Contacts of the strand formed by residues 252 - 260 (chain O) 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 O).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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250O HIS* 3.0 40.2 + - + +
251O SER* 1.3 86.7 + - - +
253O VAL* 1.3 59.2 + - - +
254O HIS* 3.8 6.6 + - + +
306O PRO 5.8 0.4 - - - +
327O ILE* 4.1 17.0 - - + -
328O SER 3.4 23.1 - - - +
329O GLN* 4.1 11.9 - - + +
427O SER 3.7 8.0 - - - +
49V LEU* 3.3 57.0 - - + +
50V LEU* 5.5 5.2 - - + +
55V MET* 4.1 14.1 - - + -
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Residues in contact with VAL 253 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
251O SER 3.5 0.6 + - - +
252O LEU* 1.3 73.1 - - - +
254O HIS* 1.3 73.3 + - - +
255O ALA* 4.0 4.8 + - + -
326O THR* 3.6 3.3 + - - +
327O ILE* 3.5 3.3 - - - -
328O SER* 2.9 33.7 + - - +
329O GLN 4.5 0.2 - - - +
330O ALA* 3.5 21.5 - - + +
333O ALA* 4.1 13.5 - - + -
337O ILE* 5.2 0.9 - - + -
427O SER 3.5 2.5 - - - -
429O ASP 3.4 34.1 - - - +
430O LEU* 3.9 10.1 - - + -
433O THR* 3.6 26.7 - - + +
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Residues in contact with HIS 254 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
155O PRO* 3.5 36.1 - - + +
156O GLN* 4.3 7.4 - - + -
159O VAL* 3.9 13.7 - - + -
250O HIS* 4.9 2.9 - + - -
252O LEU* 4.0 18.9 - - + +
253O VAL* 1.3 77.6 - - - +
255O ALA* 1.3 62.6 + - - +
325O TYR* 2.7 36.0 + - + +
326O THR 3.4 3.8 - - - -
327O ILE* 3.5 35.6 - - + +
426O ALA* 3.2 5.5 - - - +
427O SER* 3.1 35.0 + - - +
49V LEU* 5.1 7.7 - - + +
58V ARG* 5.5 1.3 - - + -
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Residues in contact with ALA 255 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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159O VAL* 5.7 0.4 - - - -
253O VAL* 4.8 4.0 - - + -
254O HIS* 1.3 77.5 - - - +
256O ALA* 1.3 60.3 + - - +
257O VAL* 5.6 1.8 - - + -
324O PHE* 4.1 2.0 - - + +
325O TYR* 3.2 8.4 - - - -
326O THR* 2.7 49.9 + - - +
337O ILE* 3.8 25.1 - - + -
424O MET* 4.8 6.1 - - + -
425O ALA 3.3 9.9 - - - +
426O ALA* 4.4 7.9 - - + -
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Residues in contact with ALA 256 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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159O VAL* 5.1 2.2 - - + -
160O LEU* 5.0 2.9 - - + -
163O LEU* 3.4 26.8 - - + +
255O ALA* 1.3 79.1 - - - +
257O VAL* 1.3 63.2 + - - +
258O VAL* 4.8 2.2 - - + -
312O PHE* 5.8 1.8 - - + -
324O PHE* 3.2 10.3 - - - +
325O TYR* 3.9 22.9 - - + -
424O MET* 3.3 6.0 - - - +
425O ALA* 3.0 31.5 + - + +
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Residues in contact with VAL 257 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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255O ALA* 5.7 1.1 - - + -
256O ALA* 1.3 73.0 - - - +
258O VAL* 1.3 66.2 + - - +
323O GLY* 3.0 3.5 - - - -
324O PHE* 2.9 62.4 + - + -
337O ILE* 4.8 2.2 - - + -
341O MET* 4.7 1.3 - - - -
417O PHE* 4.1 11.8 - - + -
422O LYS* 4.3 10.3 - - + -
423O SER 3.5 9.0 - - - +
424O MET* 3.5 28.9 - - + -
436O LEU* 4.3 12.3 - - + -
439O LEU* 3.8 24.0 - - + -
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Residues in contact with VAL 258 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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163O LEU* 3.9 22.9 - - + -
256O ALA* 4.8 1.1 - - + -
257O VAL* 1.3 83.0 - - - +
259O THR* 1.3 64.7 + - - +
312O PHE* 3.5 33.0 - - + -
321O LEU* 3.8 23.8 - - + -
322O PHE 3.0 20.4 - - - +
323O GLY* 3.9 2.0 - - - +
324O PHE 4.6 0.4 - - - +
417O PHE* 4.2 2.5 - - - -
422O LYS* 3.0 9.9 - - - +
423O SER* 2.9 45.8 + - - +
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Residues in contact with THR 259 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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239O TYR* 3.4 10.8 - - - -
258O VAL* 1.3 69.8 - - - +
260O GLU* 1.3 90.0 + - + +
321O LEU* 3.5 6.0 - - - +
322O PHE* 2.8 24.5 + - - +
416O LYS* 3.9 10.3 - - + +
417O PHE* 3.5 25.0 + - - -
420O GLY* 3.9 21.3 - - - -
421O LYS 3.4 13.5 - - - +
422O LYS* 3.2 24.8 - - - +
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Residues in contact with GLU 260 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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168O TYR* 5.0 1.4 - - - -
237O ALA 5.1 2.9 - - - +
239O TYR* 3.2 44.8 + - + +
259O THR* 1.3 93.4 - - + +
261O GLY* 1.3 68.1 + - - +
272O PHE* 4.8 2.3 - - - -
319O SER* 3.1 30.8 + - - +
320O GLY 3.4 9.2 - - - +
322O PHE* 5.1 0.7 - - - +
416O LYS* 4.1 19.3 + - - +
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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