Contacts of the helix formed by residues 252 - 261 (chain B) in PDB entry 2PY5
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 SER 252 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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250B VAL 3.2 5.3 + - - -
251B ASN* 1.3 74.7 - - - +
253B LEU* 1.3 66.7 + - - +
254B TYR 3.2 2.9 + - - -
255B PRO* 3.4 18.2 - - - +
256B ALA* 2.9 18.4 + - - +
371B LYS* 4.0 19.2 + - - -
387B ASN* 5.6 3.5 + - - +
480B LEU* 3.7 15.7 - - - -
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Residues in contact with LEU 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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250B VAL* 3.8 34.2 + - + +
251B ASN 3.6 1.4 - - - -
252B SER* 1.3 73.3 - - - +
254B TYR* 1.3 74.6 + - + +
256B ALA* 3.3 0.5 + - - +
257B GLN* 3.0 47.1 + - - +
437B ALA* 3.6 36.3 - - + +
440B THR* 4.2 4.5 - - + -
441B THR* 4.3 3.6 - - - +
457B THR* 3.3 37.5 - - + +
458B ASP* 3.7 23.8 + - + +
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Residues in contact with TYR 254 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
228B GLY* 4.5 2.9 - - - -
229B GLY* 4.0 17.3 + - - -
253B LEU* 1.3 93.0 - - + +
255B PRO* 1.3 76.6 - - + +
257B GLN* 3.0 13.5 + - - +
258B MET* 3.1 20.9 + - - +
387B ASN* 6.1 1.6 - - - +
390B TYR* 3.6 49.7 + + + -
433B ILE* 3.8 19.0 - - + +
434B THR* 4.1 15.2 + - + +
437B ALA* 3.4 25.0 - - + +
438B ARG* 6.2 0.2 - - - +
457B THR* 3.8 21.6 - - + +
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Residues in contact with PRO 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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252B SER* 3.4 25.1 - - - +
254B TYR* 1.3 93.7 - - + +
256B ALA* 1.3 55.0 + - - +
258B MET* 3.3 6.4 + - - -
259B TYR* 2.9 31.0 + - - +
364B ILE* 3.4 26.9 - - + +
386B LEU* 3.9 32.1 - - + +
387B ASN* 4.2 17.5 - - - +
480B LEU* 4.3 6.7 - - + -
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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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252B SER 2.9 20.1 + - - +
253B LEU* 3.4 6.5 - - - +
254B TYR 3.1 0.2 - - - -
255B PRO* 1.3 76.8 - - - +
257B GLN* 1.3 70.7 + - - +
259B TYR* 3.3 9.4 + - - +
260B SER* 3.3 19.2 + - - -
480B LEU* 3.8 13.8 - - + +
481B GLY* 3.4 35.7 - - - +
8005B EDO 5.7 0.4 - - - +
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Residues in contact with GLN 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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250B VAL* 5.2 1.4 - - - +
253B LEU* 3.0 35.4 + - - +
254B TYR* 3.0 7.0 + - - +
256B ALA* 1.3 84.9 - - - +
258B MET* 1.3 60.1 + - - +
261B ARG* 2.8 72.6 + - + +
263B LEU* 4.1 4.5 - - + +
433B ILE* 4.0 17.5 - - + +
436B TRP* 3.5 9.1 - - + +
437B ALA* 3.7 25.1 - - + +
440B THR* 3.1 25.4 + - - +
481B GLY* 5.5 1.2 + - - -
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Residues in contact with MET 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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254B TYR* 3.1 21.0 + - - +
255B PRO* 3.6 11.2 - - - +
257B GLN* 1.3 77.7 - - - +
259B TYR* 1.3 61.3 + - - +
261B ARG 4.9 1.2 + - - +
263B LEU* 4.0 12.8 - - - +
358B GLY 5.0 5.0 + - - -
359B LEU 5.3 0.3 + - - -
360B PHE* 3.5 60.1 + - + +
361B LYS* 5.3 0.2 - - - +
364B ILE* 3.8 11.7 - - + -
386B LEU 5.2 7.0 - - - +
389B LEU* 3.6 24.0 - - + -
390B TYR* 3.8 27.1 - - + +
433B ILE* 3.6 23.6 - - + -
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Residues in contact with TYR 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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255B PRO 2.9 18.1 + - - +
256B ALA 3.7 4.7 - - - +
257B GLN 3.2 0.2 - - - -
258B MET* 1.3 78.8 - - - +
260B SER* 1.3 63.2 + - - +
358B GLY 4.4 3.0 + - - -
360B PHE* 5.3 0.2 - - - -
361B LYS* 3.0 76.2 + - + +
364B ILE* 3.6 24.2 - - + -
365B ASP* 2.7 36.0 + - - -
480B LEU* 3.9 15.5 - - + -
9002B EDO 3.5 27.6 + - - -
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Residues in contact with SER 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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256B ALA 3.3 14.9 + - - -
259B TYR* 1.3 87.6 - - - +
261B ARG* 1.3 70.1 + - - +
357B THR* 3.6 16.4 - - - +
361B LYS* 5.2 1.1 - - - +
8003B EDO 3.8 23.9 - - - -
8005B EDO 4.7 11.5 + - - -
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Residues in contact with ARG 261 (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 GLN* 2.8 43.5 + - - +
258B MET 5.1 0.9 - - - +
260B SER* 1.3 84.4 + - - +
262B LEU* 1.3 63.7 + - - +
263B LEU* 3.3 15.2 + - + +
357B THR* 3.6 13.7 - - - +
358B GLY 5.0 0.2 + - - -
436B TRP* 3.5 52.4 - - + -
439B TYR* 3.8 19.0 - - - -
440B THR* 3.0 29.3 + - - +
8003B EDO 2.8 47.7 + - - -
8005B EDO 6.3 2.1 - - - -
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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