Contacts of the strand formed by residues 513 - 520 (chain B) in PDB entry 3HN8
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 GLY 513 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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473B LEU* 3.3 9.9 - - - +
474B ILE* 2.5 42.6 + - - -
512B VAL* 1.3 78.5 - - - +
514B LEU* 1.3 58.5 + - - -
535B VAL 3.6 10.1 - - - -
536B GLY* 4.3 4.0 - - - -
537B PRO* 4.8 1.6 - - - -
548B TRP* 4.1 11.9 - - - -
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Residues in contact with LEU 514 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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437B LEU* 4.7 6.7 - - + -
446B LEU* 4.7 11.7 - - + -
448B VAL* 3.5 34.5 - - + -
471B ALA* 4.4 5.2 - - + -
472B SER 3.3 16.2 - - - +
473B LEU* 4.2 5.6 - - + -
474B ILE* 4.2 4.5 - - - +
502B PHE* 4.5 7.2 - - + -
513B GLY* 1.3 76.5 - - - +
515B SER* 1.3 59.5 + - - +
516B ILE* 3.6 21.6 + - + -
534B ARG* 3.9 2.3 - - - +
535B VAL* 2.9 55.4 + - + +
548B TRP* 3.2 28.7 - - + +
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Residues in contact with SER 515 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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470B LYS 3.3 3.8 - - - +
472B SER* 2.9 36.7 + - - -
474B ILE* 3.4 26.4 - - - +
514B LEU* 1.3 70.6 - - - +
516B ILE* 1.3 60.8 + - - +
517B ALA* 5.0 1.9 - - - +
532B VAL* 3.6 21.0 - - - +
533B CYS 3.7 5.2 - - - -
534B ARG* 3.9 18.0 + - - +
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Residues in contact with ILE 516 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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433B LEU* 3.6 14.8 - - + -
435B PHE* 4.1 22.9 - - + -
448B VAL* 4.1 9.9 - - + -
450B ILE* 4.0 8.1 - - + -
469B VAL* 3.4 31.4 - - + -
470B LYS 3.5 4.7 - - - +
471B ALA* 3.6 15.5 - - + -
514B LEU* 3.6 39.3 - - + +
515B SER* 1.3 73.0 - - - +
517B ALA* 1.3 60.2 + - - +
532B VAL* 3.1 4.7 - - - +
533B CYS* 2.8 46.5 + - - +
535B VAL* 5.0 2.0 - - + -
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Residues in contact with ALA 517 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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469B VAL* 4.4 2.0 - - - -
470B LYS* 2.9 40.4 + - + +
515B SER* 5.0 2.2 - - - +
516B ILE* 1.3 78.9 - - - +
518B VAL* 1.3 64.8 + - - +
519B VAL* 3.5 13.1 + - + +
529B VAL* 4.7 4.9 - - + -
531B GLY 3.3 14.4 - - - +
532B VAL* 3.8 17.3 - - + +
565B LEU* 5.3 0.7 - - - -
568B GLU* 6.0 0.2 - - - +
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Residues in contact with VAL 518 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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433B LEU* 3.8 29.4 - - + -
453B ALA* 4.9 1.8 - - + -
456B LEU* 3.7 32.5 - - + -
467B PRO* 4.1 7.2 - - + -
468B TYR 3.5 8.3 - - - +
469B VAL* 4.4 9.0 - - + +
496B TYR* 5.3 0.9 - - + +
517B ALA* 1.3 72.2 - - - +
519B VAL* 1.3 63.1 + - - +
529B VAL* 3.7 0.9 - - - +
530B ILE* 2.9 35.9 + - + -
531B GLY 2.9 12.3 + - - +
565B LEU* 3.6 31.3 - - + +
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Residues in contact with VAL 519 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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467B PRO* 3.1 4.1 - - - +
468B TYR* 2.8 82.8 + - + +
470B LYS* 4.6 15.3 - - + +
517B ALA* 3.5 16.6 - - + +
518B VAL* 1.3 79.2 - - - +
520B ASP* 1.3 66.1 + - - +
527B ASN* 3.9 8.1 - - + +
528B GLU 3.5 21.1 - - - +
529B VAL* 3.9 17.5 - - + -
530B ILE* 4.1 2.9 - - - +
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Residues in contact with ASP 520 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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459B MET* 3.4 30.4 - - + +
460B ASP* 3.2 5.7 - - - +
465B SER* 4.1 0.7 - - - -
466B ASP 2.6 34.4 + - - -
519B VAL* 1.3 72.0 - - - +
521B TYR* 1.3 75.0 + - - +
522B ASP* 2.8 6.8 - - - +
527B ASN* 3.5 4.9 - - - +
528B GLU* 2.9 38.9 + - - +
530B ILE* 3.7 10.7 - - + +
602B CA 2.8 27.9 - - - -
605B CA 2.9 3.8 - - - -
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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