Contacts of the strand formed by residues 499 - 511 (chain A) in PDB entry 5IXM
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 ALA 499 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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492A GLN* 3.1 35.0 - - + +
493A TYR 3.2 6.1 - - - +
494A ASN* 3.2 11.0 - - - +
498A TRP* 1.3 81.7 - - + +
500A VAL* 1.3 63.9 + - - +
501A ASN* 4.8 4.0 - - - +
528A ILE* 2.9 34.4 - - - +
540A GLY* 5.6 3.6 - - - +
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Residues in contact with VAL 500 (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 LEU 4.0 0.2 - - - +
492A GLN* 3.2 6.2 - - - +
493A TYR* 2.9 52.9 + - + +
499A ALA* 1.3 78.1 - - - +
501A ASN* 1.3 70.0 + - - +
502A LEU* 6.0 1.6 - - + -
526A PHE* 5.7 5.4 - - + -
527A ASN 4.1 10.5 - - - +
528A ILE* 4.1 25.4 - - + +
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Residues in contact with ASN 501 (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 LEU 3.6 1.3 - - - -
492A GLN* 3.2 43.9 + - - +
499A ALA* 4.8 2.8 - - - +
500A VAL* 1.3 79.4 + - - +
502A LEU* 1.3 61.5 + - - +
525A GLY 4.1 0.2 - - - +
526A PHE* 3.5 6.9 - - - +
527A ASN* 3.0 51.3 + - - +
528A ILE 4.2 10.4 - - - +
529A GLU 5.8 0.3 - - - -
540A GLY* 3.1 26.8 + - - -
543A GLN* 4.9 1.6 - - - +
544A MET* 4.0 22.3 - - + +
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Residues in contact with LEU 502 (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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490A GLY* 3.4 2.1 - - - -
491A LEU* 2.9 55.7 + - + +
500A VAL* 6.0 1.6 - - + -
501A ASN* 1.3 74.7 - - - +
503A GLY* 1.3 61.1 + - - +
524A ILE* 4.6 18.2 - - + -
525A GLY 3.4 21.1 - - - +
526A PHE* 4.8 7.6 - - + -
544A MET* 3.8 5.2 - - - +
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Residues in contact with GLY 503 (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 VAL 3.5 7.6 - - - -
502A LEU* 1.3 79.5 - - - +
504A TYR* 1.3 60.8 + - - -
523A LYS 3.8 0.7 - - - +
524A ILE* 3.2 9.6 - - - +
525A GLY 3.1 33.8 + - - -
544A MET* 4.1 13.4 - - - -
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Residues in contact with TYR 504 (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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487A GLN* 4.7 14.8 - - - -
488A LEU* 3.4 6.1 - - - +
489A VAL* 2.9 51.3 + - + +
503A GLY* 1.3 75.1 - - - +
505A GLU* 1.3 65.7 + - - +
506A ARG* 3.7 33.9 - - + -
522A ASN* 3.4 34.8 + - + -
523A LYS 3.3 16.4 - - - -
524A ILE* 4.1 21.8 - - + -
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Residues in contact with GLU 505 (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 SER* 5.6 2.0 - - - +
487A GLN 3.3 11.2 - - - +
488A LEU* 4.2 16.7 - - + +
504A TYR* 1.3 81.9 - - - +
506A ARG* 1.3 67.5 + - - +
507A LYS* 3.3 39.0 + - + +
521A ASP 3.5 1.2 - - - +
522A ASN* 3.5 4.0 - - - -
523A LYS* 2.9 62.1 + - + +
547A SER* 4.2 12.3 + - - +
548A GLY* 3.8 20.8 - - - -
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Residues in contact with ARG 506 (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 PRO* 4.5 15.3 - - - +
485A ALA 4.9 0.2 - - - -
486A SER* 3.6 2.4 - - - -
487A GLN* 2.9 53.4 + - - +
504A TYR* 3.7 29.3 - - + +
505A GLU* 1.3 75.6 - - - +
507A LYS* 1.3 61.8 + - - +
520A TYR* 3.3 64.1 - - + +
521A ASP 3.3 4.9 - - - +
522A ASN* 3.8 15.4 + - - +
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Residues in contact with LYS 507 (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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118A THR* 5.9 1.6 + - - -
123A SER* 6.2 0.8 - - - -
124A THR* 4.4 14.8 - - + +
485A ALA 3.6 4.7 - - - +
486A SER* 4.3 5.4 - - - +
505A GLU* 3.3 30.2 + - + +
506A ARG* 1.3 76.5 - - - +
508A ILE* 1.3 66.5 + - - +
509A THR* 3.4 3.9 + - - -
520A TYR* 3.3 9.5 - - - -
521A ASP* 3.1 44.1 + - + +
523A LYS* 4.8 16.2 - - - +
547A SER 5.3 3.8 + - - -
548A GLY 5.7 0.2 - - - -
549A ILE* 3.7 43.6 - - + +
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Residues in contact with ILE 508 (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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124A THR* 4.3 6.2 - - - +
478A ASP* 6.1 1.6 - - + -
483A GLN* 3.3 30.1 - - + +
484A PRO 3.5 22.4 - - - +
485A ALA* 2.9 27.3 + - + +
507A LYS* 1.3 73.7 - - - +
509A THR* 1.3 60.2 + - - +
510A GLY 3.9 8.7 - - - +
518A SER* 4.1 5.2 - - - +
519A LYS 3.7 5.4 - - - +
520A TYR* 3.6 13.7 - - + +
549A ILE* 4.0 13.9 - - - +
69B ILE* 4.1 8.3 - - + -
70B PHE 4.6 4.3 - - - +
71B ARG* 3.3 24.0 - - - +
73B GLY* 3.7 22.7 - - - +
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Residues in contact with THR 509 (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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115A THR* 4.4 22.8 + - + +
124A THR* 3.1 35.2 + - - +
507A LYS* 3.4 8.7 + - - -
508A ILE* 1.3 74.8 - - - +
510A GLY* 1.3 56.7 + - - +
519A LYS* 2.7 26.1 + - + +
520A TYR 3.8 5.4 - - - +
521A ASP* 3.1 39.4 + - - +
72B ASN 4.2 6.8 - - - +
73B GLY* 4.7 1.5 - - - -
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Residues in contact with GLY 510 (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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508A ILE* 3.9 1.4 - - - +
509A THR* 1.3 83.7 - - - +
511A TRP* 1.3 61.7 + - - +
519A LYS* 2.9 37.7 + - - +
71B ARG 3.7 13.7 - - - +
72B ASN 3.6 12.6 + - - +
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Residues in contact with TRP 511 (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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450A TYR* 4.2 37.9 - + + -
510A GLY* 1.3 75.0 - - - +
512A ASN* 1.3 74.9 + - - +
513A ALA* 3.5 14.3 + - + +
516A GLN* 3.2 32.7 + - + -
517A THR* 3.3 31.9 - - - -
518A SER* 3.5 14.4 - - - -
519A LYS* 3.5 19.2 + - - +
71B ARG* 3.6 54.3 - - + -
72B ASN* 3.6 21.5 + - + -
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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