Contacts of the strand formed by residues 517 - 520 (chain A) 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 MET 517 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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439A GLY 3.7 4.0 - - - +
441A PHE* 3.6 28.9 - - + -
466A TRP* 3.9 10.5 - - + +
504A GLU* 3.2 35.4 - - + -
508A LEU* 4.0 22.4 - - + +
509A MET* 4.5 9.6 + - - +
512A PHE* 3.4 31.4 - - + -
515A LYS 3.6 2.2 + - - -
516A PRO* 1.3 69.2 - - - +
518A ILE* 1.3 56.7 + - - +
519A VAL* 3.5 25.7 + - + +
549A THR 3.0 9.9 + - - +
550A ARG* 3.2 13.5 - - + +
551A ALA 2.7 33.1 + - - +
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Residues in contact with ILE 518 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
439A GLY 2.8 19.5 + - - +
440A GLN* 4.1 19.5 - - + -
441A PHE* 2.9 28.0 + - - +
515A LYS* 6.0 0.7 - - + -
516A PRO* 3.1 39.5 - - + +
517A MET* 1.3 72.1 - - - +
519A VAL* 1.3 65.9 + - - +
520A TYR* 3.8 25.8 - - + +
539A PHE* 4.2 5.6 - - + -
551A ALA* 3.5 7.9 - - + +
593A GLU* 6.4 0.2 - - + -
594A LEU* 3.5 39.3 - - + -
597A VAL* 5.1 10.8 - - + -
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Residues in contact with VAL 519 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
441A PHE* 3.5 4.9 - - + -
466A TRP* 3.8 14.4 - - + -
501A GLN* 2.9 42.8 - - + +
504A GLU* 4.5 7.9 - - - +
517A MET* 3.5 34.8 - - + +
518A ILE* 1.3 78.2 - - - +
520A TYR* 1.3 61.5 + - - +
539A PHE* 4.2 2.7 - - - -
550A ARG* 5.9 0.7 - - + -
551A ALA 2.8 15.3 + - - +
552A VAL* 3.8 16.5 - - + -
553A GLU* 3.1 26.4 + - - +
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Residues in contact with TYR 520 (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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440A GLN* 2.6 40.2 + - + +
441A PHE 3.0 26.2 + - - +
442A TYR* 3.5 45.0 - + + -
443A GLY* 2.8 28.9 + - - -
501A GLN* 3.6 2.3 + - - -
518A ILE* 3.8 20.7 - - + +
519A VAL* 1.3 72.1 - - - +
521A LYS* 1.3 58.2 + - - +
522A GLY* 2.8 11.2 + - - +
532A ALA* 5.8 2.5 - - + -
537A ARG* 3.1 27.6 - - - +
539A PHE* 3.9 13.0 - + - -
553A GLU* 3.5 8.7 - - - +
597A VAL* 3.8 13.2 - - - +
598A LEU* 4.7 12.1 - - + -
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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