Contacts of the strand formed by residues 502 - 506 (chain C) in PDB entry 2BT4
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 502 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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476C ILE* 3.3 19.7 - - + +
478C ILE* 4.4 15.0 - - + -
494C LEU* 4.2 32.8 - - + -
497C CYS* 5.2 1.6 - - + -
500C LEU* 3.7 13.2 - - + +
501C PRO* 1.3 79.2 - - - +
503C VAL* 1.3 65.6 + - - +
525C ARG* 3.7 21.1 - - - +
526C ALA* 4.0 17.5 - - + -
527C ASP* 2.8 39.7 + - - +
528C GLY 3.3 4.5 + - - -
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Residues in contact with VAL 503 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
476C ILE 2.9 9.1 + - - +
477C VAL* 3.3 5.7 - - + +
478C ILE* 2.9 26.0 + - - +
502C VAL* 1.3 79.1 - - - +
504C GLU* 1.3 72.6 + - - +
505C VAL* 3.9 3.3 + - + -
527C ASP* 5.6 0.9 - - + -
528C GLY* 3.4 18.8 - - - +
530C VAL* 4.2 14.6 - - + -
541C GLY* 3.8 25.1 - - - +
544C ARG* 4.0 30.1 - - + -
545C ILE* 4.0 15.0 - - + -
548C LEU* 5.7 1.6 - - + -
1933J CYS* 5.1 2.5 - - - -
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Residues in contact with GLU 504 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
478C ILE* 3.3 11.0 - - - +
480C PRO* 4.2 5.2 - - + -
484C SER* 4.2 1.7 + - - -
503C VAL* 1.3 74.4 - - - +
505C VAL* 1.3 64.5 + - - +
506C HIS* 2.7 30.4 + - - +
520C SER* 2.7 24.4 + - - -
522C VAL* 3.6 18.7 - - + +
523C SER* 2.4 36.4 + - - -
526C ALA* 3.7 14.5 - - + +
528C GLY 2.9 8.8 + - - +
529C VAL* 3.4 9.3 - - + +
530C VAL 2.8 26.9 + - - +
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Residues in contact with VAL 505 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
477C VAL* 3.6 30.1 - - + -
478C ILE 2.8 12.6 + - - +
479C ASN* 3.1 31.4 - - + +
503C VAL* 4.3 8.5 - - + -
504C GLU* 1.3 79.6 - - - +
506C HIS* 1.3 79.5 + - - +
530C VAL* 3.4 7.9 - - + +
534C GLY 4.9 1.3 - - - +
537C GLY* 3.6 38.6 - - - +
538C TYR* 3.9 22.9 - - + +
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Residues in contact with HIS 506 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
480C PRO* 4.0 9.2 - - + -
484C SER* 3.1 31.8 - - - -
485C HIS* 5.1 0.7 - + - -
504C GLU* 2.7 29.8 + - + -
505C VAL* 1.3 80.0 + - - +
507C ILE* 1.3 59.9 - - - +
508C SER 3.4 15.0 - - - +
510C ILE* 4.1 31.4 - - + +
520C SER* 4.7 0.4 + - - -
523C SER* 5.3 0.2 + - - -
529C VAL* 4.7 5.8 - - + -
530C VAL* 2.9 12.9 + - - +
531C ALA* 3.4 13.9 - - + -
532C GLY 3.1 19.2 + - - -
533C CYS 4.4 2.3 + - - -
534C GLY 4.7 0.5 - - - +
537C GLY* 5.9 0.3 - - - -
560C CA2 3.1 32.2 + - + +
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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
------------------------------------------------------------
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