Contacts of the strand formed by residues 467 - 475 (chain C) 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 C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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456C LEU* 3.8 21.5 - - + -
465C SER* 2.9 17.7 - - - +
466C ASP* 1.3 84.9 - - - +
468C TYR* 1.3 57.3 + - - +
487C ILE 3.4 1.0 - - - -
488C LYS 2.9 38.1 + - - +
491C THR* 3.5 22.2 - - + +
494C PRO* 3.6 13.2 - - + -
496C TYR* 2.8 22.5 + - - +
518C VAL* 4.1 9.4 - - + -
519C VAL 3.2 9.2 - - - +
520C ASP* 4.4 0.9 - - - -
530C ILE* 4.6 1.1 - - + -
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Residues in contact with TYR 468 (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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467C PRO* 1.3 71.9 - - - +
469C VAL* 1.3 71.0 + - - +
470C LYS* 4.6 9.5 + - + -
484C LYS* 4.0 44.6 + - + -
485C THR* 3.9 2.7 - - - +
486C SER 3.0 25.8 - - - +
487C ILE* 3.9 25.4 - - + -
496C TYR* 3.5 3.8 - - - -
518C VAL* 3.5 4.2 - - - +
519C VAL* 2.8 84.9 + - + +
521C TYR* 4.1 11.7 - + + -
527C ASN* 3.2 29.3 + - - +
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Residues in contact with VAL 469 (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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433C LEU* 4.4 13.0 - - + -
450C ILE* 3.6 34.1 - - + -
468C TYR* 1.3 85.1 - - - +
470C LYS* 1.3 59.4 + - - +
471C ALA 3.8 1.2 + - - +
483C ARG 3.7 1.4 - - - +
484C LYS* 3.4 3.6 - - - -
485C THR* 3.1 42.7 + - + +
496C TYR* 3.7 20.4 - - + +
516C ILE* 3.4 33.7 - - + -
517C ALA 3.7 7.6 - - - +
518C VAL* 4.4 6.1 - - + +
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Residues in contact with LYS 470 (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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468C TYR* 4.6 14.4 + - + -
469C VAL* 1.3 71.9 - - - +
471C ALA* 1.3 61.3 + - - +
472C SER* 4.1 15.4 + - - +
482C LYS* 3.6 39.5 - - + +
483C ARG 3.6 7.6 - - - +
484C LYS* 3.8 17.1 - - + +
515C SER 3.3 7.1 - - - +
516C ILE* 4.4 0.2 - - - -
517C ALA* 3.0 43.4 + - + +
519C VAL* 4.6 14.5 - - + +
529C VAL* 5.7 5.1 - - - +
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Residues in contact with ALA 471 (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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448C VAL* 4.6 4.0 - - + -
450C ILE* 5.2 0.2 - - + -
469C VAL 3.8 2.2 + - - -
470C LYS* 1.3 73.9 - - - +
472C SER* 1.3 59.4 + - - +
482C LYS* 3.4 1.2 - - - +
483C ARG* 2.8 35.1 + - - -
500C LEU* 3.6 23.6 - - + -
502C PHE* 3.7 18.1 - - + -
514C LEU* 4.4 3.6 - - + -
515C SER 3.8 3.8 - - - -
516C ILE* 3.6 26.7 - - + -
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Residues in contact with SER 472 (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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470C LYS* 4.1 13.7 + - - +
471C ALA* 1.3 76.1 - - - +
473C LEU* 1.3 64.3 + - - +
474C ILE* 3.7 4.3 - - - +
479C ARG* 4.2 18.2 - - - -
481C LYS 3.2 9.0 - - - -
482C LYS* 3.9 13.5 - - - -
502C PHE* 4.6 0.6 - - - -
514C LEU* 3.3 4.7 - - - +
515C SER* 2.9 49.0 + - - +
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Residues in contact with LEU 473 (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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446C LEU* 4.5 15.7 - - + -
472C SER* 1.3 72.5 - - - +
474C ILE* 1.3 58.3 + - - +
475C SER 4.4 0.2 - - - -
479C ARG* 3.6 5.4 - - - +
480C LEU* 2.9 39.4 + - + -
481C LYS* 2.7 26.6 + - + +
502C PHE* 4.3 23.0 - - + -
503C ASP 4.8 3.4 - - - +
504C VAL* 3.6 27.8 - - + -
512C VAL* 3.4 28.0 - - + -
513C GLY 3.3 18.2 - - - +
514C LEU* 4.2 8.7 - - + +
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Residues in contact with ILE 474 (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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472C SER* 3.7 8.7 - - - +
473C LEU* 1.3 79.6 - - - +
475C SER* 1.3 65.6 + - - +
476C GLU 4.6 1.1 - - - +
477C GLY* 4.3 16.6 - - - +
478C ARG 3.4 10.5 - - - +
479C ARG* 4.9 7.9 - - + -
480C LEU* 4.2 0.2 - - - -
512C VAL* 3.3 3.0 - - - +
513C GLY* 2.5 45.8 + - - +
514C LEU* 4.6 1.6 - - - -
515C SER* 3.4 30.7 - - - +
534C ARG* 4.2 11.0 - - + +
573C SER* 3.4 24.7 - - - +
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Residues in contact with SER 475 (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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474C ILE* 1.3 75.6 - - - +
476C GLU* 1.3 81.3 + - - +
477C GLY 3.4 0.2 - - - -
478C ARG* 3.1 23.3 + - - +
480C LEU* 3.4 23.4 - - - +
511C ASN* 2.9 28.0 + - - +
512C VAL* 3.8 7.4 - - - -
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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