Contacts of the helix formed by residues 258 - 269 (chain A) in PDB entry 1P39
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 TYR 258 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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6A LEU* 4.0 18.2 - - + -
9A PRO* 3.4 19.8 - - + +
10A PHE* 2.8 42.3 + - - +
239A LEU* 4.3 4.8 - - + +
243A VAL* 3.5 38.4 - - + +
244A ARG* 3.7 35.7 + - + +
246A LYS* 2.9 21.2 + - + +
248A VAL* 4.1 14.1 - - + -
256A GLN 3.4 0.4 + - - -
257A GLU* 1.3 72.5 - - - +
259A ASP* 1.3 55.1 + - - +
261A PHE* 3.0 12.9 + + - +
262A HIS* 2.7 48.0 + - + -
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Residues in contact with ASP 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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33A LYS* 3.4 17.6 + - - +
199A PRO* 3.6 8.6 - - - +
200A PHE* 3.0 43.5 + - + +
244A ARG* 2.8 48.0 + - - +
257A GLU* 3.1 4.0 + - + +
258A TYR* 1.3 88.1 - - - +
260A TYR* 1.3 55.2 + - + +
262A HIS* 4.2 4.6 + - - -
263A MET* 2.8 32.7 + - - +
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Residues in contact with TYR 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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33A LYS* 5.6 4.4 - - + +
34A LEU* 3.9 24.4 - - - +
200A PHE* 3.8 19.5 - + - -
251A PHE* 3.9 4.8 - - + -
253A TYR* 4.6 5.3 - + + -
255A ASN* 3.0 62.2 + - + +
257A GLU* 3.0 16.1 + - + +
259A ASP* 1.3 75.5 - - + +
261A PHE* 1.3 56.6 + - - +
262A HIS 3.2 0.2 - - - -
263A MET* 3.4 33.3 - - + +
264A TYR* 2.8 34.5 + - - +
287A GLN* 4.2 13.2 - - - -
291A PHE* 3.9 18.9 - + - -
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Residues in contact with PHE 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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6A LEU* 3.7 20.4 - - + -
7A ASP 3.2 27.6 - - - -
8A LYS* 3.4 30.3 - - - -
9A PRO* 3.4 16.8 - - + -
248A VAL* 3.8 29.4 - - + -
251A PHE* 3.5 43.6 - + + -
257A GLU 3.2 6.7 + - - +
258A TYR* 3.0 14.3 + + - +
260A TYR* 1.3 75.6 - - - +
262A HIS* 1.3 62.3 + - - +
264A TYR* 3.4 6.9 - - - +
265A PHE* 3.3 41.3 - + - -
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Residues in contact with HIS 262 (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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9A PRO* 3.7 16.4 - - + -
10A PHE 3.3 24.3 + - - -
11A MET* 3.8 25.6 - - - +
197A LEU* 3.6 24.4 + - + -
198A GLN 4.1 1.3 - - - -
199A PRO* 3.3 40.7 - - + +
239A LEU* 6.4 1.3 - - + -
258A TYR* 2.7 31.0 + + + +
259A ASP* 3.7 7.1 + - - +
261A PHE* 1.3 75.7 - - - +
263A MET* 1.3 64.3 + - - +
265A PHE* 3.3 10.6 + - - +
266A MET* 3.4 13.4 + - + +
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Residues in contact with MET 263 (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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40A LEU* 4.9 0.2 - - - -
44A LEU* 3.9 19.3 - - + -
199A PRO* 4.2 8.2 - - - +
200A PHE* 3.8 18.2 - - + -
253A TYR* 4.9 3.1 - - + +
259A ASP 2.8 20.8 + - - +
260A TYR* 3.3 41.2 + - + +
262A HIS* 1.3 73.2 - - - +
264A TYR* 1.3 63.5 + - - +
266A MET* 3.0 6.5 + - - +
267A LEU* 2.9 41.5 + - + +
283A VAL* 5.7 0.9 - - + -
287A GLN* 3.4 34.5 - - + +
290A ILE* 6.1 0.7 - - - -
291A PHE* 4.3 9.2 - - + -
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Residues in contact with TYR 264 (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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251A PHE* 3.7 28.3 - + + -
252A ASP 5.8 0.4 - - - -
253A TYR* 3.9 14.4 - + + -
260A TYR 2.8 20.4 + - - +
261A PHE 3.4 7.4 - - - +
262A HIS 3.3 0.4 - - - -
263A MET* 1.3 73.0 - - - +
265A PHE* 1.3 74.9 + + - +
267A LEU* 3.7 0.7 - - - +
268A ARG* 2.9 56.0 + - - +
279A THR* 3.6 16.9 - - + +
280A LYS* 3.5 33.9 + - + +
283A VAL* 3.5 38.4 - - + +
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Residues in contact with PHE 265 (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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7A ASP 3.8 17.9 - - - -
8A LYS* 3.9 15.3 - - + -
9A PRO* 3.4 15.9 - - + -
11A MET* 3.7 29.8 - - + +
251A PHE* 5.6 0.2 - + - -
261A PHE* 3.3 38.1 - + - -
262A HIS 3.3 4.8 + - - +
263A MET 3.2 0.6 - - - -
264A TYR* 1.3 95.7 - + - +
266A MET* 1.3 57.6 + - - +
268A ARG* 3.2 45.1 - - - +
269A THR* 3.5 10.7 - - - +
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Residues in contact with MET 266 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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11A MET* 3.9 15.7 - - + -
44A LEU* 3.8 19.3 - - + +
45A GLY* 3.9 3.1 - - - +
48A PHE* 3.7 34.0 - - + -
196A MET* 3.7 39.0 - - + -
197A LEU 4.1 3.4 - - - +
199A PRO* 3.3 39.3 - - + -
262A HIS* 3.4 12.1 + - + +
263A MET* 3.0 6.5 + - - +
265A PHE* 1.3 76.1 - - - +
267A LEU* 1.3 67.8 + - + +
269A THR* 2.5 26.7 + - - -
270A VAL* 3.8 5.8 - - - +
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Residues in contact with LEU 267 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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44A LEU* 3.8 20.9 - - + +
47A LEU* 4.2 7.0 - - + -
263A MET* 2.9 43.4 + - + +
264A TYR 3.9 2.9 - - - +
266A MET* 1.3 76.3 - - + +
268A ARG* 1.3 61.1 + - - +
269A THR 3.0 5.4 - - - -
270A VAL* 3.1 34.7 + - + +
282A LYS* 4.0 2.1 - - - -
283A VAL* 4.0 18.4 - - + -
286A LEU* 3.5 19.0 - - + +
287A GLN* 4.0 29.8 - - + +
290A ILE* 3.9 15.7 - - + -
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Residues in contact with ARG 268 (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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264A TYR* 2.9 35.7 + - + +
265A PHE* 3.2 60.6 - - - +
267A LEU* 1.3 76.9 - - - +
269A THR* 1.3 61.9 + - + +
279A THR* 3.5 36.3 + - + +
282A LYS* 3.0 23.5 + - - +
283A VAL* 3.8 8.2 - - + +
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Residues in contact with THR 269 (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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48A PHE* 3.4 28.2 - - + -
51A SER* 3.9 4.6 - - - -
55A ARG* 3.3 35.7 + - - +
265A PHE 3.5 18.6 - - - +
266A MET 2.5 17.2 + - - -
267A LEU 3.0 0.2 - - - -
268A ARG* 1.3 82.8 - - + +
270A VAL* 1.3 60.9 + - - +
271A TYR* 3.5 12.1 - - - -
282A LYS* 4.7 0.4 - - - -
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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