Contacts of the strand formed by residues 620 - 627 (chain C) in PDB entry 3HR4
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 ARG 620 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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584C ARG 3.4 14.4 + - - +
585C LEU* 3.2 13.7 - - + -
586C LEU 2.6 30.1 + - - -
618C LYS 5.5 2.2 + - - -
619C PHE* 1.3 90.3 - - - +
621C TYR* 1.3 55.3 + - - +
651C SER* 3.7 27.3 + - - +
653C LEU* 4.2 22.2 - - + +
683C THR* 4.3 28.9 + - - +
684C PHE* 4.7 16.5 - - + -
616G ASN 3.9 17.0 + - - -
617G ASN* 5.0 2.0 + - - +
618G LYS* 3.8 28.5 - - - +
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Residues in contact with TYR 621 (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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585C LEU* 4.5 1.3 - - - -
586C LEU* 3.1 23.1 - - + +
587C LEU* 4.7 1.3 - - - -
619C PHE* 4.2 3.4 - - + -
620C ARG* 1.3 77.0 - - - +
622C ALA* 1.3 67.1 + - - +
623C VAL* 4.1 7.0 - - + -
642C ASP* 3.4 24.6 + - - -
645C LEU* 3.4 39.0 - - + -
646C SER* 3.7 25.4 + - - -
650C ALA* 3.2 30.9 + - + -
651C SER 3.1 7.1 + - - -
652C GLN* 2.9 44.5 + - + +
653C LEU* 2.9 29.5 + - - +
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Residues in contact with ALA 622 (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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586C LEU 3.2 3.9 + - - +
587C LEU* 3.6 16.4 - - + -
588C VAL* 3.0 25.1 + - - +
621C TYR* 1.3 84.3 - - - +
623C VAL* 1.3 64.4 + - - +
653C LEU* 4.5 1.8 - - + -
654C THR* 3.4 37.5 - - + +
672C TRP* 3.5 11.5 - - + -
676C THR* 3.9 2.5 - - + -
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Residues in contact with VAL 623 (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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588C VAL* 3.4 23.6 - - + +
621C TYR* 4.1 10.5 - - + -
622C ALA* 1.3 79.2 - - - +
624C PHE* 1.3 71.0 + - - +
638C ALA* 3.7 27.6 - - + +
641C ILE* 4.5 5.2 - - + -
642C ASP* 3.7 32.9 + - + +
645C LEU* 4.5 7.2 - - + -
654C THR 4.7 3.4 + - - -
656C MET* 3.4 17.9 - - + +
657C GLY 3.0 21.6 + - - -
672C TRP* 3.3 10.6 - - - -
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Residues in contact with PHE 624 (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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553C LEU* 5.1 1.6 - - + -
588C VAL 2.8 11.4 + - - +
589C VAL* 3.3 9.8 - - + +
590C THR 3.0 24.3 + - - -
623C VAL* 1.3 79.4 - - - +
625C GLY* 1.3 58.8 + - - +
626C LEU* 3.5 29.4 - - + -
657C GLY* 3.5 16.2 - - - -
658C GLU 3.7 15.3 - - - -
659C GLY* 3.5 27.1 - - - -
665C GLN* 4.9 0.7 - - + -
668C ALA 3.8 6.3 - - - -
669C PHE* 3.2 57.2 - + + -
672C TRP* 3.6 34.3 - + + -
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Residues in contact with GLY 625 (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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590C THR 3.1 8.3 - - - -
623C VAL 4.3 0.2 - - - -
624C PHE* 1.3 75.2 - - - +
626C LEU* 1.3 59.5 + - - -
635C CYS* 3.3 12.8 - - - -
638C ALA* 3.3 23.6 - - - +
656C MET* 4.3 0.4 - - - +
657C GLY 2.9 10.2 + - - -
658C GLU* 3.3 1.2 - - - -
659C GLY 2.7 31.4 + - - -
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Residues in contact with LEU 626 (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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549C LYS* 4.3 3.4 - - + -
550C SER* 3.1 36.3 - - - +
553C LEU* 3.7 19.7 - - + -
589C VAL* 4.2 11.9 - - + -
590C THR 2.9 8.8 + - - +
591C SER* 3.8 1.0 - - - -
592C THR* 3.3 25.5 + - - -
624C PHE* 3.5 30.7 - - + -
625C GLY* 1.3 76.3 - - - -
627C GLY* 1.3 58.3 + - - +
635C CYS* 3.8 7.1 - - - -
659C GLY 3.6 4.0 - - - -
665C GLN* 3.4 37.0 - - + +
999C FMN 3.8 14.8 - - - +
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Residues in contact with GLY 627 (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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626C LEU* 1.3 78.5 - - - +
628C SER* 1.3 60.8 + - - -
634C PHE* 3.3 6.3 - - - -
635C CYS* 4.1 1.4 - - - -
659C GLY 3.2 3.8 + - - -
660C ASP* 3.1 10.0 - - - -
661C GLU 2.9 21.9 + - - -
665C GLN* 3.9 0.2 - - - +
999C FMN 3.4 35.9 - - - -
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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