Contacts of the helix formed by residues 252 - 261 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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250A VAL 3.2 4.8 + - - -
251A ASN* 1.3 75.5 - - - +
253A LEU* 1.3 67.7 + - - +
254A TYR 3.2 2.9 + - - -
255A PRO* 3.4 18.2 - - - +
256A ALA* 2.8 18.0 + - - +
371A LYS* 4.1 10.9 + - - -
387A ASN* 6.1 0.2 - - - -
480A LEU* 3.6 15.9 - - - -
8001A EDO 3.7 27.9 + - - -
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Residues in contact with LEU 253 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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250A VAL* 3.8 34.0 + - + +
251A ASN 3.6 1.0 - - - -
252A SER* 1.3 73.6 - - - +
254A TYR* 1.3 74.2 + - + +
256A ALA* 3.3 0.5 + - - +
257A GLN* 3.0 45.1 + - - +
437A ALA* 3.7 36.6 - - + +
440A THR* 4.3 3.4 - - - -
441A THR* 4.3 5.8 - - - +
457A THR* 3.4 35.4 - - + +
458A ASP* 3.7 23.6 + - + +
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Residues in contact with TYR 254 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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228A GLY* 4.5 1.2 - - - -
229A GLY* 4.1 17.8 + - - -
253A LEU* 1.3 91.6 - - + +
255A PRO* 1.4 76.5 - - + +
257A GLN* 3.0 13.6 + - - +
258A MET* 3.0 20.3 + - - +
387A ASN* 6.5 0.7 - - - -
390A TYR* 3.6 44.4 + + + -
433A ILE* 3.8 19.6 - - + +
434A THR* 4.0 22.6 + - + +
437A ALA* 3.4 26.0 - - + +
457A THR* 3.8 21.4 - - + +
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Residues in contact with PRO 255 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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252A SER* 3.4 26.0 - - - +
254A TYR* 1.4 92.1 - - + +
256A ALA* 1.3 55.6 + - - +
258A MET* 3.3 11.2 + - - -
259A TYR* 2.9 30.3 + - - +
364A ILE* 3.5 23.0 - - + +
386A LEU* 3.9 32.5 - - + +
387A ASN* 4.3 15.9 - - - +
480A LEU* 4.4 7.4 - - + +
8001A EDO 5.0 1.3 - - - +
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Residues in contact with ALA 256 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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252A SER 2.8 23.1 + - - +
253A LEU* 3.4 5.8 - - - +
255A PRO* 1.3 71.1 - - - +
257A GLN* 1.3 64.6 - - - +
259A TYR* 3.3 9.7 + - - +
260A SER* 3.3 19.1 + - - -
480A LEU* 3.8 14.5 - - + +
481A GLY* 3.3 36.8 - - - +
9008A EDO 3.8 11.2 + - - +
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Residues in contact with GLN 257 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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253A LEU* 3.0 33.4 + - - +
254A TYR* 3.0 7.4 + - - +
256A ALA* 1.3 74.4 - - - +
258A MET* 1.3 59.5 + - - +
261A ARG* 2.9 70.8 + - + +
263A LEU* 4.0 5.6 - - + +
433A ILE* 4.0 17.5 - - + +
436A TRP* 3.5 9.9 - - + +
437A ALA* 3.7 23.3 - - + +
440A THR* 3.1 17.2 + - - -
9008A EDO 3.0 26.8 + - - -
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Residues in contact with MET 258 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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254A TYR* 3.0 21.6 + - - +
255A PRO* 3.6 11.9 - - - +
257A GLN* 1.3 75.5 - - - +
259A TYR* 1.3 61.7 + - - +
260A SER 3.6 0.2 + - - -
261A ARG 4.7 1.0 + - - +
263A LEU* 3.9 13.3 - - - +
358A GLY 4.9 6.1 + - - -
359A LEU 5.2 0.2 + - - -
360A PHE* 3.5 60.5 + - + +
364A ILE* 3.8 10.1 - - + -
386A LEU 5.1 7.2 - - - +
389A LEU* 3.8 22.2 - - + -
390A TYR* 3.9 22.7 - - + +
433A ILE* 3.6 26.7 - - + -
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Residues in contact with TYR 259 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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255A PRO 2.9 16.9 + - - +
256A ALA 3.7 5.8 - - - +
257A GLN 3.2 0.4 - - - -
258A MET* 1.3 79.5 - - - +
260A SER* 1.3 64.1 + - - +
357A THR* 5.3 0.5 - - - -
358A GLY* 4.5 15.1 + - - -
360A PHE* 5.2 2.0 - - - -
361A LYS* 3.1 48.5 + - + +
364A ILE* 3.7 24.7 - - + -
365A ASP* 2.6 30.5 + - - -
480A LEU* 3.9 17.3 - - + -
8012A EDO 3.4 19.1 - - - -
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Residues in contact with SER 260 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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256A ALA 3.3 14.2 + - - -
259A TYR* 1.3 86.8 - - - +
261A ARG* 1.3 66.9 + - - +
357A THR* 3.7 7.7 - - - +
8004A EDO 2.7 35.1 + - - -
9008A EDO 3.6 19.9 + - - -
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Residues in contact with ARG 261 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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257A GLN* 2.9 44.3 + - - +
258A MET 4.9 1.2 - - - +
260A SER* 1.3 86.3 - - - +
262A LEU* 1.3 64.4 + - - +
263A LEU* 3.3 14.9 + - + +
357A THR* 3.6 14.4 - - - +
358A GLY 5.0 0.2 + - - -
436A TRP* 3.5 57.2 - - + +
439A TYR* 3.8 20.4 - - - -
440A THR* 3.0 26.7 + - - +
8004A EDO 4.5 6.5 - - - -
9008A EDO 3.7 17.8 - - - -
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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