Contacts of the strand formed by residues 364 - 375 (chain L) in PDB entry 2B4X
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 VAL 364 (chain L).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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87L PHE* 5.6 0.2 - - + -
90L THR* 4.6 2.7 - - + -
343L LEU* 2.7 54.1 + - + +
344L PHE* 3.4 36.4 - - + +
351L LEU* 4.5 7.2 - - + -
363L TYR* 1.3 74.4 - - - +
365L SER* 1.3 64.1 + - - +
366L ASP 3.7 20.4 - - - +
367L ALA* 4.6 2.9 - - + +
388L VAL* 3.7 25.8 - - + -
389L VAL 3.3 16.2 - - - +
390L ILE* 4.3 4.5 - - + +
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Residues in contact with SER 365 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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332L LYS* 4.9 1.2 - - - +
344L PHE* 4.5 5.5 - - - +
363L TYR* 3.3 16.5 + - - -
364L VAL* 1.3 74.4 - - - +
366L ASP* 1.3 73.7 + - - +
389L VAL* 2.8 32.7 + - - +
391L ALA* 3.9 1.8 - - - -
392L GLY* 3.0 38.5 + - - -
393L ARG 3.6 8.0 + - - -
394L SER* 3.2 22.9 + - - -
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Residues in contact with ASP 366 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
330L SER* 3.4 8.6 + - - -
332L LYS* 3.4 26.9 - - - +
344L PHE* 4.5 4.3 - - - -
364L VAL* 3.4 6.5 - - - +
365L SER* 1.3 87.0 + - - +
367L ALA* 1.3 61.4 + - - +
368L PHE* 2.6 49.0 - - + -
387L ALA 4.0 0.5 - - - +
389L VAL* 2.9 30.8 + - - +
393L ARG 3.9 12.8 - - - +
394L SER* 4.4 6.4 + - - -
395L LEU 4.4 10.8 - - - +
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Residues in contact with ALA 367 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87L PHE* 3.8 21.8 - - + -
330L SER* 3.6 5.2 + - - -
331L LEU* 3.0 50.9 + - + -
332L LYS 5.0 0.4 - - - +
344L PHE* 4.5 10.0 - - + -
364L VAL* 4.8 1.6 - - + -
366L ASP* 1.3 81.4 + - - +
368L PHE* 1.3 62.8 + - - +
387L ALA 3.1 10.1 - - - +
388L VAL* 4.3 6.3 - - + -
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Residues in contact with PHE 368 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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201L VAL* 3.7 20.6 - - - +
202L ILE* 4.5 9.2 - - + -
203L PRO* 3.4 35.4 - - + -
206L ALA* 3.5 26.5 - - + -
329L PHE 3.7 11.9 - - - +
330L SER* 4.7 7.6 - - - -
331L LEU* 4.6 1.6 - - - -
366L ASP* 2.6 40.4 - - + -
367L ALA* 1.3 75.3 - - - +
369L HIS* 1.3 61.0 + - - +
385L SER 4.0 0.4 - - - +
386L THR* 3.4 5.9 - - - +
387L ALA* 2.8 42.3 + - + +
389L VAL* 4.6 9.2 - - + -
393L ARG 5.1 1.1 - - - -
395L LEU* 4.9 9.9 - - - -
398L ASN* 5.7 11.0 - - + -
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Residues in contact with HIS 369 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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78L LEU* 3.7 17.2 - - + +
79L SER 3.2 40.5 + - - -
82L SER* 3.9 5.8 - - - -
83L ILE* 3.5 11.7 - - + +
201L VAL* 4.9 2.1 - - - +
328L GLY* 3.3 2.6 - - - -
329L PHE* 3.0 59.0 + + + -
331L LEU* 4.3 9.6 - - + +
367L ALA 4.4 0.2 + - - -
368L PHE* 1.3 76.1 - - - +
370L LYS* 1.3 78.5 + - - +
371L ALA* 3.9 3.3 - - + +
384L ALA* 3.9 14.1 - - + +
385L SER 3.3 10.3 + - - -
386L THR* 2.8 27.8 + - - +
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Residues in contact with LYS 370 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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197L ARG 5.1 2.7 - - - -
198L ILE* 3.3 32.8 - - + +
199L THR 5.1 2.2 - - - +
200L ASP* 2.9 39.7 + - - +
201L VAL* 4.1 17.0 - - + +
326L GLU* 4.1 25.5 + - - +
327L ASP 3.4 16.4 + - - +
328L GLY* 4.3 8.2 - - - +
369L HIS* 1.3 78.4 - - - +
371L ALA* 1.3 65.5 + - - +
372L PHE* 6.3 0.2 - - - -
384L ALA* 3.1 2.6 - - - +
385L SER 2.7 37.3 + - - -
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Residues in contact with ALA 371 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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77L PHE* 3.5 20.9 - - + +
78L LEU* 3.5 33.0 - - - -
198L ILE* 3.7 3.5 - - - +
326L GLU* 3.5 4.5 - - - +
327L ASP 2.8 31.5 + - - +
369L HIS* 3.9 6.0 - - + +
370L LYS* 1.3 76.8 - - - +
372L PHE* 1.3 63.5 + - - +
383L ALA 3.2 9.0 - - - +
384L ALA* 4.0 4.3 - - + -
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Residues in contact with PHE 372 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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77L PHE* 3.1 8.5 - - - -
197L ARG* 3.8 54.5 - - + +
198L ILE* 3.8 11.9 - - + -
324L ARG* 3.2 43.7 - - - -
325L ILE 3.8 3.8 - - - -
326L GLU* 3.4 26.2 - - + -
370L LYS* 6.3 0.2 - - - -
371L ALA* 1.3 78.2 - - - +
373L LEU* 1.3 59.9 + - - +
374L GLU* 3.7 17.3 - - + -
381L GLU* 3.4 22.2 - - + -
382L ALA* 2.9 7.7 - - - -
383L ALA* 2.5 42.9 + - + +
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Residues in contact with LEU 373 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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77L PHE* 3.2 39.7 - - + -
281L MET* 4.3 9.9 - - + -
323L PHE* 4.4 15.0 - - + -
324L ARG* 3.1 3.9 - - - +
325L ILE* 2.8 42.7 + - + +
372L PHE* 1.3 76.7 - - - +
374L GLU* 1.3 69.2 + - - +
375L VAL* 4.1 25.1 - - + -
380L SER* 4.1 8.5 - - - -
381L GLU 3.4 9.0 - - - +
382L ALA* 4.2 1.6 - - + -
410L VAL* 4.4 8.5 - - + -
412L ILE* 4.0 23.1 - - + -
426L VAL* 4.8 5.8 - - + -
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Residues in contact with GLU 374 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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197L ARG* 4.3 12.7 + - - -
323L PHE 3.4 11.9 - - - +
324L ARG* 3.0 44.3 + - + +
372L PHE* 3.7 15.7 - - + -
373L LEU* 1.3 79.7 - - - +
375L VAL* 1.3 64.2 + - - +
376L ASN* 3.8 23.7 + - + +
379L GLY 3.8 0.5 - - - +
380L SER* 2.9 5.0 - - - -
381L GLU* 2.9 41.2 + - + +
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Residues in contact with VAL 375 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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225L TRP* 3.7 29.4 - - + +
252L MET* 4.4 6.1 - - + -
281L MET* 4.2 11.7 - - + -
320L MET* 4.2 18.6 - - - -
321L PRO 4.4 0.7 - - - +
322L ARG* 3.3 5.3 - - - +
323L PHE* 2.7 66.2 + - + +
373L LEU* 4.1 12.3 - - + -
374L GLU* 1.3 77.6 - - - +
376L ASN* 1.3 66.2 + - - +
379L GLY 3.6 1.8 - - - -
380L SER* 4.0 9.6 - - - -
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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