Contacts of the strand formed by residues 394 - 401 (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 ASP 394 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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327C LYS* 3.4 35.7 - - + +
385C TYR* 3.4 2.8 - - - -
386C ASP* 2.6 41.6 + - + +
388C ASP* 3.6 1.7 + - - -
392C ARG 3.2 4.3 - - - +
393C HIS* 1.3 70.3 - - - +
395C LEU* 1.3 63.5 + - - +
601C CA 2.8 22.1 - - - -
606C CA 2.8 23.6 - - - -
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Residues in contact with LEU 395 (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* 3.4 19.8 + - - -
383C SER* 4.7 0.7 - - - -
384C VAL 3.1 20.4 - - - +
385C TYR* 3.4 37.1 - - + +
393C HIS 3.7 2.4 + - - -
394C ASP* 1.3 69.8 - - - +
396C ILE* 1.3 61.5 + - - +
397C GLY* 3.5 21.1 - - - +
398C GLN* 4.4 15.3 - - + +
423C GLY 4.1 9.0 - - - +
425C SER* 3.2 48.5 - - - +
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Residues in contact with ILE 396 (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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324C LEU* 3.8 19.1 - - + -
325C PRO* 3.4 32.6 - - + +
327C LYS* 4.1 22.1 + - + +
333C SER* 4.2 9.9 - - - -
335C PRO* 4.0 14.8 - - + -
384C VAL* 2.7 31.6 + - + +
385C TYR 3.6 20.9 - - - +
386C ASP* 3.7 16.8 - - + +
395C LEU* 1.3 76.4 - - - +
397C GLY* 1.3 56.6 + - - +
420C ILE* 4.5 3.9 - - + +
422C GLU* 3.5 24.6 - - - +
423C GLY 5.3 0.5 + - - -
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Residues in contact with GLY 397 (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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384C VAL 2.7 30.4 + - - +
395C LEU* 3.5 9.5 - - - +
396C ILE* 1.3 83.5 - - - +
398C GLN* 1.3 64.5 + - - +
420C ILE* 3.4 17.5 - - - -
421C LEU 3.5 11.7 - - - -
422C GLU* 4.5 1.1 - - - -
423C GLY 5.4 0.7 - - - -
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Residues in contact with GLN 398 (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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381C HIS* 3.6 18.6 + - + +
382C PHE 3.1 9.2 - - - +
383C SER* 3.4 23.9 + - - +
384C VAL 4.7 0.2 - - - +
385C TYR* 5.5 2.2 + - - -
395C LEU* 4.4 10.3 - - + +
397C GLY* 1.3 79.7 - - - +
399C VAL* 1.3 64.8 + - - +
420C ILE* 3.7 0.8 - - - +
421C LEU* 2.8 40.6 + - + +
425C SER* 3.6 23.5 + - - -
429C ASP* 3.0 24.5 + - - +
432C GLU* 3.1 14.8 - - - +
455C ASN* 5.7 0.8 - - - +
564C GLN* 3.3 14.3 - - - +
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Residues in contact with VAL 399 (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* 4.2 11.4 - - + -
303C PHE* 4.6 9.2 - - + -
380C LEU 4.7 0.2 - - - -
381C HIS* 3.5 5.9 - - - -
382C PHE* 2.9 64.1 + - + +
384C VAL* 5.5 2.0 - - + -
398C GLN* 1.3 80.3 - - - +
400C VAL* 1.3 67.2 + - - +
401C LEU* 5.1 2.2 - - + -
418C ARG* 4.6 11.2 - - + +
419C ASP 3.8 7.6 - - - +
420C ILE* 3.7 31.6 - - + -
421C LEU* 4.5 4.5 - - - -
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Residues in contact with VAL 400 (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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342C LEU* 5.5 0.2 - - + -
379C LYS* 4.2 18.4 - - + -
380C LEU 3.7 9.6 - - - +
381C HIS* 4.0 9.9 - - + -
399C VAL* 1.3 80.1 - - - +
401C LEU* 1.3 71.0 + - - +
402C ASP 3.7 2.6 + - - -
418C ARG* 5.2 5.5 + - - +
421C LEU* 4.7 5.0 - - + +
432C GLU* 3.6 44.9 - - + +
454C SER* 4.2 12.1 - - - +
562C TRP* 3.9 43.5 + - + -
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Residues in contact with LEU 401 (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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303C PHE* 3.6 39.9 - - + -
305C LEU* 4.4 8.1 - - + -
316C VAL* 5.9 0.7 - - + -
379C LYS* 3.6 8.3 - - - +
380C LEU* 3.0 60.5 + - + -
382C PHE* 4.2 11.7 - - + -
399C VAL* 4.1 2.9 + - + -
400C VAL* 1.3 79.1 - - - +
402C ASP* 1.3 67.7 + - - +
404C LEU* 3.7 8.0 - - + +
407C LEU* 3.6 27.1 - - + -
418C ARG* 3.9 20.6 - - + +
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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