Contacts of the strand formed by residues 379 - 386 (chain A) 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 A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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341A LEU* 3.4 4.7 - - - +
342A LEU* 2.8 46.5 + - + +
343A PRO* 6.5 0.7 - - - -
376A ALA 5.6 1.6 - - - +
377A GLN 5.7 1.3 - - - -
378A ARG* 1.3 85.9 - - - +
380A LEU* 1.3 64.4 + - - +
400A VAL* 4.2 10.5 - - + +
401A LEU 3.6 17.3 - - - +
402A ASP* 4.6 13.0 - - - +
403A ASN 5.7 0.2 - - - +
404A LEU* 4.2 5.6 - - - -
452A LYS* 5.1 13.9 - - - +
453A ALA 4.5 2.0 + - - -
454A SER* 3.2 31.3 + - - +
493A ASN* 3.2 34.2 - - - +
562A TRP* 5.2 4.0 - - + -
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Residues in contact with LEU 380 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
305A LEU* 4.1 4.5 - - + -
314A LEU* 4.6 2.0 - - + -
316A VAL* 3.4 29.4 - - + -
339A ILE* 4.5 5.8 - - + -
340A TYR 3.5 15.3 - - - +
341A LEU* 3.6 24.5 - - + -
368A PHE* 4.2 15.9 - - + -
379A LYS* 1.3 74.7 - - - +
381A HIS* 1.3 62.5 + - - +
382A PHE* 4.0 18.6 - - + -
400A VAL* 3.7 6.4 - - - +
401A LEU* 3.0 51.5 + - + +
404A LEU* 3.7 23.2 - - + +
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Residues in contact with HIS 381 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
339A ILE* 3.7 0.3 - - - -
340A TYR* 2.9 53.4 + + + +
342A LEU* 4.1 33.4 - - + -
380A LEU* 1.3 75.9 - - - +
382A PHE* 1.3 70.1 + - - +
383A SER* 3.6 22.8 + - - -
398A GLN* 3.6 27.8 + - + +
399A VAL 3.5 4.7 - - - -
400A VAL* 4.0 14.3 - - + +
432A GLU* 3.7 24.0 + - - -
454A SER* 4.7 0.4 - - - -
455A ASN* 4.6 13.8 + - - -
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Residues in contact with PHE 382 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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301A ILE* 5.1 6.5 - - + -
303A PHE* 3.2 36.3 - + - -
316A VAL* 4.0 23.3 - - + -
318A ILE* 4.7 8.3 - - + -
337A VAL* 3.9 14.6 - - + -
338A LYS 3.4 2.2 - - - -
339A ILE* 3.7 39.7 - - + -
380A LEU* 4.0 23.6 - - + -
381A HIS* 1.3 79.7 + - - +
383A SER* 1.3 60.4 + - - +
384A VAL* 4.0 5.5 + - + +
398A GLN* 3.1 8.5 - - - +
399A VAL* 2.9 57.4 + - + +
401A LEU* 4.2 7.9 - - + -
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Residues in contact with SER 383 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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337A VAL* 3.3 2.6 - - - -
338A LYS* 2.8 48.8 + - - +
340A TYR* 3.8 11.6 - - - -
381A HIS* 3.6 11.2 + - - -
382A PHE* 1.3 69.4 - - - +
384A VAL* 1.3 63.0 + - - +
385A TYR* 3.7 26.1 + - - -
395A LEU* 4.7 0.7 - - - -
397A GLY 3.7 4.5 - - - -
398A GLN* 3.4 25.2 + - - -
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Residues in contact with VAL 384 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
301A ILE* 4.8 10.8 - - + -
324A LEU* 4.5 13.9 - - + -
335A PRO* 4.6 4.0 - - + -
336A TYR 3.7 9.6 - - - +
337A VAL* 4.3 15.7 - - + +
362A PHE* 5.6 2.9 - - + -
382A PHE* 5.1 5.8 - - + +
383A SER* 1.3 74.1 - - - +
385A TYR* 1.3 57.3 + - - +
395A LEU* 3.1 9.4 - - - +
396A ILE* 2.7 60.1 + - + -
397A GLY 2.7 17.7 + - - +
399A VAL* 5.5 3.1 - - + -
420A ILE* 4.0 23.6 - - + -
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Residues in contact with TYR 385 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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335A PRO* 3.1 3.8 - - - +
336A TYR* 2.8 59.1 + - + +
338A LYS* 3.6 44.4 + - + -
340A TYR* 5.5 0.4 - - - -
383A SER* 3.7 24.8 + - - -
384A VAL* 1.3 74.5 - - - +
386A ASP* 1.3 60.3 + - - +
393A HIS* 4.1 17.9 - - + -
394A ASP 3.4 7.4 - - - -
395A LEU* 3.4 41.8 - - + +
396A ILE* 3.6 5.8 - - - +
398A GLN* 5.5 1.7 + - - -
425A SER* 5.1 7.2 + - - -
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Residues in contact with ASP 386 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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327A LYS* 3.8 21.5 - - + -
328A ASP* 2.9 14.6 - - - +
333A SER* 3.4 1.5 - - - -
334A ASP 2.5 35.8 + - - +
336A TYR* 4.0 1.1 - - - -
385A TYR* 1.3 72.5 - - - +
387A PHE* 1.3 63.8 + - - +
388A ASP* 2.7 14.6 - - - +
393A HIS* 3.5 7.4 - - - +
394A ASP* 2.6 36.4 + - + +
396A ILE* 3.7 9.0 - - + +
600A CA 3.1 6.4 - - - -
606A CA 2.6 26.3 - - - -
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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