Contacts of the strand formed by residues 335 - 342 (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 335 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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324C LEU* 3.6 21.3 - - + -
333C SER* 2.9 27.6 - - - +
334C ASP* 1.3 76.9 - - - +
336C TYR* 1.3 60.8 + - - +
354C HIS* 3.0 35.7 + - - +
357C THR* 3.5 15.0 - - + +
360C PRO* 3.7 30.5 - - + -
362C PHE* 4.0 7.7 - - + -
384C VAL* 4.6 2.5 - - + -
385C TYR 3.1 9.0 - - - +
386C ASP* 4.5 0.2 - - - -
396C ILE* 4.0 9.4 - - + -
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Residues in contact with TYR 336 (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* 1.3 74.2 - - - +
337C VAL* 1.3 66.9 + - - +
338C LYS* 4.0 19.3 + - + -
350C GLN* 3.7 39.5 + - + -
351C THR* 3.4 12.3 - - - +
352C LYS 3.5 15.7 - - - +
353C VAL* 3.9 13.2 - - + -
362C PHE* 4.0 3.8 - - - -
384C VAL* 3.7 1.9 - - - +
385C TYR* 2.8 64.4 + - + +
387C PHE* 3.7 24.9 - + + -
393C HIS* 3.2 36.3 - + - +
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Residues in contact with VAL 337 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
301C ILE* 4.9 4.5 - - + -
318C ILE* 3.8 24.7 - - + -
336C TYR* 1.3 80.0 - - - +
338C LYS* 1.3 73.9 + - - +
339C ILE* 4.0 3.4 - - + +
349C PHE 3.8 0.7 - - - +
350C GLN* 3.7 2.6 - - - -
351C THR* 2.7 51.9 + - + +
362C PHE* 3.7 22.9 - - + -
382C PHE* 3.9 18.2 - - + -
383C SER 3.3 7.2 - - - +
384C VAL* 4.3 12.6 - - + -
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Residues in contact with LYS 338 (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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336C TYR* 4.0 19.2 + - + -
337C VAL* 1.3 79.6 - - - +
339C ILE* 1.3 59.9 + - - +
340C TYR* 3.5 31.9 + - + +
348C LYS* 3.9 19.5 - - + +
349C PHE 3.5 5.6 - - - +
350C GLN* 3.5 34.5 - - + +
381C HIS 4.5 0.2 - - - -
382C PHE* 3.4 1.2 - - - -
383C SER* 2.8 35.7 + - - +
385C TYR* 3.6 34.3 + - + -
393C HIS* 6.3 0.2 - - - +
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Residues in contact with ILE 339 (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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316C VAL* 5.3 2.5 - - + -
318C ILE* 3.4 28.5 - - + -
337C VAL* 4.0 8.5 - - + +
338C LYS* 1.3 80.7 - - - +
340C TYR* 1.3 69.8 + - - +
347C LYS 3.3 1.2 - - - +
348C LYS* 2.9 28.3 - - - +
349C PHE* 3.0 18.2 + - + +
366C PHE* 3.7 33.7 - - + -
368C PHE* 3.8 27.8 - - + -
380C LEU* 4.5 1.6 - - + -
381C HIS 3.6 2.9 - - - -
382C PHE* 3.7 29.8 - - + -
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Residues in contact with TYR 340 (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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338C LYS* 3.5 38.3 + - + +
339C ILE* 1.3 75.9 - - - +
341C LEU* 1.3 59.5 + - - +
342C LEU* 3.9 20.0 - - + -
344C ASP 4.2 3.1 - - - +
345C ARG* 3.2 28.5 - - - -
346C LYS 3.9 2.7 - - - -
347C LYS 3.6 4.5 - - - -
348C LYS* 3.7 33.6 + - + +
368C PHE* 5.1 0.7 - - - -
380C LEU* 3.5 10.2 - - - +
381C HIS* 2.9 52.2 + + + +
383C SER* 3.8 19.0 + - - -
385C TYR* 5.5 0.2 - - - -
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Residues in contact with LEU 341 (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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314C LEU* 4.0 17.0 - - + -
340C TYR* 1.3 75.0 - - - +
342C LEU* 1.3 68.2 + - - +
344C ASP* 3.2 23.0 + - - +
347C LYS* 4.0 19.7 + - + +
368C PHE* 3.9 34.5 - - + -
370C VAL* 4.2 11.4 - - + -
378C ARG* 3.1 56.0 + - + +
379C LYS 3.4 5.8 - - - +
380C LEU* 3.5 22.4 - - + -
404C LEU* 4.3 5.8 - - + -
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Residues in contact with LEU 342 (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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340C TYR* 4.1 14.4 - - + -
341C LEU* 1.3 73.0 - - - +
343C PRO* 1.3 68.1 - - + +
344C ASP 3.3 6.7 - - - +
345C ARG* 5.5 6.3 - - + -
378C ARG* 2.7 33.0 + - - +
379C LYS* 2.8 45.5 + - + +
381C HIS* 4.1 32.1 - - + -
400C VAL* 5.5 0.4 - - + -
454C SER* 3.4 25.1 - - - +
455C ASN* 4.8 12.8 - - + +
493C ASN* 4.5 7.0 - - - +
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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