Contacts of the strand formed by residues 443 - 451 (chain A) in PDB entry 2YWE
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 THR 443 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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144A ARG* 2.9 21.9 + - - +
148A GLN* 4.6 4.0 - - - +
413A ILE* 3.7 28.9 - - + -
414A THR 3.6 7.9 - - - +
415A PRO* 5.0 2.6 - - - +
438A TYR* 3.3 5.6 - - - -
439A LEU* 2.7 46.3 + - + -
440A ASP* 2.8 35.9 + - - +
441A PRO 3.7 0.2 - - - -
442A ASN* 1.3 76.9 + - - +
444A VAL* 1.3 63.1 + - - +
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Residues in contact with VAL 444 (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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412A ILE 3.6 0.9 - - - +
413A ILE* 3.5 6.1 - - - +
414A THR* 2.9 36.4 + - + +
416A LYS* 4.2 9.4 - - + -
419A VAL* 3.6 34.5 - - + -
436A MET* 4.0 22.7 - - + -
437A THR 3.4 8.3 - - - +
438A TYR* 3.4 35.0 - - + +
439A LEU* 4.7 0.4 - - - -
443A THR* 1.3 76.6 - - - +
445A TYR* 1.3 72.7 + - - +
446A LEU* 4.1 8.3 - - + -
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Residues in contact with TYR 445 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
112A ALA* 6.5 0.2 - - - -
115A VAL* 5.1 18.4 - - + +
411A THR* 3.4 26.6 - - + +
412A ILE 3.3 10.3 - - - -
413A ILE* 4.2 15.9 - - + +
435A ASN* 3.5 14.1 - - - -
436A MET* 3.2 5.7 - - - -
437A THR* 2.6 59.2 + - - +
439A LEU* 3.8 21.1 - - + +
444A VAL* 1.3 76.5 - - - +
446A LEU* 1.3 62.2 + - - +
447A GLU* 2.4 48.0 + - + +
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Residues in contact with LEU 446 (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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410A VAL 3.5 0.7 - - - +
411A THR* 3.2 5.0 - - - -
412A ILE* 2.8 52.3 + - + +
414A THR* 4.8 7.0 - - + -
419A VAL* 4.7 8.5 - - + -
422A ILE* 4.0 27.1 - - + -
423A ILE* 4.4 16.2 - - + -
433A GLN* 4.0 15.3 - - - +
435A ASN 3.4 3.4 - - - +
436A MET* 3.5 40.8 - - + -
444A VAL* 4.1 8.7 - - + -
445A TYR* 1.3 77.2 - - - +
447A GLU* 1.3 64.7 + - - +
448A TYR* 4.3 15.3 - - + -
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Residues in contact with GLU 447 (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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409A LEU* 4.4 21.9 - - + +
410A VAL 3.2 4.7 - - - +
411A THR* 4.2 9.4 - - + +
433A GLN* 3.6 0.5 - - - -
434A LYS* 2.8 34.0 + - + +
435A ASN* 3.0 33.9 + - + +
445A TYR* 2.4 45.4 + - + +
446A LEU* 1.3 73.8 - - - +
448A TYR* 1.3 67.4 + - - +
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Residues in contact with TYR 448 (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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408A VAL 3.6 0.3 - - - +
409A LEU* 3.5 2.8 - - - +
410A VAL* 2.6 46.7 + - + +
412A ILE* 4.7 3.8 - - + -
423A ILE* 3.4 26.4 + - + +
426A CYS* 3.8 37.9 - - + -
427A GLN* 4.8 4.5 + - + +
431A GLY* 3.7 12.1 - - - -
432A ILE 3.5 12.6 - - - -
433A GLN* 2.9 59.5 + - + +
434A LYS* 4.8 0.2 - - - -
446A LEU* 4.3 23.8 - - + -
447A GLU* 1.3 80.8 - - - +
449A GLU* 1.3 62.1 + - - +
450A MET* 4.0 15.9 - - + -
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Residues in contact with GLU 449 (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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407A PHE* 4.5 4.2 - - + -
408A VAL 3.4 7.9 - - - +
409A LEU* 4.1 8.7 - - + +
430A ARG 4.0 1.9 - - - +
431A GLY* 3.2 4.2 - - - -
432A ILE* 2.8 44.4 + - + +
434A LYS* 3.4 39.1 + - + +
448A TYR* 1.3 72.8 - - - +
450A MET* 1.3 56.8 + - - +
478A ILE* 3.9 16.5 - - + +
481A ARG* 2.6 45.3 + - - +
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Residues in contact with MET 450 (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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407A PHE* 3.4 7.7 - - - -
408A VAL* 2.9 33.4 + - - +
410A VAL* 3.9 19.7 - - + -
426A CYS* 3.6 35.0 - - - +
429A LYS* 3.2 38.6 - - + +
430A ARG 4.4 0.2 - - - -
431A GLY* 3.6 10.1 - - - -
448A TYR* 4.0 10.5 - - + -
449A GLU* 1.3 79.5 - - - +
451A PRO* 1.3 74.0 - - + +
452A LEU 3.5 0.2 + - - -
454A GLU* 5.0 0.9 - - + -
455A ILE* 3.6 28.0 - - + -
459A PHE* 4.2 6.7 - - + -
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Residues in contact with PRO 451 (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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405A GLU* 3.3 27.1 - - - +
406A PRO 3.6 7.2 - - - +
407A PHE* 3.8 17.0 - - + -
429A LYS 3.5 17.7 - - - +
430A ARG* 3.5 44.0 - - + +
450A MET* 1.3 87.1 - - + +
452A LEU* 1.3 64.8 + - - +
453A SER* 3.7 3.1 - - - +
454A GLU* 3.1 11.8 + - + -
455A ILE* 3.4 12.2 + - - +
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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