Contacts of the strand formed by residues 394 - 401 (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 ASP 394 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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327B LYS* 3.4 35.9 - - + +
385B TYR* 3.4 3.0 - - - -
386B ASP* 2.6 42.3 + - + +
388B ASP* 3.6 1.7 + - - -
392B ARG* 3.2 4.0 - - - +
393B HIS* 1.3 70.9 - - - +
395B LEU* 1.3 61.8 + - - +
601B CA 2.7 22.9 - - - -
606B CA 2.7 23.4 - - - -
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Residues in contact with LEU 395 (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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327B LYS* 3.4 20.3 + - - -
383B SER* 4.7 1.1 - - - -
384B VAL 3.2 20.2 - - - +
385B TYR* 3.4 36.7 - - + +
393B HIS 3.7 2.2 + - - -
394B ASP* 1.3 69.4 - - - +
396B ILE* 1.3 60.3 + - - +
397B GLY* 3.5 22.4 - - - +
398B GLN* 4.3 14.6 - - + +
423B GLY 4.1 9.4 - - - +
425B SER* 3.2 48.7 - - - +
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Residues in contact with ILE 396 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
324B LEU* 3.7 19.7 - - + -
325B PRO* 3.4 31.9 - - + +
327B LYS* 4.1 22.1 + - + +
333B SER* 4.2 9.4 - - - -
335B PRO* 4.0 15.9 - - + -
384B VAL* 2.7 29.6 + - + +
385B TYR 3.7 20.4 - - - +
386B ASP* 3.7 16.2 - - + +
394B ASP 3.4 0.2 + - - -
395B LEU* 1.3 76.2 - - - +
397B GLY* 1.3 57.8 + - - +
420B ILE* 4.5 3.3 - - + +
422B GLU* 3.5 24.8 - - - +
423B GLY 5.3 0.2 + - - -
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Residues in contact with GLY 397 (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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384B VAL 2.7 31.9 + - - +
395B LEU* 3.5 10.2 - - - +
396B ILE* 1.3 80.7 - - - +
398B GLN* 1.3 65.3 + - - +
420B ILE* 3.4 17.7 - - - +
421B LEU 3.5 11.9 - - - -
422B GLU* 4.5 1.1 - - - -
423B GLY 5.4 0.2 - - - -
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Residues in contact with GLN 398 (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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381B HIS* 3.6 18.7 + - + +
382B PHE 3.1 8.7 - - - +
383B SER* 3.4 24.2 + - - +
384B VAL 4.7 0.2 - - - +
385B TYR* 5.5 2.2 + - - -
395B LEU* 4.3 10.1 - - + +
397B GLY* 1.3 79.3 - - - +
399B VAL* 1.3 65.7 + - - +
420B ILE* 3.7 1.2 - - - +
421B LEU* 2.8 39.7 + - + +
425B SER* 3.6 23.1 + - - -
429B ASP* 3.0 24.8 + - - +
432B GLU* 3.1 15.0 - - - +
455B ASN* 5.7 0.8 - - - +
564B GLN* 3.3 16.2 - - - +
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Residues in contact with VAL 399 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
301B ILE* 4.1 11.4 - - + -
303B PHE* 4.6 7.9 - - + -
380B LEU 4.7 0.2 - - - -
381B HIS* 3.5 4.9 - - - -
382B PHE* 2.9 64.0 + - + +
384B VAL* 5.5 2.5 - - + -
398B GLN* 1.3 81.9 - - - +
400B VAL* 1.3 68.3 - - - +
401B LEU* 4.2 3.1 + - + -
418B ARG* 4.7 12.3 - - + +
419B ASP 3.8 8.1 - - - +
420B ILE* 3.7 31.0 - - + -
421B LEU* 4.5 4.9 - - - -
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Residues in contact with VAL 400 (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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379B LYS* 4.2 17.3 - - + -
380B LEU 3.7 9.6 - - - +
381B HIS* 4.0 11.0 - - + +
398B GLN 5.7 0.4 - - - -
399B VAL* 1.3 80.1 - - - +
401B LEU* 1.3 71.1 + - - +
402B ASP 3.7 2.1 + - - -
418B ARG* 5.1 5.5 + - - +
421B LEU* 4.7 5.2 - - + +
432B GLU* 3.6 44.4 - - + +
454B SER* 4.2 12.3 - - - +
562B TRP* 3.9 44.8 + - + -
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Residues in contact with LEU 401 (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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303B PHE* 3.5 40.2 - - + -
305B LEU* 4.4 7.9 - - + -
316B VAL* 5.9 0.4 - - + -
379B LYS* 3.7 8.5 - - - +
380B LEU* 3.0 60.7 + - + -
382B PHE* 4.2 11.9 - - + -
399B VAL* 4.2 3.3 + - + -
400B VAL* 1.3 77.7 - - - +
402B ASP* 1.3 68.0 + - - +
404B LEU* 3.7 7.3 - - + +
407B LEU* 3.6 28.0 - - + -
418B ARG* 3.9 20.4 - - + +
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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