Contacts of the strand formed by residues 518 - 528 (chain A) in PDB entry 3ASW
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 SER 518 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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366A ILE* 3.4 18.6 - - - +
368A LYS* 6.4 1.1 - - - -
370A ASN* 4.4 1.8 - - - -
371A GLY* 3.6 8.7 - - - -
372A ALA* 3.0 28.7 + - - -
507A GLU* 3.3 5.0 - - - +
508A ASN* 2.9 37.8 + - - +
516A ASP 3.9 6.1 - - - -
517A TYR* 1.3 82.5 - - - +
519A ILE* 1.3 63.1 + - - +
477B SER 5.1 4.2 + - - +
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Residues in contact with ILE 519 (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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366A ILE* 3.7 4.4 - - - +
372A ALA* 3.8 1.8 - - - -
409A TYR* 6.0 0.9 - - + -
505A ILE* 3.7 30.1 - - + -
506A GLN 3.4 8.1 - - - +
507A GLU* 4.0 9.6 - - + +
517A TYR* 3.2 33.4 - - + +
518A SER* 1.3 75.5 + - - +
520A PHE* 1.3 63.0 + - - +
477B SER* 3.3 39.9 + - - +
478B SER 3.6 3.8 + - - -
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Residues in contact with PHE 520 (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 ALA* 3.7 8.7 - - + -
365A GLY* 3.5 39.5 - - - -
366A ILE* 3.8 12.6 - - + -
372A ALA* 3.6 21.3 - - + +
373A ASN 4.3 0.7 - - - +
374A ILE* 3.6 35.5 - - + +
505A ILE* 3.3 6.4 - - - +
506A GLN 2.9 32.2 + - - +
519A ILE* 1.3 75.6 - - - +
521A GLY* 1.3 61.4 + - - +
522A TRP* 3.8 14.1 - + - -
478B SER* 3.7 24.5 - - - -
479B GLY* 3.4 30.5 - - - -
480B GLY* 4.0 1.3 - - - -
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Residues in contact with GLY 521 (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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374A ILE* 5.1 0.2 - - - -
503A GLN* 5.0 4.7 - - - -
504A VAL 3.4 7.6 - - - -
505A ILE* 4.3 9.9 - - - -
520A PHE* 1.3 77.7 - - - +
522A TRP* 1.3 64.1 + - - +
523A ASN* 5.3 0.9 - - - -
478B SER 3.2 12.9 + - - -
479B GLY* 3.1 4.6 - - - -
480B GLY 3.1 23.2 + - - -
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Residues in contact with TRP 522 (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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360A SER* 6.0 5.2 - - - -
361A SER 4.7 8.5 - - - -
364A ALA* 3.5 28.5 - - + -
374A ILE* 3.9 11.4 - - + +
375A SER* 3.7 10.5 - - - -
376A SER* 3.0 34.6 + - - +
446A TYR* 3.7 14.1 + - - -
502A THR 4.4 0.2 - - - -
503A GLN* 3.1 6.9 - - - +
504A VAL* 2.9 45.0 + - + +
520A PHE* 3.8 15.0 - + - -
521A GLY* 1.3 73.5 - - - -
523A ASN* 1.3 64.0 + - - +
524A ASN* 3.8 5.3 + - - -
480B GLY* 3.4 25.1 - - - -
481B GLY* 3.4 32.8 - - - -
482B SER* 2.9 24.2 + - - +
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Residues in contact with ASN 523 (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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414A GLN* 3.4 27.8 + - - +
415A ASP* 5.0 4.6 + - - -
502A THR 3.4 2.5 - - - -
503A GLN* 2.7 40.9 + - - +
521A GLY 5.3 0.4 - - - -
522A TRP* 1.3 73.2 + - - +
524A ASN* 1.3 63.4 + - - +
480B GLY 3.0 14.8 + - - +
481B GLY* 3.1 3.8 - - - -
482B SER 3.0 27.2 + - - +
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Residues in contact with ASN 524 (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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376A SER* 2.6 45.4 + - - +
377A GLN* 3.2 22.4 - - - +
378A ILE* 3.5 13.2 - - + +
392A GLN* 2.9 18.8 - - - +
414A GLN* 3.1 9.4 + - - -
501A LYS* 3.5 0.9 - - - -
502A THR* 3.0 41.1 + - - +
522A TRP* 3.8 0.9 + - - -
523A ASN* 1.3 80.9 - - - +
525A GLU* 1.3 63.4 + - - +
526A ASN* 5.3 0.2 - - - +
482B SER* 3.2 13.8 + - - +
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Residues in contact with GLU 525 (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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378A ILE* 4.5 1.8 - - - -
414A GLN* 4.7 4.5 + - - +
499A ASN* 3.6 24.2 - - + +
500A LEU 3.7 18.4 - - - +
501A LYS* 3.8 28.1 - - + +
524A ASN* 1.3 77.6 - - - +
526A ASN* 1.3 80.1 + - - +
482B SER 3.9 3.4 + - - -
483B SER* 3.1 27.1 - - - -
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Residues in contact with ASN 526 (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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236A SER* 5.4 0.4 - - - -
270A ASP* 3.6 14.7 - - + +
377A GLN* 5.1 0.6 + - - -
378A ILE* 3.0 48.3 + - - +
381A VAL* 4.3 11.9 - - + +
499A ASN* 5.8 3.1 + - - +
500A LEU 4.3 3.8 + - - -
524A ASN* 5.3 0.6 - - - +
525A GLU* 1.3 109.4 + - - +
527A VAL* 1.3 63.1 + - - +
483B SER* 4.0 1.0 - - - +
484B GLY* 2.9 28.3 - - - +
485B GLY* 4.2 1.3 - - - +
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Residues in contact with VAL 527 (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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236A SER* 4.7 9.8 + - - +
271A VAL* 5.4 1.6 - - - +
526A ASN* 1.3 74.9 - - - +
528A VAL* 1.3 60.8 + - - +
529A ARG* 4.8 22.4 - - - +
484B GLY 2.9 12.0 + - - +
485B GLY* 3.1 22.8 - - - -
486B GLY 3.1 5.5 + - - -
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Residues in contact with VAL 528 (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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271A VAL* 5.4 4.7 - - + -
383A THR* 6.5 0.9 - - + -
527A VAL* 1.3 74.4 - - - +
529A ARG* 1.3 67.4 + - - +
530A TYR* 3.8 29.6 + - + +
486B GLY 3.2 8.3 - - - +
487B HIS 5.2 6.1 - - - -
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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