Contacts of the strand formed by residues 556 - 568 (chain N) in PDB entry 2AS5
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 556 (chain N).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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554M SER 4.1 5.9 + - - -
555M GLY* 3.3 37.7 + - - -
556M ARG* 4.4 19.1 - - - +
552N GLU* 3.0 38.4 + - + +
554N SER* 4.3 17.6 + - - +
555N GLY* 1.3 82.8 - - - +
557N ILE* 1.3 65.4 + - - +
558N VAL* 3.3 6.3 + - + +
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Residues in contact with ILE 557 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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392N ALA 4.9 4.3 - - - +
393N SER* 3.9 28.7 - - - -
394N LEU 5.3 1.1 - - - +
549N HIS* 3.9 29.8 - - + -
550N ILE 4.2 4.7 - - - +
551N PRO* 4.9 8.7 - - + -
555N GLY 4.2 2.6 + - - +
556N ARG* 1.3 72.2 - - - +
558N VAL* 1.3 60.5 + - - +
559N SER* 3.8 13.7 + - - +
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Residues in contact with VAL 558 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
405N SER* 4.3 15.7 - - - +
408N TYR* 4.7 11.0 - - + -
548N VAL 3.8 0.2 - - - +
549N HIS* 3.7 1.5 - - - -
550N ILE* 3.0 42.8 + - + +
552N GLU* 4.0 22.7 - - + +
556N ARG* 3.5 18.8 - - + +
557N ILE* 1.3 70.7 - - - +
559N SER* 1.3 62.8 + - - +
560N LEU* 3.5 23.9 - - + +
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Residues in contact with SER 559 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
395N PRO* 4.5 7.7 - - - +
401N LEU* 4.0 38.3 - - - +
402N SER* 4.4 4.2 + - - +
405N SER* 4.8 4.5 + - - -
548N VAL 3.4 5.2 - - - -
549N HIS* 3.0 27.9 + - - -
557N ILE* 3.8 11.3 + - - +
558N VAL* 1.3 72.1 - - - +
560N LEU* 1.3 68.6 + - - +
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Residues in contact with LEU 560 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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401N LEU* 4.7 0.7 - - - -
402N SER 3.7 6.3 - - - +
403N SER 4.0 3.4 - - - +
404N GLN* 3.9 22.2 - - - +
405N SER* 4.1 8.7 - - - +
408N TYR* 3.5 40.4 - - + -
409N GLU 4.0 2.9 - - - +
410N LEU* 3.9 14.8 - - + +
445N LEU* 4.8 1.8 - - + -
547N ARG* 3.5 2.9 - - - +
548N VAL* 2.9 41.4 + - + +
550N ILE* 4.5 11.0 - - + -
558N VAL* 3.5 30.5 - - + +
559N SER* 1.3 83.3 - - - +
561N GLN* 1.3 63.9 + - - +
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Residues in contact with GLN 561 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
397N LEU 5.1 2.6 + - - -
399N TRP 4.6 6.7 + - - -
400N PRO* 5.5 0.8 - - - +
401N LEU* 3.8 29.0 + - + +
402N SER 3.3 7.7 + - - +
403N SER* 3.1 23.5 + - - +
410N LEU* 3.6 4.0 - - - +
459N PHE* 4.1 4.0 - - - -
468N LEU* 3.6 27.5 - - - +
545N VAL* 3.7 13.6 - - + +
546N PHE 3.0 20.0 - - - +
547N ARG* 2.6 47.0 + - - +
560N LEU* 1.3 79.3 - - - +
562N THR* 1.3 64.5 + - - +
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Residues in contact with THR 562 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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403N SER* 4.2 11.6 - - - -
410N LEU* 3.1 44.2 + - + +
411N ARG 4.3 6.5 - - - +
412N ILE* 4.8 10.5 - - + +
443N VAL* 6.0 0.2 - - + -
545N VAL* 4.6 0.2 - - - -
546N PHE* 2.8 47.0 + - + +
561N GLN* 1.3 80.2 - - - +
563N ALA* 1.3 71.9 + - - +
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Residues in contact with ALA 563 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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412N ILE* 3.9 8.4 - - - +
415N GLN* 4.8 0.2 + - - -
468N LEU* 4.1 23.5 - - + +
543N ARG* 4.0 31.4 - - + +
544N LEU 3.5 5.8 - - - -
545N VAL* 4.1 8.5 - - + +
561N GLN* 5.1 0.2 - - - +
562N THR* 1.3 86.9 + - - +
564N SER* 1.3 63.2 + - - +
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Residues in contact with SER 564 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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412N ILE* 3.8 9.2 - - - -
415N GLN* 3.2 16.8 - - - +
416N PRO* 3.8 14.1 - - - -
543N ARG* 3.6 20.3 + - - -
544N LEU* 2.8 45.8 + - - +
546N PHE* 4.6 0.4 - - - -
563N ALA* 1.3 78.1 - - - +
565N ASN* 1.3 75.1 + - - +
567N ILE* 3.9 2.8 - - - +
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Residues in contact with ASN 565 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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415N GLN* 2.6 45.7 + - + +
416N PRO* 4.6 5.3 - - + +
542N VAL 4.0 0.3 - - - +
543N ARG* 4.2 0.8 - - - -
564N SER* 1.3 88.3 + - - +
566N PRO* 1.3 77.7 - - + +
567N ILE* 3.1 10.2 - - - +
581N GLU 5.6 1.9 + - - -
582N ARG* 4.0 33.3 + - - +
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Residues in contact with PRO 566 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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417N LYS 4.8 0.9 - - - +
418N PRO* 4.3 4.2 - - - +
463N ALA* 4.1 15.3 - - + +
541N ARG* 3.7 32.8 - - + +
542N VAL 3.0 12.8 - - - +
543N ARG* 4.0 15.0 - - + +
564N SER 4.4 2.0 - - - +
565N ASN* 1.3 93.4 - - + +
567N ILE* 1.3 59.8 + - - +
579N MET* 4.2 19.8 - - + +
580N VAL 6.1 1.3 - - - +
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Residues in contact with ILE 567 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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416N PRO* 4.1 12.6 - - + -
417N LYS 3.8 14.8 - - - +
418N PRO 3.3 14.6 - - - +
419N HIS 4.0 0.9 - - - -
420N HIS* 3.5 36.8 - - + +
433N VAL* 5.2 3.4 - - + -
518N ILE* 5.3 1.1 - - + -
541N ARG* 3.2 5.4 - - - -
542N VAL* 2.6 51.6 + - + +
544N LEU* 3.3 32.5 - - + -
564N SER* 3.9 2.9 - - - +
565N ASN 3.1 18.6 - - - +
566N PRO* 1.3 73.7 - - - +
568N GLU* 1.3 66.7 + - - +
569N CYS* 4.6 3.4 - - - -
579N MET* 5.5 0.9 - - - -
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Residues in contact with GLU 568 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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418N PRO 3.1 9.3 + - - +
419N HIS* 3.9 17.6 - - + +
420N HIS 3.2 21.7 + - - -
540N THR* 2.7 38.4 + - - +
541N ARG* 3.7 17.0 - - + +
567N ILE* 1.3 74.3 - - - +
569N CYS* 1.3 62.1 + - - +
570N SER 3.2 22.5 + - - +
573N SER* 3.0 41.2 - - - +
574N ALA* 4.4 1.0 - - + +
577N LEU* 5.1 4.9 - - + +
579N MET* 4.3 15.1 - - - -
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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