Contacts of the strand formed by residues 379 - 386 (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 LYS 379 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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341B LEU* 3.4 4.4 - - - +
342B LEU* 2.8 49.5 + - + +
343B PRO* 6.5 0.7 - - - -
376B ALA 5.6 1.6 - - - +
377B GLN 5.7 1.1 - - - -
378B ARG* 1.3 85.4 - - - +
380B LEU* 1.3 64.7 + - - +
400B VAL* 4.2 10.8 - - + -
401B LEU 3.7 16.8 - - - +
402B ASP* 4.6 13.2 - - - +
404B LEU* 4.2 5.6 - - - -
452B LYS* 5.1 13.4 - - - +
453B ALA 4.5 2.4 + - - -
454B SER* 3.2 30.7 + - - +
493B ASN* 3.2 33.2 - - - +
562B TRP* 5.2 3.8 - - + -
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Residues in contact with LEU 380 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
305B LEU* 4.1 4.3 - - + -
314B LEU* 4.6 1.6 - - + -
316B VAL* 3.4 29.4 - - + -
339B ILE* 4.5 5.4 - - + -
340B TYR 3.5 15.3 - - - +
341B LEU* 3.5 24.9 - - + -
368B PHE* 4.2 16.6 - - + -
379B LYS* 1.3 75.5 - - - +
381B HIS* 1.3 62.2 + - - +
382B PHE* 4.0 18.6 - - + -
400B VAL* 3.7 6.2 - - - +
401B LEU* 3.0 51.6 + - + +
404B LEU* 3.7 23.9 - - + +
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Residues in contact with HIS 381 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
339B ILE* 3.6 0.3 - - - -
340B TYR* 2.9 53.3 + + + +
342B LEU* 4.2 33.7 - - + -
380B LEU* 1.3 78.6 - - - +
382B PHE* 1.3 70.0 + - - +
383B SER* 3.6 22.6 + - - -
398B GLN* 3.6 26.3 + - + +
399B VAL 3.5 4.5 - - - -
400B VAL* 4.0 14.6 - - + +
432B GLU* 3.7 24.6 + - - -
454B SER* 4.7 0.4 - - - -
455B ASN* 4.6 12.7 + - - -
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Residues in contact with PHE 382 (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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301B ILE* 5.1 7.0 - - + -
303B PHE* 3.2 37.0 - + - -
316B VAL* 4.0 22.7 - - + -
318B ILE* 4.7 8.7 - - + -
337B VAL* 3.9 13.9 - - + -
338B LYS 3.4 2.5 - - - -
339B ILE* 3.7 39.9 - - + -
380B LEU* 4.0 22.7 - - + -
381B HIS* 1.3 80.2 + - - +
383B SER* 1.3 60.6 + - - +
384B VAL* 4.0 4.9 + - + -
398B GLN* 3.1 9.4 - - - +
399B VAL* 2.9 56.2 + - + +
401B LEU* 4.2 7.2 - - + -
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Residues in contact with SER 383 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
337B VAL* 3.3 1.9 - - - -
338B LYS* 2.8 48.9 + - - +
340B TYR* 3.8 11.0 - - - -
381B HIS* 3.6 11.4 + - - -
382B PHE* 1.3 69.8 - - - +
384B VAL* 1.3 63.6 + - - +
385B TYR* 3.7 25.2 + - - -
395B LEU* 4.7 0.4 - - - -
397B GLY 3.7 4.3 - - - -
398B GLN* 3.4 26.1 + - - -
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Residues in contact with VAL 384 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
301B ILE* 4.8 11.4 - - + -
324B LEU* 4.4 13.5 - - + -
335B PRO* 4.6 3.8 - - + -
336B TYR 3.7 10.1 - - - +
337B VAL* 4.3 14.6 - - + +
362B PHE* 5.6 3.6 - - + -
382B PHE* 5.2 5.6 - - + +
383B SER* 1.3 73.5 - - - +
385B TYR* 1.3 56.7 + - - +
395B LEU* 3.2 5.9 - - - +
396B ILE* 2.7 61.9 + - + -
397B GLY 2.7 20.8 + - - +
399B VAL* 5.5 3.1 - - + -
420B ILE* 4.0 23.8 - - + -
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Residues in contact with TYR 385 (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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335B PRO* 3.1 4.5 - - - +
336B TYR* 2.8 57.9 + - + -
338B LYS* 3.6 45.1 + - + -
340B TYR* 5.5 0.4 - - - -
383B SER* 3.7 25.5 + - - -
384B VAL* 1.3 74.5 - - - +
386B ASP* 1.3 60.1 + - - +
393B HIS* 4.0 17.3 - - + -
394B ASP 3.4 7.0 - - - -
395B LEU* 3.4 43.6 - - + +
396B ILE* 3.7 5.6 - - - +
398B GLN* 5.5 1.9 + - - -
425B SER* 5.1 7.5 + - - -
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Residues in contact with ASP 386 (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* 3.8 21.1 - - + -
328B ASP* 3.0 11.4 - - - +
333B SER* 4.3 1.3 - - - -
334B ASP 2.5 36.0 + - - +
336B TYR* 4.0 0.9 - - - -
385B TYR* 1.3 72.5 - - - +
387B PHE* 1.3 61.4 + - - +
388B ASP* 2.7 28.2 - - - +
393B HIS* 3.5 7.8 - - - +
394B ASP* 2.6 36.0 + - + +
396B ILE* 3.7 9.0 - - + +
600B CA 2.9 11.8 - - - -
606B CA 2.7 12.7 - - - -
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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
------------------------------------------------------------
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