Contacts of the strand formed by residues 467 - 475 (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 PRO 467 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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456B LEU* 3.8 20.9 - - + -
465B SER* 2.9 18.2 - - - +
466B ASP* 1.3 83.8 - - - +
468B TYR* 1.3 57.2 + - - +
487B ILE 3.4 0.9 - - - -
488B LYS 2.9 38.0 + - - +
491B THR* 3.5 22.7 - - + +
494B PRO* 3.6 14.1 - - + -
496B TYR* 2.8 22.5 + - - +
518B VAL* 4.1 9.6 - - + -
519B VAL 3.1 10.1 - - - +
520B ASP* 4.3 0.7 - - - -
530B ILE* 4.6 1.1 - - + -
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Residues in contact with TYR 468 (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* 1.3 74.1 - - - +
469B VAL* 1.3 71.6 + - - +
470B LYS* 4.6 9.9 + - + -
484B LYS* 4.0 44.4 + - + -
485B THR* 3.9 3.6 - - - +
486B SER 3.0 26.2 - - - +
487B ILE* 3.9 24.7 - - + -
496B TYR* 3.5 4.0 - - - -
517B ALA 3.9 0.2 - - - +
518B VAL* 3.5 4.3 - - - +
519B VAL* 2.8 85.8 + - + +
521B TYR* 4.1 11.4 - + + -
527B ASN* 3.2 30.2 + - - +
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Residues in contact with VAL 469 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
433B LEU* 4.3 12.8 - - + -
450B ILE* 3.6 34.3 - - + -
468B TYR* 1.3 84.1 - - - +
470B LYS* 1.3 60.1 - - - +
471B ALA 3.8 0.6 + - - +
483B ARG 3.7 1.7 - - - +
484B LYS* 3.4 3.8 - - - -
485B THR* 3.1 41.3 + - + +
496B TYR* 3.7 19.5 - - + +
516B ILE* 3.4 33.7 - - + -
517B ALA 3.7 8.3 - - - +
518B VAL* 4.4 6.5 - - + +
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Residues in contact with LYS 470 (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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468B TYR* 4.2 15.1 + - + -
469B VAL* 1.3 72.1 - - - +
471B ALA* 1.3 61.3 + - - +
472B SER* 4.1 14.1 + - - +
482B LYS* 3.6 41.0 - - + +
483B ARG 3.6 7.9 - - - +
484B LYS* 3.8 16.0 - - + +
515B SER 3.3 7.1 - - - +
516B ILE* 4.4 0.7 - - - -
517B ALA* 2.9 43.3 + - + +
519B VAL* 4.6 14.2 - - + +
529B VAL* 5.7 5.1 - - - +
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Residues in contact with ALA 471 (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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448B VAL* 4.5 4.0 - - + -
469B VAL 3.8 1.6 + - - -
470B LYS* 1.3 73.6 - - - +
472B SER* 1.3 59.4 + - - +
482B LYS* 3.4 1.2 - - - +
483B ARG* 2.8 35.9 + - - -
500B LEU* 3.6 23.6 - - + -
502B PHE* 3.7 15.7 - - + -
514B LEU* 4.4 5.4 - - + -
515B SER 3.8 3.4 - - - -
516B ILE* 3.6 27.3 - - + +
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Residues in contact with SER 472 (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* 4.1 13.3 + - - +
471B ALA* 1.3 76.5 - - - +
473B LEU* 1.3 64.4 + - - +
474B ILE* 3.5 4.2 + - - +
479B ARG* 4.2 19.3 - - - -
481B LYS 3.2 9.6 - - - -
482B LYS* 3.9 13.7 - - - -
502B PHE* 5.0 0.2 - - - -
514B LEU* 3.3 4.5 - - - +
515B SER* 2.9 49.7 + - - +
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Residues in contact with LEU 473 (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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390A PHE* 4.8 9.0 - - + -
446B LEU* 4.5 16.2 - - + -
472B SER* 1.3 71.8 - - - +
474B ILE* 1.3 59.2 + - - +
479B ARG* 3.6 4.7 - - - +
480B LEU* 2.9 38.9 + - + -
481B LYS* 2.7 25.0 + - + +
502B PHE* 4.3 23.0 - - + -
503B ASP 4.8 2.0 - - - +
504B VAL* 3.6 28.9 - - + -
512B VAL* 3.4 27.8 - - + -
513B GLY 3.3 18.2 - - - +
514B LEU* 4.2 8.1 - - + -
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Residues in contact with ILE 474 (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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472B SER* 3.7 9.2 - - - +
473B LEU* 1.3 78.7 - - - +
475B SER* 1.3 64.6 - - - +
476B GLU 4.6 0.7 - - - +
477B GLY* 4.3 15.3 - - - +
478B ARG 3.4 10.1 - - - +
479B ARG* 4.9 8.1 - - + -
512B VAL* 3.3 3.0 - - - +
513B GLY* 2.5 46.7 + - - +
514B LEU 4.7 0.7 - - - -
515B SER* 3.4 31.0 - - - +
534B ARG* 4.2 11.2 - - + +
573B SER* 3.4 26.0 - - - +
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Residues in contact with SER 475 (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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390A PHE* 4.6 12.2 - - - +
391A SER* 5.2 6.3 - - - -
474B ILE* 1.3 75.8 - - - +
476B GLU* 1.3 81.5 + - - +
477B GLY 3.4 0.9 - - - -
478B ARG* 3.1 22.5 + - - +
480B LEU* 3.4 22.3 - - - +
511B ASN* 2.8 28.8 + - - +
512B VAL* 3.7 8.0 - - - +
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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