Contacts of the strand formed by residues 549 - 554 (chain B) in PDB entry 1D0N
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 549 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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509B MET* 3.4 15.1 + - - +
514B GLY 5.1 3.5 + - - -
515B LYS 5.0 0.9 + - - -
516B PRO* 3.2 23.1 - - - +
517B MET 3.1 17.7 + - - -
541B VAL* 4.7 6.7 - - - -
542B ARG 3.1 16.6 - - - +
543B ALA* 3.5 15.9 - - + -
547B GLY 3.7 8.3 - - - +
548B ALA* 1.3 84.8 - - - +
550B ARG* 1.3 62.4 - - - +
586B ALA 3.6 21.9 + - - +
587B GLU* 4.8 1.6 - - - +
589B THR* 6.0 0.2 - - - +
590B GLY* 4.4 5.9 - - - -
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Residues in contact with ARG 550 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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502B GLY 3.2 24.7 + - - -
503B LYS* 5.1 3.2 - - - +
504B GLU* 3.5 40.9 + - - +
509B MET* 3.6 34.1 - - + +
516B PRO* 4.4 0.9 - - - -
517B MET* 3.3 19.7 - - + +
519B VAL* 5.1 1.3 - - + -
540B GLN 3.4 2.1 - - - +
541B VAL* 3.4 4.8 - - - -
542B ARG* 3.0 74.5 + - + +
549B THR* 1.3 77.4 - - - +
551B ALA* 1.3 57.5 + - - +
552B VAL* 3.5 25.5 - - + +
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Residues in contact with ALA 551 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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516B PRO* 4.6 4.6 - - + +
517B MET 2.9 6.5 + - - -
518B ILE* 3.7 19.6 - - + +
519B VAL* 2.9 30.3 + - - +
539B PHE* 4.5 5.7 - - + -
540B GLN 3.3 5.8 - - - -
541B VAL* 4.0 12.8 - - + +
550B ARG* 1.3 71.9 - - - +
552B VAL* 1.3 61.2 + - - +
553B GLU 4.1 0.2 - - - -
590B GLY 5.5 0.2 - - - +
594B LEU* 3.8 30.1 - - + -
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Residues in contact with VAL 552 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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501B GLN* 5.5 3.6 - - + +
502B GLY* 4.7 13.0 - - - +
504B GLU* 4.5 2.7 - - - +
519B VAL* 3.5 30.7 - - + -
539B PHE* 4.0 2.0 - - - -
540B GLN* 2.9 39.7 + - + +
542B ARG* 6.4 0.4 - - + -
550B ARG* 3.5 37.7 - - + +
551B ALA* 1.3 74.6 - - - +
553B GLU* 1.3 74.4 + - - +
554B ILE* 3.3 19.6 + - + +
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Residues in contact with GLU 553 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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501B GLN* 5.7 0.7 + - - -
519B VAL 2.9 16.6 + - - +
520B TYR* 3.4 13.5 - - - +
521B LYS* 3.6 45.2 + - + +
522B GLY* 4.3 2.3 + - - -
532B ALA 5.1 3.1 - - - +
534B ALA* 5.3 3.3 - - - +
537B ARG* 2.7 54.6 + - + +
538B LEU 3.4 13.2 - - - +
539B PHE* 3.6 17.7 - - + -
552B VAL* 1.3 74.9 - - - +
554B ILE* 1.3 73.8 + - - +
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Residues in contact with ILE 554 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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521B LYS* 4.8 5.8 - - - -
538B LEU* 2.9 28.2 + - + +
540B GLN* 4.2 25.4 - - + +
552B VAL* 3.4 28.0 - - + +
553B GLU* 1.3 88.7 - - - +
555B ILE* 1.3 89.2 + - + +
556B PRO* 3.4 6.6 - - - +
560B ALA* 4.5 16.4 - - + +
567B PHE* 5.8 1.8 - - + -
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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