Contacts of the strand formed by residues 524 - 531 (chain C) in PDB entry 5UHA
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 VAL 524 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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517C ARG* 3.4 47.6 - - + +
518C LYS 3.9 3.6 - - - +
519C VAL* 4.0 7.2 - - + -
523C VAL* 1.3 76.0 - - - +
525C SER* 1.3 64.5 + - - +
526C ASP* 4.2 5.8 + - - +
548C ILE* 4.0 15.5 - - + -
551C ASP 4.8 2.8 - - - +
552C GLY* 2.7 26.0 + - - +
554C PHE* 3.8 20.0 - - + -
579C MET* 3.8 21.8 - - - -
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Residues in contact with SER 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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517C ARG* 4.0 10.2 - - - +
518C LYS* 2.7 34.0 + - - +
520C VAL* 4.6 14.1 - - - -
523C VAL 3.3 4.9 + - - -
524C VAL* 1.3 75.0 - - - +
526C ASP* 1.3 60.1 + - - +
527C GLU* 3.0 37.5 + - - +
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Residues in contact with ASP 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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46C GLU* 4.0 25.9 - - - +
47C PRO* 5.7 3.0 - - - +
517C ARG* 5.0 14.4 + - - +
524C VAL* 4.6 5.4 - - - +
525C SER* 1.3 71.2 + - - +
527C GLU* 1.3 63.9 + - - +
528C ILE* 3.4 18.5 + - - +
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Residues in contact with GLU 527 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
518C LYS* 3.1 66.9 + - + +
525C SER* 3.0 17.2 + - - +
526C ASP* 1.3 77.0 - - - +
528C ILE* 1.3 68.5 + - - +
529C VAL* 5.7 3.4 - - + +
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Residues in contact with ILE 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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47C PRO 4.2 9.4 - - - +
48C LEU* 3.4 38.1 - - + -
515C PRO* 4.0 16.4 - - + -
516C TYR 3.5 27.8 - - - +
517C ARG* 4.6 11.7 - - + -
526C ASP* 3.4 18.5 + - - +
527C GLU* 1.3 80.5 - - - +
529C VAL* 1.3 66.2 + - - +
530C TYR* 5.5 7.3 - - + -
581C VAL* 4.9 0.4 - - + -
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Residues in contact with VAL 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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516C TYR 3.4 17.6 + - - +
518C LYS* 5.2 8.3 - - + -
527C GLU* 5.7 4.0 - - + +
528C ILE* 1.3 78.6 - - - +
530C TYR* 1.3 74.7 + - - +
531C LEU* 3.2 17.1 - - + +
578C TYR* 3.5 39.3 - - + +
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Residues in contact with TYR 530 (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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48C LEU* 5.3 7.1 - - - +
51C PRO* 5.1 11.4 - - - +
503C TYR 4.0 9.6 + - - -
505C ARG* 3.2 53.5 + - + +
513C GLU* 3.2 28.6 - - + +
514C THR* 3.4 9.4 - - - -
515C PRO* 3.3 51.5 - - + +
528C ILE* 5.5 5.8 - - + -
529C VAL* 1.3 89.9 - - - +
531C LEU* 1.3 61.6 + - - +
535C GLU* 4.4 4.3 - - - +
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Residues in contact with LEU 531 (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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482C ARG* 3.3 6.2 + - - -
513C GLU* 3.2 4.8 - - - -
514C THR* 3.2 25.0 + - - +
516C TYR* 3.8 31.2 - - + -
529C VAL* 3.2 34.3 - - + +
530C TYR* 1.3 77.2 - - - +
532C THR* 1.3 71.0 + - - +
535C GLU* 3.9 13.0 - - + +
536C GLU* 3.9 27.6 - - + +
539C HIS* 4.7 7.0 - - + -
541C VAL* 5.6 0.2 - - + -
578C TYR* 4.0 28.9 - - + +
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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