Contacts of the strand formed by residues 379 - 386 (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 LYS 379 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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341C LEU* 3.4 4.6 - - - +
342C LEU* 2.8 49.5 + - + +
343C PRO* 6.5 0.7 - - - -
376C ALA 5.6 1.3 - - - +
377C GLN 5.7 1.3 - - - -
378C ARG* 1.3 84.5 - - - +
380C LEU* 1.3 64.8 + - - +
400C VAL* 4.2 10.3 - - + -
401C LEU 3.6 16.2 - - - +
402C ASP* 4.6 12.8 - - - +
403C ASN 5.7 0.2 - - - +
404C LEU* 4.2 6.1 - - - -
452C LYS* 5.1 14.4 - - - +
453C ALA 4.5 2.2 + - - -
454C SER* 3.2 31.1 + - - +
493C ASN* 3.2 34.7 - - - +
562C TRP* 5.2 3.7 - - + -
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Residues in contact with LEU 380 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
305C LEU* 4.1 4.0 - - + -
314C LEU* 4.6 2.5 - - + -
316C VAL* 3.4 29.4 - - + -
339C ILE* 4.5 5.2 - - + -
340C TYR 3.5 14.8 - - - +
341C LEU* 3.5 24.0 - - + -
368C PHE* 4.2 16.6 - - + -
379C LYS* 1.3 74.9 - - - +
381C HIS* 1.3 61.8 + - - +
382C PHE* 4.0 18.8 - - + -
400C VAL* 3.7 6.6 - - - +
401C LEU* 3.0 53.3 + - + +
404C LEU* 3.7 23.2 - - + +
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Residues in contact with HIS 381 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
339C ILE* 3.6 0.7 - - - -
340C TYR* 2.9 53.2 + + + +
342C LEU* 4.1 33.4 - - + -
380C LEU* 1.3 76.5 - - - +
382C PHE* 1.3 70.4 + - - +
383C SER* 3.6 22.2 + - - -
398C GLN* 3.6 28.3 + - + +
399C VAL 3.5 4.5 - - - -
400C VAL* 4.0 14.4 - - + -
432C GLU* 3.7 24.3 + - - -
454C SER* 4.7 0.2 - - - -
455C ASN* 4.6 13.5 + - - -
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Residues in contact with PHE 382 (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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301C ILE* 5.1 6.5 - - + -
303C PHE* 3.2 36.6 - + - -
316C VAL* 4.0 23.1 - - + -
318C ILE* 4.7 8.3 - - + -
337C VAL* 3.9 14.6 - - + -
338C LYS 3.4 2.0 - - - -
339C ILE* 3.7 40.8 - - + -
380C LEU* 4.0 24.0 - - + -
381C HIS* 1.3 76.7 + - - +
383C SER* 1.3 62.5 + - - +
384C VAL* 4.0 4.9 - - + -
398C GLN* 3.1 9.2 - - - +
399C VAL* 2.9 57.3 + - + +
401C LEU* 4.2 8.1 - - + -
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Residues in contact with SER 383 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
337C VAL* 3.3 2.2 - - - -
338C LYS* 2.8 48.5 + - - +
340C TYR* 3.8 11.7 - - - -
381C HIS* 3.6 11.2 + - - -
382C PHE* 1.3 70.3 - - - +
384C VAL* 1.3 63.1 + - - +
385C TYR* 3.7 26.0 + - - -
395C LEU* 4.7 0.9 - - - -
397C GLY 3.7 5.2 - - - -
398C GLN* 3.4 24.0 + - - -
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Residues in contact with VAL 384 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
301C ILE* 4.8 10.8 - - + -
324C LEU* 4.4 14.1 - - + -
335C PRO* 4.6 4.3 - - + -
336C TYR 3.7 9.6 - - - +
337C VAL* 4.3 14.8 - - + +
362C PHE* 5.6 3.4 - - + -
382C PHE* 5.2 5.4 - - + +
383C SER* 1.3 75.0 - - - +
385C TYR* 1.3 57.2 + - - +
395C LEU* 3.1 8.8 - - - +
396C ILE* 2.7 59.9 + - + -
397C GLY 2.7 19.1 + - - +
399C VAL* 5.5 2.9 - - + -
420C ILE* 4.0 24.5 - - + -
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Residues in contact with TYR 385 (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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335C PRO* 3.1 4.7 - - - +
336C TYR* 2.8 57.9 + - + +
338C LYS* 3.6 44.1 + - + -
340C TYR* 5.5 0.4 - - - -
383C SER* 3.7 25.3 + - - -
384C VAL* 1.3 74.0 - - - +
386C ASP* 1.3 60.2 + - - +
387C PHE 3.9 0.2 - - - -
393C HIS* 4.1 18.8 - - + -
394C ASP 3.4 7.2 - - - -
395C LEU* 3.4 42.0 - - + +
396C ILE* 3.6 5.6 - - - +
398C GLN* 5.5 1.9 + - - -
425C SER* 5.1 7.8 + - - -
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Residues in contact with ASP 386 (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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327C LYS* 3.8 21.3 - - + -
328C ASP* 3.0 10.6 - - - +
333C SER* 3.4 1.1 - - - -
334C ASP* 2.5 36.3 + - - +
336C TYR* 4.0 0.9 - - - -
385C TYR* 1.3 72.1 - - - +
387C PHE* 1.3 60.5 + - - +
388C ASP* 2.7 28.1 - - - +
393C HIS* 3.5 7.3 - - - +
394C ASP* 2.6 36.5 + - + +
396C ILE* 3.7 9.2 - - + +
600C CA 3.0 12.6 - - - -
606C CA 2.7 12.1 - - - -
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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