Contacts of the strand formed by residues 335 - 342 (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 PRO 335 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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324B LEU* 3.6 21.5 - - + -
333B SER* 2.9 26.9 - - - +
334B ASP* 1.3 76.3 - - - +
336B TYR* 1.3 59.5 + - - +
354B HIS* 3.1 35.1 + - - +
357B THR* 3.5 14.4 - - + +
360B PRO* 3.7 30.3 - - + -
362B PHE* 4.0 8.0 - - + -
384B VAL* 4.6 2.5 - - + -
385B TYR 3.1 9.4 - - - +
396B ILE* 4.0 9.6 - - + -
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Residues in contact with TYR 336 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
335B PRO* 1.3 74.0 - - - +
337B VAL* 1.3 65.4 + - - +
338B LYS* 4.0 20.0 + - + -
350B GLN* 3.7 39.1 + - + -
351B THR* 3.4 11.7 - - - +
352B LYS 3.5 16.4 - - - +
353B VAL* 3.8 14.4 - - + -
362B PHE* 4.0 4.3 - - - -
384B VAL* 3.7 1.9 - - - +
385B TYR* 2.8 65.6 + - + +
387B PHE* 3.7 24.7 - + + -
393B HIS* 3.2 36.7 - + - +
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Residues in contact with VAL 337 (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 4.7 - - + -
318B ILE* 3.8 23.6 - - + -
336B TYR* 1.3 79.4 - - - +
338B LYS* 1.3 75.6 + - - +
339B ILE* 3.9 3.3 + - + +
349B PHE 3.8 0.5 - - - +
350B GLN* 3.7 3.0 - - - -
351B THR* 2.7 52.6 + - + +
362B PHE* 3.7 23.8 - - + -
382B PHE* 3.9 18.6 - - + -
383B SER 3.3 8.3 - - - +
384B VAL* 4.3 12.6 - - + -
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Residues in contact with LYS 338 (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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336B TYR* 4.0 18.2 + - + -
337B VAL* 1.3 80.1 - - - +
339B ILE* 1.3 59.2 - - - +
340B TYR* 3.5 32.8 + - + +
348B LYS* 3.9 20.2 - - + +
349B PHE 3.6 5.4 - - - +
350B GLN* 3.5 34.5 - - + +
382B PHE* 3.4 1.0 - - - -
383B SER* 2.8 36.3 + - - +
385B TYR* 3.6 34.2 + - + -
393B HIS* 6.3 0.2 - - - +
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Residues in contact with ILE 339 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
316B VAL* 5.3 2.7 - - + -
318B ILE* 3.4 28.9 - - + -
337B VAL 4.0 8.3 - - - +
338B LYS* 1.3 80.8 - - - +
340B TYR* 1.3 70.3 + - - +
347B LYS 3.3 1.4 - - - +
348B LYS* 2.9 27.6 - - - +
349B PHE* 3.0 19.1 + - + +
366B PHE* 3.7 33.9 - - + -
368B PHE* 3.8 28.9 - - + -
380B LEU* 4.5 0.9 - - + -
381B HIS 3.6 2.5 - - - -
382B PHE* 3.7 28.9 - - + -
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Residues in contact with TYR 340 (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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338B LYS* 3.5 38.6 + - + +
339B ILE* 1.3 75.2 - - - +
341B LEU* 1.3 60.4 + - - +
342B LEU* 3.9 20.0 - - + -
344B ASP 4.2 3.1 - - - +
345B ARG* 3.2 28.0 - - - -
346B LYS 3.9 9.0 - - - -
347B LYS 3.6 4.7 - - - -
348B LYS* 3.8 26.6 + - + +
368B PHE* 5.2 0.9 - - - -
380B LEU* 3.5 10.2 - - - +
381B HIS* 2.9 52.2 + + + +
383B SER* 3.8 19.0 + - - -
385B TYR* 5.5 0.2 - - - -
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Residues in contact with LEU 341 (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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314B LEU* 4.0 17.3 - - + -
340B TYR* 1.3 74.7 - - - +
342B LEU* 1.3 68.7 + - - +
344B ASP* 3.2 22.9 + - - +
347B LYS* 4.0 19.1 + - - +
368B PHE* 3.9 34.1 - - + -
370B VAL* 4.2 12.1 - - + -
378B ARG* 3.1 55.8 + - + +
379B LYS 3.4 5.4 - - - +
380B LEU* 3.5 22.9 - - + -
404B LEU* 4.3 5.6 - - + -
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Residues in contact with LEU 342 (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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340B TYR* 4.1 21.5 - - + -
341B LEU* 1.3 72.3 - - - +
343B PRO* 1.3 68.3 - - + +
344B ASP 3.3 6.7 - - - +
345B ARG* 5.4 6.1 - - + -
378B ARG* 2.7 33.6 + - - +
379B LYS* 2.8 45.6 + - + +
381B HIS* 4.2 23.1 - - + -
400B VAL* 5.5 0.7 - - + -
454B SER* 3.4 25.1 - - - +
455B ASN* 4.8 12.3 - - + +
493B ASN* 4.5 7.2 - - - +
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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