE* 4.0 5.6 - - + -
517A ILE* 3.6 23.1 - - + -
529A ILE* 3.5 35.2 - - + -
538A LYS* 5.9 2.0 - - - +
540A PHE* 3.9 14.4 - + + -
552A ARG 4.0 1.8 - - - -
553A THR* 1.3 85.7 + - - +
555A PRO* 1.3 89.4 - - + +
556A ALA 3.2 2.8 + - - -
557A LEU* 3.9 13.0 - - + -
562A ILE* 5.7 1.1 - - + -
580A LEU* 5.5 1.3 - - + -
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Residues in contact with PRO 555 (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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529A ILE* 5.0 8.6 - - + +
554A PHE* 1.3 98.9 - - + +
556A ALA* 1.3 69.6 + - - +
557A LEU* 3.3 5.9 + - - +
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Residues in contact with ALA 556 (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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494A ILE* 3.9 22.2 - - + -
495A VAL 3.4 7.9 - - - -
496A ARG* 3.9 18.7 - - + +
554A PHE 3.2 3.2 + - - -
555A PRO* 1.3 75.8 - - - +
557A LEU* 1.3 59.8 + - - +
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Residues in contact with LEU 557 (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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493A LYS 3.6 0.2 - - - +
494A ILE* 3.2 8.9 - - - +
495A VAL* 2.8 47.9 + - + +
519A TYR* 3.9 42.4 - - + +
529A ILE* 3.9 14.1 - - + -
554A PHE* 3.9 23.1 - - + -
555A PRO 4.3 2.9 - - - +
556A ALA* 1.3 74.8 - - - +
558A SER* 1.3 58.6 + - - +
559A THR* 3.1 40.4 - - + -
562A ILE* 4.4 5.6 - - + -
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Residues in contact with SER 558 (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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492A GLU* 2.7 32.6 + - - +
493A LYS 3.4 4.0 - - - -
494A ILE* 3.5 20.1 - - - +
519A TYR* 4.8 5.9 - - - -
521A ASN* 3.6 13.5 + - - -
557A LEU* 1.3 73.9 - - - +
559A THR* 1.3 62.9 + - - +
585A VAL* 3.9 5.7 - - - +
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Residues in contact with THR 559 (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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489A LEU* 3.8 7.6 - - + +
492A GLU* 3.8 6.0 - - - +
493A LYS 2.8 26.0 + - - +
495A VAL* 4.1 9.6 - - + -
519A TYR* 3.6 5.9 - - + +
520A SER* 2.9 33.6 + - - -
521A ASN* 3.4 8.1 - - - -
557A LEU* 3.1 28.7 - - + -
558A SER* 1.3 76.7 - - - +
560A ARG* 1.3 58.5 + - - +
561A PHE 3.1 20.3 + - - +
562A ILE* 3.9 13.2 - - + -
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Residues in contact with ARG 560 (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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488A ASP* 3.0 34.7 + - - +
489A LEU* 2.9 35.9 + - - +
490A GLY* 3.2 27.1 + - - -
491A GLU* 3.6 24.2 - - - +
492A GLU* 4.0 1.8 - - + +
520A SER 3.5 0.6 + - - +
521A ASN* 2.9 21.7 + - - +
559A THR* 1.3 75.5 + - - +
561A PHE* 1.3 88.6 + - + +
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Residues in contact with PHE 561 (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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486A GLN* 3.8 20.9 - - + -
487A ILE 3.3 2.7 - - - +
488A ASP* 3.4 39.3 - - + -
519A TYR* 3.3 5.0 - - - +
520A SER 3.0 30.6 + - - +
521A ASN 3.9 14.8 - - - -
522A ASN 4.5 3.8 - - - -
523A GLY* 4.3 13.7 - - - -
526A TRP* 3.4 22.7 - + + -
559A THR* 3.1 16.0 + - - +
560A ARG* 1.3 113.0 - - + +
562A ILE* 1.3 62.6 + - - +
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Residues in contact with ILE 562 (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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485A LEU 3.8 0.3 - - - +
486A GLN* 3.3 5.4 - - - +
487A ILE* 2.8 40.8 + - + +
489A LEU* 4.9 3.6 - - + -
495A VAL* 4.5 14.4 - - + -
517A ILE* 4.2 13.7 - - + -
518A GLY 3.5 9.9 - - - +
519A TYR* 4.1 5.6 - - + -
526A TRP* 4.1 1.3 - - - -
554A PHE* 5.7 1.3 - - + -
557A LEU* 4.4 9.0 - - + -
559A THR* 3.9 23.6 - - + -
561A PHE* 1.3 74.8 - - - +
563A ARG* 1.3 66.4 + - - +
564A ILE* 3.9 28.5 - - + -
580A LEU* 4.0 33.4 - - + -
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Residues in contact with ARG 563 (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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484A TRP* 3.4 58.9 - - + +
485A LEU 3.2 10.8 - - - +
486A GLN* 2.9 27.5 + - + -
517A ILE* 3.4 5.7 - - - -
518A GLY 2.8 33.8 + - - +
523A GLY 5.5 1.2 + - - -
526A TRP* 3.3 42.3 - - + +
562A ILE* 1.3 75.0 - - - +
564A ILE* 1.3 63.6 + - - +
565A TYR* 3.5 34.6 + - + +
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Residues in contact with ILE 564 (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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484A TRP* 3.2 5.5 - - - -
485A LEU* 2.9 46.0 + - + +
487A ILE* 5.7 1.6 - - + -
498A ILE* 3.7 24.9 - - + -
515A PHE* 4.0 24.2 - - + -
516A LYS 3.7 1.3 - - - -
517A ILE* 3.9 17.7 - - + -
562A ILE* 3.9 17.3 - - + -
563A ARG* 1.3 78.1 - - - +
565A TYR* 1.3 63.8 + - - +
566A PRO* 3.4 7.3 - - + +
574A LEU* 5.3 1.8 - - + -
576A LEU* 4.1 20.6 - - + -
578A MET* 4.0 23.8 - - + -
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Residues in contact with TYR 565 (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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482A ASN* 4.9 12.6 - - + -
483A GLU 3.6 14.8 - - - +
484A TRP* 3.9 21.3 - + + -
515A PHE* 3.2 1.5 - - - -
516A LYS* 2.9 40.7 + - + +
518A GLY* 3.8 13.5 - - - -
526A TRP* 4.2 18.5 - - - +
528A MET* 3.9 29.5 - - + -
563A ARG* 3.5 43.5 + - + +
564A ILE* 1.3 70.5 - - - +
566A PRO* 1.3 69.7 - - - +
3287A GOL 3.1 7.3 + - - +
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Residues in contact with PRO 566 (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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473A LEU* 4.3 4.9 - - + -
483A GLU* 3.5 32.6 - - + +
484A TRP* 4.3 2.0 - - - -
485A LEU 5.1 0.2 - - - +
513A ARG* 3.9 28.0 + - + +
514A LYS 3.6 8.3 - - - +
515A PHE* 3.9 6.0 - - + -
564A ILE* 3.4 12.5 - - + +
565A TYR* 1.3 87.0 - - - +
567A GLU* 1.3 64.9 + - - +
568A ARG 3.8 0.5 + - - -
574A LEU* 3.9 32.5 - - + -
3287A GOL 3.7 2.5 + - - -
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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