Contacts of the strand formed by residues 336 - 344 (chain B) in PDB entry 3N9V
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 TYR 336 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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429A PRO* 3.7 24.1 - - + +
293B ALA* 3.4 13.7 - - - +
294B PRO* 2.7 45.3 + - - +
295B ASP 4.4 2.0 - - - -
297B TYR* 3.5 27.5 - + - -
330B LEU* 3.7 35.4 - - + -
331B HIS* 3.4 21.6 - - - +
334B ALA* 3.7 17.5 + - + -
335B LYS* 1.3 80.0 - - - +
337B ALA* 1.3 59.7 + - - +
352B TYR* 4.2 8.5 - - + -
353B VAL* 3.4 7.9 - - - +
354B LYS* 3.3 31.0 - - + -
355B GLN* 4.6 1.1 - - - -
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Residues in contact with ALA 337 (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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427A PRO* 3.6 23.8 - - + +
428A ASP* 5.6 0.7 - - - +
429A PRO* 5.0 0.2 - - - -
336B TYR* 1.3 75.0 - - - +
338B LYS* 1.3 63.5 + - - +
339B VAL* 3.4 3.6 + - + +
352B TYR* 3.2 7.2 - - - -
353B VAL* 2.8 36.0 + - + +
355B GLN* 4.3 12.5 - - + +
358B ALA* 4.6 19.7 - - + -
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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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365A GLU* 5.2 4.0 + - - -
425A CYS* 2.4 44.8 - - - +
426A GLN 4.6 9.0 - - - +
427A PRO* 3.1 29.3 + - + +
429A PRO* 5.2 2.2 - - + +
323B PHE* 3.5 40.1 - - + -
337B ALA* 1.3 71.3 - - - +
339B VAL* 1.3 64.8 - - - +
340B LYS* 4.1 16.4 - - - +
341B LEU* 4.6 19.4 - - + +
350B LEU* 5.5 1.1 - - + -
351B LEU 3.8 9.6 - - - +
352B TYR* 4.0 15.8 - - + -
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Residues in contact with VAL 339 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
365A GLU* 5.5 2.8 - - - +
337B ALA* 4.0 4.7 - - + +
338B LYS* 1.3 76.5 - - - +
340B LYS* 1.3 64.1 + - - +
351B LEU* 2.8 34.5 + - + +
353B VAL* 3.8 39.0 - - + -
358B ALA* 6.0 1.6 - - + -
361B ILE* 3.7 15.7 - - + -
364B VAL* 3.7 33.5 - - + +
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Residues in contact with LYS 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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340A LYS* 4.3 19.0 - - - +
365A GLU* 5.6 4.5 + - - -
338B LYS* 3.6 11.2 - - - +
339B VAL* 1.3 86.5 - - + +
341B LEU* 1.3 80.3 + - - +
342B ILE* 6.1 0.4 - - - +
350B LEU* 3.4 3.5 - - - +
351B LEU* 2.8 32.4 + - + +
364B VAL* 3.9 26.2 - - + -
365B GLU* 5.8 0.2 - - - +
366B ALA* 4.1 20.8 - - + +
385B ILE* 3.8 35.2 - - + +
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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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319B GLU* 3.8 44.2 - - + +
323B PHE* 4.4 15.0 - - + -
338B LYS* 4.6 16.0 - - + +
340B LYS* 1.3 90.1 + - - +
342B ILE* 1.3 78.6 + - - +
343B ARG* 4.1 4.7 - - + +
348B MET* 4.2 6.1 - - + -
349B LEU 3.5 4.3 - - - -
350B LEU* 3.5 26.5 - - + -
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Residues in contact with ILE 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 LYS* 4.3 0.9 - - + +
341B LEU* 1.3 79.7 - - - +
343B ARG* 1.3 68.7 + - - +
347B ILE 3.9 0.5 - - - +
348B MET* 3.3 3.6 - - - +
349B LEU* 2.9 45.8 + - + +
366B ALA* 3.8 32.1 - - + +
367B GLU* 4.1 3.1 - - - +
368B THR* 3.6 28.9 - - + -
383B VAL* 3.6 23.8 - - + -
384B ALA 4.3 3.8 - - - +
385B ILE* 3.9 14.4 - - + -
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Residues in contact with ARG 343 (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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304B LEU* 3.9 25.8 - - - -
310B ALA* 5.6 0.6 - - - +
314B HIS* 2.9 76.2 + - + -
315B ASP* 4.1 1.8 + - - +
316B THR* 3.3 24.2 + - - +
319B GLU* 2.7 37.8 + - - +
341B LEU* 4.1 3.0 - - + +
342B ILE* 1.3 80.9 - - - +
344B LEU* 1.3 60.5 + - - +
345B VAL* 2.7 50.2 + - - +
347B ILE 3.2 10.8 - - - +
348B MET* 4.0 11.9 - - + -
368B THR* 4.1 8.1 - - - +
383B VAL* 4.3 2.7 - - - -
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Residues in contact with LEU 344 (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 HIS* 5.0 2.0 - - - +
343B ARG* 1.3 72.4 - - - +
345B VAL* 1.3 67.3 + - + +
346B GLY 2.9 10.7 + - - -
347B ILE* 2.9 27.2 + - + +
368B THR* 3.9 21.8 - - + +
369B VAL 3.8 8.5 - - - +
370B GLY* 3.7 28.5 - - - +
378B GLY* 3.8 32.2 - - - +
380B LYS 4.8 1.6 - - - +
382B GLY 4.6 2.9 - - - +
383B VAL* 3.8 15.0 - - + +
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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