Contacts of the strand formed by residues 504 - 510 (chain B) in PDB entry 1DY7
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 504 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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459B THR* 3.4 31.4 - - + +
460B LEU* 3.7 22.9 - - - +
461B ASN 5.8 0.7 - - - -
467B SER* 4.0 10.8 - - - +
502B GLN* 3.9 11.9 + - + +
503B PRO* 1.3 78.9 - - - +
505B VAL* 1.3 65.6 + - - +
506B VAL* 3.6 1.7 + - - +
521B VAL* 4.7 0.2 - - - -
522B TRP* 2.9 88.4 + - + +
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Residues in contact with VAL 505 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
457B ASP* 4.2 5.1 - - + +
459B THR* 2.7 32.4 + - - -
467B SER 2.9 15.5 + - - +
468B GLY* 3.5 31.0 - - - +
469B SER 4.5 2.2 - - - +
470B VAL* 3.8 28.9 - - + -
492B ILE* 3.8 17.5 - - + -
493B ALA* 3.9 10.1 - - + +
504B ARG* 1.3 72.1 - - - +
506B VAL* 1.3 56.3 + - - +
519B PHE* 4.0 18.6 - - + -
520B SER 3.1 11.4 - - - +
521B VAL* 4.3 5.6 - - + -
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Residues in contact with VAL 506 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
443B LEU* 4.2 5.6 - - + -
444B PHE* 3.6 26.0 - - + -
457B ASP* 3.7 1.6 - - - -
459B THR* 3.5 24.7 - - + +
504B ARG 4.3 2.2 - - - +
505B VAL* 1.3 77.3 - - - +
507B GLN* 1.3 72.7 + - + +
519B PHE* 4.6 4.0 - - - -
520B SER* 2.9 35.9 + - - +
522B TRP* 4.1 22.0 - - + -
554B THR* 4.5 13.9 - - - +
556B LYS* 3.1 13.2 + - - -
602B DHE 4.4 8.7 - - + -
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Residues in contact with GLN 507 (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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391B ARG* 4.6 2.2 - - - +
444B PHE* 3.5 34.8 - - + -
446B LYS* 6.1 0.4 - - + -
457B ASP* 2.8 19.4 + - - +
506B VAL* 1.3 75.6 - - + +
508B GLY* 1.3 72.0 + - - +
509B GLU* 4.6 1.6 - - - +
518B TRP 3.3 1.6 - - - +
519B PHE* 3.9 3.1 - - - -
554B THR 5.1 1.1 - - - +
555B GLY* 3.4 6.5 - - - -
556B LYS* 2.6 88.1 + - - +
557B PHE* 3.6 10.7 - - - -
602B DHE 3.2 28.5 + - + +
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Residues in contact with GLY 508 (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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444B PHE* 4.7 6.3 + - - +
446B LYS* 3.4 35.1 - - - +
457B ASP* 4.8 0.6 + - - +
507B GLN* 1.3 83.0 + - - +
509B GLU* 1.3 60.1 + - - +
517B VAL* 4.0 4.3 - - - -
518B TRP 3.2 8.7 - - - -
519B PHE* 3.4 25.9 - - - -
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Residues in contact with GLU 509 (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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169B PHE* 3.7 14.5 - - + -
391B ARG* 4.0 9.2 + - - -
446B LYS* 3.4 26.6 + - - +
507B GLN* 4.6 1.9 + - - +
508B GLY* 1.3 74.9 - - - +
510B PHE* 1.3 64.6 + - - +
517B VAL* 3.7 4.3 - - - +
518B TRP* 2.8 33.1 + - - +
556B LYS* 3.4 38.9 - - + +
557B PHE* 3.5 3.0 - - - -
558B ASN* 2.7 37.1 + - - +
561B ASN* 4.1 9.1 - - - +
562B THR* 3.8 8.0 + - - -
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Residues in contact with PHE 510 (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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169B PHE* 3.5 3.7 - - - -
446B LYS* 3.9 21.0 - - + +
447B THR* 3.4 37.7 - - - -
448B HIS* 3.7 26.0 - + + -
451B SER* 3.9 11.2 - - - -
455B TYR* 3.7 24.0 - + - -
509B GLU* 1.3 78.7 + - - +
511B ASN* 1.4 66.5 + - - +
514B GLY* 3.8 11.9 - - - -
516B GLU 3.3 18.8 - - - -
517B VAL* 4.0 17.5 - - + -
536B ASP* 3.7 20.6 - - + -
558B ASN* 3.2 17.5 - - - +
561B ASN* 3.0 22.4 + - - +
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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