Contacts of the strand formed by residues 552 - 556 (chain C) in PDB entry 2HDX
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 PHE 552 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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527C TRP* 3.9 14.4 - + + -
541C VAL* 4.0 4.7 - - - -
550C GLY 3.7 9.0 - - - -
551C VAL* 1.3 77.7 - - - +
553C LEU* 1.3 79.2 + - - +
554C VAL* 4.9 1.3 - - + -
566C LEU* 3.7 20.6 - - + -
567C THR 3.1 14.6 - - - +
568C PHE* 3.8 10.8 - - + -
601C LEU* 3.9 19.7 - - + -
605C ARG* 3.8 20.9 - - - -
621C LEU* 3.9 22.4 - - + -
623C SER 3.0 38.8 + - - -
624C TYR* 3.1 27.7 - + + -
625C VAL* 2.9 26.3 + - - +
531E MET* 4.3 11.9 - - + -
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Residues in contact with LEU 553 (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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527C TRP* 3.6 6.1 - - - -
529C HIS* 3.7 21.5 - - + +
532C LEU* 4.1 21.5 - - + -
537C ALA* 4.1 15.3 - - + +
540C LEU* 4.1 16.4 - - + -
541C VAL* 4.1 20.2 - - + -
552C PHE* 1.3 84.6 - - - +
554C VAL* 1.3 76.9 + - - +
555C ARG* 4.1 12.6 - - + +
566C LEU* 3.7 2.9 - - - +
567C THR* 3.0 37.0 + - - +
625C VAL* 4.2 7.0 - - + +
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Residues in contact with VAL 554 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
527C TRP* 2.9 39.8 + - + -
528C PHE* 3.6 19.6 - - + -
529C HIS* 2.8 29.1 + - - +
552C PHE* 4.9 1.8 - - + -
553C LEU* 1.3 78.0 - - - +
555C ARG* 1.3 69.0 + - - +
564C CYS* 4.3 14.4 - - + -
565C VAL 3.5 8.3 - - - +
566C LEU* 4.3 15.7 - - + -
579C LEU* 4.3 9.6 - - + -
597C ILE* 4.3 15.5 - - + -
601C LEU* 4.4 7.6 - - + -
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Residues in contact with ARG 555 (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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528C PHE* 4.8 0.9 - - - -
530C GLY 3.3 13.9 - - - +
532C LEU* 3.4 27.4 + - + +
534C ARG* 3.8 17.2 - - - +
537C ALA* 3.7 20.8 - - - +
553C LEU* 4.1 7.4 - - + -
554C VAL* 1.3 78.3 - - - +
556C GLN* 1.3 67.1 + - - +
557C SER* 5.5 0.4 - - - +
558C GLU* 6.1 2.2 - - - +
564C CYS* 3.3 6.5 - - - +
565C VAL* 2.8 60.7 + - + +
567C THR* 2.9 15.7 + - - -
576C HIS* 2.7 31.3 + - - -
813I PTR 2.8 41.4 + - - -
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Residues in contact with GLN 556 (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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623A SER* 3.2 13.7 - - - -
624A TYR* 2.8 78.5 + - + +
626A PRO* 4.6 6.9 - - - +
528C PHE* 3.3 33.0 - - + -
530C GLY 2.7 14.7 + - - +
531C MET* 3.3 18.4 + - - +
532C LEU 4.4 4.0 - - - +
555C ARG* 1.3 80.2 + - - +
557C SER* 1.3 66.4 + - - +
558C GLU* 3.5 2.3 + - - +
563C GLU 4.2 4.0 - - - +
564C CYS* 4.3 7.6 - - - -
565C VAL* 5.7 0.2 - - - -
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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