Contacts of the strand formed by residues 252 - 260 (chain B) in PDB entry 5V8V
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 252 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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247B SER* 4.0 9.9 + - - -
248B ASP 3.3 20.9 - - - -
249B PRO* 2.9 44.6 - - + +
250B GLN 3.6 0.6 - - - -
251B HIS* 1.3 79.5 - - - +
253B GLU* 1.3 60.2 + - - +
254B GLY 3.5 21.1 - - - -
255B ASN* 5.3 0.4 - - - -
256B PHE* 3.3 38.6 - + - -
390B TYR* 3.7 17.7 - + + -
403B ALA* 3.6 28.9 - - + -
404B LEU 3.5 8.1 - - - +
406B ARG* 2.8 21.0 + - - +
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Residues in contact with GLU 253 (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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252B TYR* 1.3 74.3 - - - +
254B GLY* 1.3 69.4 + - - +
255B ASN 3.9 0.7 + - - +
403B ALA* 4.0 11.1 - - - +
404B LEU* 3.0 50.4 + - + +
405B ALA 5.5 0.4 - - - -
406B ARG* 3.7 28.2 - - - +
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Residues in contact with GLY 254 (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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252B TYR* 3.5 18.4 - - - -
253B GLU* 1.3 81.0 - - - +
255B ASN* 1.3 67.1 + - - -
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Residues in contact with ASN 255 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
252B TYR* 5.3 0.7 - - - -
253B GLU 4.7 0.9 - - - +
254B GLY* 1.3 78.9 + - - -
256B PHE* 1.3 70.3 + - - +
257B HIS* 3.5 2.8 + - - +
402B PHE 4.0 4.5 - - - +
403B ALA* 4.4 6.7 - - - +
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Residues in contact with PHE 256 (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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247B SER* 3.7 19.1 - - - -
252B TYR* 3.3 39.3 - + - -
255B ASN* 1.3 80.0 - - - +
257B HIS* 1.3 58.4 + - - +
258B TYR* 3.6 42.7 + - + -
390B TYR* 3.6 33.4 - + - -
392B GLU* 3.8 17.9 - - + -
401B GLY* 3.6 24.7 - - - -
402B PHE 3.5 8.3 - - - +
403B ALA* 3.7 10.5 - - + -
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Residues in contact with HIS 257 (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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255B ASN 3.5 1.5 + - - +
256B PHE* 1.3 72.0 - - - +
258B TYR* 1.3 73.0 + - - +
259B ILE* 3.9 10.3 + - + +
338B LEU 3.3 17.9 - - - -
339B GLY* 2.9 34.3 + - - -
341B LYS* 3.1 39.8 + - + +
343B TYR* 2.6 30.1 + - - +
400B ILE 3.8 1.2 - - - +
401B GLY* 3.5 1.2 - - - -
402B PHE* 3.0 29.1 + - - +
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Residues in contact with TYR 258 (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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256B PHE* 3.6 34.1 - - + +
257B HIS* 1.3 83.1 + - - +
259B ILE* 1.3 68.1 + - - +
339B GLY* 5.4 0.3 - - - -
392B GLU* 2.7 32.6 + - - -
394B ASP* 5.1 1.3 - - + -
399B ARG* 3.3 60.9 + - + +
400B ILE 3.4 2.2 - - - -
401B GLY* 3.4 26.7 - - - -
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Residues in contact with ILE 259 (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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257B HIS* 3.9 16.8 - - + +
258B TYR* 1.3 79.4 - - - +
260B ASN* 1.3 75.0 + - + +
269B ILE* 4.2 20.8 - - + +
270B GLN* 4.9 7.0 - - + +
338B LEU* 3.9 19.5 - - + -
339B GLY* 3.8 27.8 - - - +
343B TYR* 4.5 0.4 - - - +
399B ARG* 3.3 5.0 - - - -
400B ILE* 2.9 34.8 + - - +
402B PHE* 3.7 35.9 - - + -
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Residues in contact with ASN 260 (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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259B ILE* 1.3 82.9 - - - +
261B LEU* 1.3 70.7 + - - +
262B ILE* 3.8 0.7 + - - +
269B ILE* 3.4 17.0 - - - +
270B GLN 4.6 1.7 + - - -
397B ASN 4.9 5.5 + - - -
398B ASN 4.1 9.4 + - - -
399B ARG* 4.4 4.2 - - - +
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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