Contacts of the strand formed by residues 258 - 266 (chain E) in PDB entry 3PUY
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 PHE 258 (chain E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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111E GLU 4.1 0.2 - - - +
112E ALA* 3.7 18.8 - - - +
113E LEU* 4.7 1.1 + - - +
155E TYR* 3.7 39.2 + + + -
158E TRP* 3.4 56.1 - + + -
159E PRO* 5.2 1.6 - - - +
168E ALA* 4.6 3.1 - - + -
257E PRO* 1.3 74.8 - - - +
259E VAL* 1.3 61.7 + - - +
260E GLY 3.9 0.7 + - - -
328E GLU* 3.3 25.8 - - + -
330E MET* 4.0 23.8 - - + -
331E PRO* 4.5 13.7 - - + -
336E MET* 4.6 2.2 - - + -
339E PHE* 3.9 17.3 - + - -
340E TRP* 3.3 33.7 - + - -
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Residues in contact with VAL 259 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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64E HIS* 3.0 18.4 - - - -
92E PHE* 4.2 4.3 - - + -
110E VAL* 4.1 14.1 - - + -
111E GLU 3.9 2.2 - - - +
112E ALA* 4.6 0.9 - - - -
155E TYR* 6.3 0.2 - - - -
257E PRO 4.0 2.2 - - - +
258E PHE* 1.3 74.8 - - - +
260E GLY* 1.3 61.0 + - - +
261E VAL* 3.9 8.5 - - + -
324E ALA* 3.2 46.7 - - + +
327E GLY 4.0 0.7 - - - +
328E GLU 2.7 34.8 + - - +
329E ILE* 3.7 26.2 - - + +
330E MET* 3.3 15.2 + - - +
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Residues in contact with GLY 260 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63E ALA* 5.3 9.4 - - - -
64E HIS* 3.6 5.6 - - - -
111E GLU* 2.9 51.8 + - - +
155E TYR* 5.9 0.6 + - - -
258E PHE 3.9 0.8 + - - -
259E VAL* 1.3 72.2 - - - +
261E VAL* 1.3 64.0 + - - -
262E LEU* 3.6 2.6 + - - +
330E MET* 4.9 9.2 - - - -
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Residues in contact with VAL 261 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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63E ALA* 4.4 1.3 - - - -
64E HIS* 2.9 42.9 + - + +
92E PHE* 5.2 0.4 - - + -
93E THR* 4.2 24.9 - - + +
96E ALA* 4.1 18.2 - - + -
97E VAL* 4.7 0.2 - - + -
107E PRO* 3.7 31.0 - - + -
109E ALA 3.5 7.2 - - - +
110E VAL* 4.4 6.1 - - + -
259E VAL* 4.1 18.6 - - + -
260E GLY* 1.3 71.1 - - - -
262E LEU* 1.3 64.7 + - - +
263E SER* 3.2 13.8 + - - +
329E ILE* 4.2 5.8 - - + -
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Residues in contact with LEU 262 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11E ILE* 5.4 2.5 - - + -
15E LYS* 4.2 35.2 - - + +
61E PHE* 4.2 18.4 - - + +
62E TRP* 4.0 26.9 - - - +
63E ALA* 4.2 5.6 - - - +
107E PRO* 3.5 1.9 - - - +
108E ILE* 2.6 50.3 + - + -
109E ALA* 2.8 36.6 + - + +
111E GLU* 6.5 0.4 - - + -
260E GLY 3.6 3.2 + - - +
261E VAL* 1.3 70.8 - - - +
263E SER* 1.3 58.1 + - - +
299E LEU* 4.5 8.1 - - + -
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Residues in contact with SER 263 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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60E ILE 3.4 1.6 - - - +
61E PHE* 3.3 6.9 - - - +
62E TRP 3.1 38.1 + - - +
64E HIS* 3.7 4.6 - - - +
67E PHE* 3.6 7.0 - - - -
97E VAL* 3.1 21.1 - - - +
105E ALA* 3.7 20.9 - - - -
106E TYR 3.2 9.4 - - - -
108E ILE* 4.4 4.0 - - - +
261E VAL* 3.2 17.3 + - - +
262E LEU* 1.3 75.3 + - - +
264E ALA* 1.3 60.4 + - - +
265E GLY 4.1 0.2 - - - -
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Residues in contact with ALA 264 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59E ILE* 4.0 6.3 - - + -
60E ILE 3.4 4.7 - - - -
61E PHE* 3.6 28.3 - - + -
105E ALA* 3.2 3.5 - - - -
106E TYR* 2.8 45.7 + - + +
108E ILE* 4.1 3.1 - - + +
263E SER* 1.3 73.1 - - - +
265E GLY* 1.3 60.4 + - - +
280E LEU* 3.6 26.2 - - + +
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Residues in contact with GLY 265 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59E ILE* 3.4 7.0 - - - +
60E ILE* 2.9 39.9 + - - +
67E PHE* 3.4 20.2 - - - -
76E LEU* 4.6 3.6 - - - -
79E ILE* 5.9 0.2 - - - -
104E ILE 4.0 6.1 - - - -
105E ALA* 4.0 6.1 - - - -
264E ALA* 1.3 73.9 - - - +
266E ILE* 1.3 64.3 + - - -
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Residues in contact with ILE 266 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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58E ASP 3.5 10.3 - - - +
59E ILE* 4.7 1.1 - - + -
76E LEU* 3.3 9.3 - - - -
77E ALA* 2.9 35.7 + - + +
79E ILE* 4.2 24.7 - - + +
104E ILE 4.5 4.6 + - - -
106E TYR* 4.5 9.4 - - + -
264E ALA 4.4 0.2 + - - -
265E GLY* 1.3 73.6 - - - +
267E ASN* 1.3 72.8 + - - +
270E SER* 4.6 3.8 - - - -
273E LYS* 3.9 46.4 - - + +
276E ALA* 4.1 17.0 - - + -
277E LYS* 4.2 9.6 - - + +
280E LEU* 4.3 11.2 - - + -
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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