Contacts of the strand formed by residues 556 - 568 (chain M) 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 M).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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552M GLU* 3.0 42.9 + - + +
554M SER* 4.3 15.0 + - - +
555M GLY* 1.3 85.6 - - - +
557M ILE* 1.3 65.0 + - - +
558M VAL* 3.3 5.4 + - + +
554N SER 4.3 5.3 + - - -
555N GLY* 3.2 38.5 + - - -
556N ARG* 4.4 18.1 - - - +
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Residues in contact with ILE 557 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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393M SER* 3.8 29.2 - - - -
394M LEU 5.5 0.2 - - - +
395M PRO* 6.0 0.7 - - + -
549M HIS* 3.9 30.1 - - + +
550M ILE 4.1 5.4 - - - +
551M PRO* 4.8 8.7 - - + -
555M GLY 4.2 2.9 + - - +
556M ARG* 1.3 69.9 - - - +
558M VAL* 1.3 60.7 + - - +
559M SER* 3.6 13.8 + - - +
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Residues in contact with VAL 558 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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405M SER* 4.4 15.5 - - - +
408M TYR* 4.6 11.7 - - + -
549M HIS* 3.7 1.6 - - - -
550M ILE* 3.0 43.8 + - + +
552M GLU* 4.0 23.3 - - + +
556M ARG* 3.6 16.8 - - + +
557M ILE* 1.3 70.6 - - - +
559M SER* 1.3 60.4 + - - +
560M LEU* 3.4 25.4 - - + +
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Residues in contact with SER 559 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
395M PRO* 4.4 8.7 - - - +
401M LEU* 4.0 39.2 - - - +
402M SER 4.4 2.4 + - - +
405M SER* 4.8 4.3 + - - -
548M VAL 3.4 4.5 - - - -
549M HIS* 3.0 28.0 + - - -
557M ILE* 3.6 11.7 + - - +
558M VAL* 1.3 71.5 - - - +
560M LEU* 1.3 67.6 + - - +
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Residues in contact with LEU 560 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
401M LEU* 4.9 0.4 - - - -
402M SER 3.6 6.5 - - - +
403M SER 4.1 3.1 - - - +
404M GLN* 4.0 18.2 - - - +
405M SER* 4.1 7.2 - - - +
408M TYR* 3.4 43.5 - - + +
409M GLU* 4.0 4.7 - - - +
410M LEU* 3.5 14.0 - - + +
445M LEU* 4.8 1.6 - - + -
547M ARG* 3.4 1.6 - - - +
548M VAL* 2.8 40.5 + - + +
550M ILE* 4.4 11.0 - - + -
558M VAL* 3.4 32.8 - - + +
559M SER* 1.3 84.1 - - - +
561M GLN* 1.3 63.1 + - - +
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Residues in contact with GLN 561 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
397M LEU 5.2 2.0 + - - -
399M TRP 5.2 1.4 + - - -
400M PRO* 5.5 2.4 - - - +
401M LEU* 3.8 32.1 + - + +
402M SER 3.2 8.1 + - - +
403M SER* 3.0 25.1 + - - +
410M LEU* 3.5 4.2 - - - +
459M PHE* 4.7 1.6 - - - -
468M LEU* 3.5 29.1 - - - +
545M VAL* 3.7 14.9 - - + +
546M PHE 2.9 19.7 - - - +
547M ARG* 2.5 49.3 + - + +
560M LEU* 1.3 76.4 - - - +
562M THR* 1.3 64.6 + - - +
563M ALA 5.0 0.2 - - - +
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Residues in contact with THR 562 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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403M SER* 4.1 11.3 - - - -
410M LEU* 3.1 42.1 + - + +
411M ARG 4.3 7.0 - - - +
412M ILE* 5.0 9.3 - - + +
546M PHE* 2.8 45.4 + - + -
561M GLN* 1.3 79.8 - - - +
563M ALA* 1.3 72.1 + - - +
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Residues in contact with ALA 563 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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412M ILE* 3.9 9.5 - - - +
415M GLN* 4.8 0.2 + - - -
468M LEU* 4.1 21.7 - - + +
543M ARG* 3.9 33.0 - - - +
544M LEU 3.5 7.9 - - - +
545M VAL* 4.2 7.8 - - + +
561M GLN* 5.0 0.4 - - - +
562M THR* 1.3 85.9 + - - +
564M SER* 1.3 63.4 + - - +
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Residues in contact with SER 564 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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412M ILE* 3.8 9.9 - - - -
415M GLN* 3.1 16.8 - - - +
416M PRO* 3.8 11.4 - - - -
543M ARG* 3.5 20.7 + - - +
544M LEU* 2.7 50.0 + - - +
546M PHE* 4.6 0.2 - - - -
563M ALA* 1.3 78.2 - - - +
565M ASN* 1.3 74.2 + - - +
567M ILE* 3.8 3.3 - - - +
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Residues in contact with ASN 565 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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415M GLN* 2.5 43.2 + - + +
416M PRO* 4.9 4.5 - - + +
542M VAL 4.0 0.3 - - - +
543M ARG* 4.3 0.8 - - - -
564M SER* 1.3 88.6 + - - +
566M PRO* 1.3 79.1 - - + +
567M ILE* 3.1 9.2 - - - +
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Residues in contact with PRO 566 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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417M LYS 4.8 0.7 - - - +
418M PRO* 4.1 9.5 - - - +
463M ALA* 4.2 15.0 - - + +
541M ARG* 3.6 32.5 - - + +
542M VAL 3.1 11.4 - - - +
543M ARG* 4.1 15.7 - - + +
565M ASN* 1.3 93.9 - - + +
567M ILE* 1.3 63.4 + - - +
579M MET* 5.8 2.8 - - - +
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Residues in contact with ILE 567 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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416M PRO* 4.1 11.0 - - + -
417M LYS 3.9 15.0 - - - +
418M PRO 3.4 13.2 - - - +
419M HIS 4.0 0.7 - - - -
420M HIS* 3.6 32.8 - - + +
433M VAL* 5.1 3.1 - - + -
518M ILE* 5.3 1.3 - - + -
541M ARG* 3.2 5.6 - - - -
542M VAL* 2.6 51.7 + - + +
544M LEU* 3.3 32.3 - - + +
564M SER* 3.8 2.9 - - - +
565M ASN 3.1 19.5 - - - +
566M PRO* 1.3 74.6 - - - +
568M GLU* 1.3 68.8 + - - +
569M CYS* 3.8 6.1 + - - -
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Residues in contact with GLU 568 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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418M PRO 3.1 5.0 + - - +
419M HIS* 3.7 23.0 - - + +
420M HIS 3.1 23.4 + - - -
540M THR* 2.6 39.2 + - - +
541M ARG* 3.7 18.6 - - + +
567M ILE* 1.3 73.4 - - - +
569M CYS* 1.3 63.1 + - - +
570M SER 3.2 16.9 + - - +
573M SER* 2.8 44.1 - - - +
574M ALA* 5.4 0.6 - - + +
577M LEU* 5.2 4.8 - - + +
579M MET* 5.2 8.9 - - - -
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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