Contacts of the strand formed by residues 366 - 375 (chain I) 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 ASP 366 (chain I).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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206I ALA 5.9 1.8 - - - +
213I LEU 3.4 1.2 + - - -
214I VAL* 3.2 12.1 - - + +
215I LEU 2.9 24.1 + - - -
330I SER* 3.0 26.7 + - - -
332I LYS* 3.4 31.8 + - - +
364I VAL* 3.4 9.4 - - - +
365I SER* 1.3 83.1 - - - +
367I ALA* 1.3 77.0 + - - +
368I PHE* 3.7 27.1 - - + -
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Residues in contact with ALA 367 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87I PHE* 3.7 17.9 - - + -
215I LEU* 3.3 13.7 - - + +
330I SER* 3.3 6.8 - - - -
331I LEU* 2.9 56.0 + - + -
332I LYS* 4.4 5.1 - - - +
335I LEU* 4.6 0.7 - - + -
344I PHE* 4.9 5.6 - - + -
364I VAL* 5.1 1.1 - - + -
366I ASP* 1.3 81.9 + - - +
368I PHE* 1.3 62.1 - - - +
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Residues in contact with PHE 368 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
201I VAL* 4.0 11.3 - - - +
202I ILE* 3.3 34.5 - - + -
203I PRO* 3.7 24.7 - - + -
206I ALA* 4.0 31.9 - - + -
207I ILE* 6.0 0.2 - - + -
214I VAL* 4.1 12.6 - - + -
215I LEU 2.8 10.9 + - - +
216I VAL* 3.4 8.3 - - + +
217I ASN* 3.2 23.4 + - - +
329I PHE 3.1 19.5 - - - +
330I SER* 3.8 20.9 - - - -
331I LEU* 4.3 2.0 - - - -
366I ASP* 3.7 31.6 - - + -
367I ALA* 1.3 75.5 - - - +
369I HIS* 1.3 60.6 + - - +
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Residues in contact with HIS 369 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78I LEU* 3.7 18.0 - - + -
79I SER* 3.2 30.2 + - - -
82I SER* 3.5 26.2 - - - -
83I ILE* 4.4 9.6 - - + -
201I VAL* 5.3 3.4 - - - +
217I ASN* 2.5 42.5 + - - +
218I THR* 3.8 4.3 - - - -
219I ILE 4.9 0.7 - - - -
327I ASP 3.6 0.5 - - - +
328I GLY* 3.3 4.0 - - - -
329I PHE* 2.8 52.0 + + + +
331I LEU* 3.9 12.1 - - + +
368I PHE* 1.3 73.6 - - - +
370I LYS* 1.3 76.1 + - - +
371I ALA* 3.8 5.3 - - + +
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Residues in contact with LYS 370 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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198I ILE* 3.6 37.1 - - + +
199I THR 5.4 0.7 - - - +
200I ASP* 2.9 36.3 + - - +
201I VAL* 4.7 13.1 - - + +
217I ASN 3.7 3.0 + - - -
218I THR* 2.9 27.4 + - - -
326I GLU* 3.4 41.0 + - + +
327I ASP* 3.1 23.2 - - - +
328I GLY* 3.9 16.0 - - - +
369I HIS* 1.3 82.0 + - - +
371I ALA* 1.3 60.6 + - - +
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Residues in contact with ALA 371 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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77I PHE* 3.3 41.0 - - + +
78I LEU* 3.6 17.7 - - - -
198I ILE* 5.0 0.4 - - - -
218I THR* 5.0 0.7 - - - -
219I ILE 5.9 0.2 - - - -
325I ILE 3.7 0.7 - - - +
326I GLU* 3.3 5.9 - - - +
327I ASP 3.0 30.6 + - - -
369I HIS* 3.8 7.8 + - + +
370I LYS* 1.3 76.1 - - - +
372I PHE* 1.3 61.9 + - - +
422I PHE* 4.8 6.3 - - + -
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Residues in contact with PHE 372 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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77I PHE* 3.6 7.8 - - - -
197I ARG* 3.9 45.3 - - + +
198I ILE* 4.3 22.1 - - + +
219I ILE 5.6 2.2 + - - +
221I PHE 5.7 1.0 + - - +
324I ARG* 3.5 58.1 - - + -
325I ILE 3.5 8.1 - - - -
326I GLU* 4.0 24.9 - - + +
370I LYS 4.5 0.2 + - - -
371I ALA* 1.3 76.0 - - - +
373I LEU* 1.3 70.5 + - - +
374I GLU* 4.0 20.6 - - + -
422I PHE* 5.2 7.5 - - - -
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Residues in contact with LEU 373 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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77I PHE* 3.4 40.6 - - + -
221I PHE* 5.1 8.7 - - + +
274I PHE* 6.3 0.2 - - + -
281I MET* 4.9 0.9 - - - -
323I PHE* 3.9 13.4 - - + +
324I ARG* 3.3 2.1 - - - +
325I ILE* 2.7 44.2 + - + +
372I PHE* 1.3 81.3 - - - +
374I GLU* 1.3 63.6 + - - +
375I VAL* 3.9 22.7 - - + -
380I SER* 3.9 21.5 - - - +
410I VAL* 4.6 8.5 - - + -
412I ILE* 4.2 23.3 - - + -
422I PHE* 6.1 1.6 - - + -
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Residues in contact with GLU 374 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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323I PHE 3.4 7.9 - - - +
324I ARG* 3.0 38.5 + - + +
372I PHE* 4.0 20.2 - - + -
373I LEU* 1.3 76.6 - - - +
375I VAL* 1.3 68.5 + - - +
376I ASN* 4.8 11.0 + - + +
379I GLY 3.3 11.8 - - - +
380I SER* 3.5 23.7 + - - +
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Residues in contact with VAL 375 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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225I TRP* 3.5 31.9 - - + -
252I MET* 4.3 9.9 - - + -
281I MET* 4.4 12.1 - - + -
320I MET* 4.7 0.7 - - + -
322I ARG* 3.3 10.9 - - - +
323I PHE* 2.7 72.5 + - + +
373I LEU* 3.9 16.6 - - + -
374I GLU* 1.3 78.7 - - - +
376I ASN* 1.3 66.1 + - - +
379I GLY 3.5 4.7 - - - +
380I SER* 5.9 0.2 - - - +
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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