Contacts of the strand formed by residues 524 - 529 (chain C) in PDB entry 1DD1
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 TRP 524 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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370B VAL* 4.0 20.2 - - + -
328C TYR* 3.6 1.8 - - - -
329C PHE* 2.7 79.7 + + + +
331C MET 2.7 27.4 + - - -
332C ASP* 5.1 0.2 - - - -
502C ARG* 4.1 22.2 - - + -
503C MET 3.1 15.5 - - - +
504C SER* 3.8 4.0 - - - -
505C PHE* 4.5 1.8 - - - -
518C ILE* 3.3 49.2 + - + -
519C LYS* 3.9 15.0 - - + -
521C THR* 3.2 25.6 - - - +
523C CYS* 1.3 75.1 - - - +
525C ILE* 1.3 77.9 + - - +
526C GLU* 4.3 9.6 - - + -
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Residues in contact with ILE 525 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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326C ILE* 4.0 17.5 - - + -
327C ALA 3.2 10.3 - - - +
328C TYR* 4.1 16.8 - - + -
350C VAL* 4.6 19.3 - - + -
362C PHE* 5.3 0.4 - - + -
364C LEU* 4.7 0.4 - - + -
387C VAL* 4.9 1.6 - - + -
389C LEU* 4.9 2.5 - - + -
501C LEU 4.0 0.3 - - - +
502C ARG* 3.4 5.7 - - - +
503C MET* 2.9 60.1 + - + +
505C PHE* 3.8 28.0 - - + -
524C TRP* 1.3 86.1 - - - +
526C GLU* 1.3 60.7 + - - +
527C ILE* 3.4 23.3 - - + -
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Residues in contact with GLU 526 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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368B SER* 3.0 30.2 + - - -
325C SER 3.4 4.0 - - - +
326C ILE* 3.5 0.9 - - - -
327C ALA* 2.9 37.4 + - + +
329C PHE* 4.3 14.2 - - + -
500C ILE* 3.5 23.2 - - + +
501C LEU 3.4 2.5 - - - -
502C ARG* 2.8 43.6 + - + -
524C TRP* 4.3 11.2 - - + -
525C ILE* 1.3 75.0 - - - +
527C ILE* 1.3 59.7 + - - +
528C HIS* 3.4 18.6 + - + -
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Residues in contact with ILE 527 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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323C TRP* 5.5 0.7 - - + -
324C CYS* 3.8 28.9 - - + -
325C SER 3.3 8.7 - - - +
326C ILE* 4.0 11.9 - - + -
389C LEU* 3.9 21.5 - - + -
397C VAL* 6.5 0.7 - - + -
500C ILE* 3.3 8.1 - - - +
501C LEU* 2.7 57.4 + - + +
502C ARG* 5.4 0.2 - - - -
503C MET* 5.2 6.3 - - + -
525C ILE* 3.4 39.7 - - + +
526C GLU* 1.3 75.6 - - - +
528C HIS* 1.3 64.2 + - - +
529C LEU* 3.8 10.6 + - + +
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Residues in contact with HIS 528 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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356B PRO* 6.2 0.7 - - + -
366B GLN* 3.1 34.6 + - + -
367B LEU* 4.8 1.4 - - + +
368B SER* 3.9 7.8 + - - -
324C CYS* 3.0 26.0 - - - -
325C SER* 2.8 31.9 + - - +
327C ALA* 6.2 1.2 - - + +
499C CYS 4.1 2.7 - - - -
500C ILE* 3.7 16.3 - - + +
526C GLU* 3.4 35.6 + - + +
527C ILE* 1.3 75.0 - - - +
529C LEU* 1.3 63.1 + - - +
530C HIS* 3.4 4.6 - - + +
533C LEU* 3.9 24.0 - - + -
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Residues in contact with LEU 529 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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323C TRP* 3.8 8.3 - - + +
324C CYS* 4.1 14.1 - - + -
395C GLY 5.4 0.4 - - - +
397C VAL* 4.2 22.0 - - + -
438C PHE* 3.9 35.7 - - + -
499C CYS 3.0 28.2 + - - +
500C ILE* 4.8 0.7 - - - -
501C LEU* 3.9 24.2 - - + -
527C ILE* 4.1 13.0 - - + -
528C HIS* 1.3 74.4 - - - +
530C HIS* 1.3 60.9 + - - +
531C ARG 3.5 1.1 - - - +
532C ALA* 3.4 15.3 + - + +
533C LEU* 3.0 30.2 + - - +
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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