Contacts of the strand formed by residues 252 - 260 (chain B) in PDB entry 3H1J
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 LEU 252 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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250B HIS* 3.0 37.6 + - + +
251B SER* 1.3 86.5 + - - +
253B VAL* 1.3 62.1 + - - +
254B HIS* 3.8 7.7 + - + +
306B PRO 5.9 0.4 - - - +
327B ILE* 4.1 16.2 - - + -
328B SER* 3.5 24.5 - - - +
329B GLN* 4.2 10.8 - - + +
427B SER 3.7 6.9 - - - +
428B GLY* 4.1 0.2 - - - -
49I LEU* 3.2 59.2 - - + +
50I LEU* 5.7 3.4 - - + -
55I MET* 4.6 9.2 - - + -
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Residues in contact with VAL 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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251B SER 3.5 1.1 + - - +
252B LEU* 1.3 72.7 - - - +
254B HIS* 1.3 69.6 + - - +
255B ALA* 3.9 4.9 + - + -
326B THR* 3.6 3.1 + - - +
327B ILE* 3.5 4.0 - - - -
328B SER* 2.9 34.5 + - - +
330B ALA* 3.6 27.1 - - + -
333B ALA* 4.2 12.1 - - + -
337B ILE* 5.2 1.1 - - + -
426B ALA* 5.1 0.2 - - + -
427B SER 3.4 3.6 - - - +
429B ASP 3.6 26.2 - - - +
430B LEU* 4.0 12.1 - - + -
433B THR* 3.7 27.4 - - + +
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Residues in contact with HIS 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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155B PRO* 3.5 35.7 - - + +
156B GLN* 4.2 7.0 - - + -
159B VAL* 3.9 14.4 - - + -
250B HIS* 4.9 2.3 - + - -
252B LEU* 4.0 16.3 - - + +
253B VAL* 1.3 77.2 - - - +
255B ALA* 1.3 59.8 + - - +
325B TYR* 2.7 35.7 + + - +
326B THR 3.4 3.8 - - - -
327B ILE* 3.4 37.1 - - + +
426B ALA* 3.1 6.3 - - - +
427B SER* 3.1 34.5 + - - +
49I LEU* 4.7 10.9 - - + +
58I ARG* 4.7 3.4 - - + -
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Residues in contact with ALA 255 (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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159B VAL* 5.7 0.2 - - - -
253B VAL* 4.8 4.3 - - + -
254B HIS* 1.3 76.2 - - - +
256B ALA* 1.3 60.8 + - - +
257B VAL* 5.7 2.2 - - + -
324B PHE* 4.5 2.0 - - + -
325B TYR* 3.1 10.2 - - - -
326B THR* 2.8 49.5 + - - +
337B ILE* 3.9 25.4 - - + -
424B MET* 4.9 5.2 - - + -
425B ALA 3.3 9.6 - - - +
426B ALA* 4.4 7.6 - - + -
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Residues in contact with ALA 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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159B VAL* 5.1 2.0 - - + -
160B LEU* 5.0 3.4 - - + -
163B LEU* 3.4 28.0 - - + +
255B ALA* 1.3 77.2 - - - +
257B VAL* 1.3 62.1 + - - +
258B VAL* 4.2 1.8 - - + -
312B PHE* 5.8 2.5 - - + -
324B PHE 3.3 8.3 - - - +
325B TYR* 3.9 23.3 - - + -
424B MET* 3.3 4.7 - - - +
425B ALA* 2.9 34.1 + - + +
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Residues in contact with VAL 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 ALA* 5.7 1.6 - - + -
256B ALA* 1.3 72.4 - - - +
258B VAL* 1.3 65.9 + - - +
323B GLY* 3.0 3.8 - - - -
324B PHE* 2.9 62.5 + - + -
337B ILE* 4.8 2.5 - - + -
341B MET* 4.7 2.9 - - - -
417B PHE* 4.1 18.3 - - + -
422B LYS* 4.4 14.4 - - + -
423B SER 3.5 8.3 - - - +
424B MET* 3.6 27.4 - - + -
436B LEU* 4.4 6.1 - - + -
439B LEU* 3.9 19.5 - - + -
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Residues in contact with VAL 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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163B LEU* 3.9 23.6 - - + -
256B ALA* 4.8 0.9 - - + -
257B VAL* 1.3 84.2 - - - +
259B THR* 1.3 64.6 + - - +
312B PHE* 3.4 33.0 - - + -
321B LEU* 3.8 23.3 - - + -
322B PHE 3.0 20.0 - - - +
323B GLY* 3.9 2.0 - - - +
417B PHE* 4.2 1.8 - - - -
422B LYS* 3.1 9.7 - - - +
423B SER* 2.9 45.1 + - - +
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Residues in contact with THR 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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239B TYR* 3.4 11.0 - - - -
258B VAL* 1.3 71.1 - - - +
260B GLU* 1.3 87.4 + - + +
321B LEU* 3.3 7.0 - - - -
322B PHE* 2.8 27.9 + - - -
416B LYS* 4.0 10.5 - - + +
417B PHE* 3.5 22.6 + - - -
420B GLY* 3.9 21.1 - - - -
421B LYS 3.4 14.1 - - - +
422B LYS* 3.3 23.2 - - - +
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Residues in contact with GLU 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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168B TYR* 4.8 1.6 - - - -
237B ALA 5.0 2.8 - - - +
239B TYR* 3.2 50.1 + - + +
259B THR* 1.3 91.6 - - + +
261B GLY* 1.3 68.7 + - - +
272B PHE* 4.9 2.8 - - - -
319B SER* 3.1 29.4 + - - +
320B GLY 3.3 5.2 - - - +
322B PHE* 5.1 1.4 - - - +
416B LYS* 4.1 16.9 - - - +
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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