Contacts of the helix formed by residues 265 - 278 (chain A) in PDB entry 3F61
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 THR 265 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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127A ASN* 5.8 2.0 - - - -
130A HIS* 5.7 0.7 - - - -
195A ALA* 5.4 5.2 - - + -
199A VAL* 4.0 7.2 - - - +
263A TYR* 3.3 7.0 - - - +
264A GLN* 1.3 87.4 - - + +
266A ALA* 1.3 63.7 + - - +
267A ALA* 3.5 11.7 + - - +
268A GLU* 3.0 39.4 + - - +
269A MET 3.3 8.8 + - - -
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Residues in contact with ALA 266 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
123A CYS* 3.5 34.7 - - - +
126A LEU* 3.8 16.6 - - + -
127A ASN* 3.7 16.8 - - - +
130A HIS* 4.3 12.6 + - + +
199A VAL* 4.1 12.8 - - + +
202A LEU* 6.1 0.2 - - + -
265A THR* 1.3 72.4 - - - +
267A ALA* 1.3 58.8 + - - +
269A MET* 3.3 4.4 + - - -
270A ARG* 3.0 28.6 + - - +
313A MG 4.6 0.7 - - - -
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Residues in contact with ALA 267 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
127A ASN* 4.0 17.6 - - - +
265A THR* 3.1 10.3 + - - +
266A ALA* 1.3 79.2 - - - +
268A GLU* 1.3 56.1 + - - +
270A ARG* 3.3 3.2 + - - +
271A ALA* 2.9 28.9 + - - +
313A MG 3.6 21.5 - - - -
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Residues in contact with GLU 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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253A LYS* 5.1 4.3 + - - -
262A ARG 4.9 0.3 - - - +
263A TYR* 3.7 21.2 - - + -
264A GLN* 3.0 40.6 + - - +
265A THR* 3.0 25.9 + - - +
267A ALA* 1.3 73.2 - - - +
269A MET* 1.3 66.8 + - - +
271A ALA* 3.3 8.5 + - - +
272A ASP* 3.1 18.4 + - - +
275A ARG* 4.9 1.4 + - - -
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Residues in contact with MET 269 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
119A ILE* 4.1 12.3 - - + -
123A CYS* 3.9 7.6 - - - -
199A VAL* 4.0 28.0 - - + +
202A LEU* 4.0 26.5 - - + -
203A GLY* 3.9 25.1 - - - +
206A LEU* 4.2 12.8 - - + -
250A VAL* 5.2 1.3 - - + -
254A ALA* 4.0 14.1 - - + -
263A TYR* 3.6 32.5 - - + -
265A THR 3.3 6.9 + - - +
266A ALA* 3.3 9.6 + - - +
268A GLU* 1.3 77.5 - - - +
270A ARG* 1.3 64.4 + - - +
272A ASP* 3.2 5.5 + - - +
273A LEU* 2.9 31.3 + - + +
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Residues in contact with ARG 270 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
120A ALA* 3.5 34.7 + - + +
121A ASP* 5.0 5.1 + - - -
123A CYS* 3.6 19.5 - - + -
124A GLN* 3.5 42.5 + - - +
266A ALA 3.0 7.5 + - - +
267A ALA 3.6 8.3 - - - +
269A MET* 1.3 76.6 - - - +
271A ALA* 1.3 59.7 - - - +
273A LEU* 3.1 6.4 + - - +
274A VAL* 2.8 55.6 + - + +
313A MG 3.8 11.0 - - - -
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Residues in contact with ALA 271 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
267A ALA 2.9 18.1 + - - +
268A GLU* 3.3 8.7 + - - +
270A ARG* 1.3 77.8 - - - +
272A ASP* 1.3 56.5 + - - +
274A VAL* 3.4 7.5 + - - +
275A ARG* 3.0 51.6 + - - +
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Residues in contact with ASP 272 (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* 4.0 4.7 - - + -
263A TYR* 2.6 44.2 + - + +
268A GLU 3.1 6.0 + - - +
269A MET 3.7 2.9 - - - +
271A ALA* 1.3 74.3 - - - +
273A LEU* 1.3 65.7 + - - +
275A ARG* 2.9 23.7 + - - +
276A VAL* 3.1 26.9 + - - +
282A PRO* 3.5 7.8 - - - +
283A GLU* 2.8 25.3 + - - -
284A ALA* 3.1 22.9 + - - +
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Residues in contact with LEU 273 (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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116A ILE* 3.4 39.0 - - + +
119A ILE* 3.8 26.2 - - + -
120A ALA* 3.9 22.4 - - + +
123A CYS* 4.1 4.5 - - - -
206A LEU* 4.0 18.2 - - + -
247A LEU* 5.0 4.3 - - + -
250A VAL* 3.8 23.1 - - + -
269A MET* 2.9 31.9 + - + +
270A ARG* 3.5 6.5 - - - +
272A ASP* 1.3 75.4 - - - +
274A VAL* 1.3 58.3 + - - +
276A VAL* 3.3 6.0 + - + +
277A HIS 2.9 23.0 + - - -
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Residues in contact with VAL 274 (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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120A ALA* 4.9 6.3 - - + -
270A ARG* 2.8 58.9 + - + +
271A ALA* 3.6 7.9 - - - +
273A LEU* 1.3 69.5 - - - +
275A ARG* 1.3 67.9 + - + +
277A HIS* 3.0 8.3 + - + +
278A ASN* 2.9 44.0 + - - +
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Residues in contact with ARG 275 (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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268A GLU 4.9 1.4 + - - -
271A ALA* 3.0 29.0 + - - +
272A ASP* 2.9 45.9 + - - +
274A VAL* 1.3 76.7 - - + +
276A VAL* 1.3 60.4 + - - +
278A ASN* 3.0 8.7 + - - -
280A GLU* 2.8 57.7 + - + +
281A PRO 3.4 19.3 - - - +
282A PRO* 4.4 2.5 - - + -
283A GLU* 3.6 38.6 + - - +
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Residues in contact with VAL 276 (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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116A ILE* 3.7 21.9 - - + +
244A SER* 4.9 2.9 - - - +
246A ASP* 4.3 15.0 - - + +
247A LEU* 4.2 18.2 - - + -
250A VAL* 3.9 22.4 - - + -
272A ASP 3.1 14.4 + - - +
273A LEU* 3.7 7.4 - - - +
275A ARG* 1.3 72.6 - - - +
277A HIS* 1.3 68.5 + - - +
279A GLY* 3.0 13.6 + - - -
280A GLU 3.8 6.1 - - - -
282A PRO* 4.0 20.2 - - + -
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Residues in contact with HIS 277 (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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113A LYS* 3.8 38.5 + - + +
116A ILE* 3.9 20.0 - - + +
117A GLU* 2.8 44.1 + - + +
273A LEU 2.9 13.8 + - - +
274A VAL* 3.0 13.0 + - - +
276A VAL* 1.3 77.9 - - - +
278A ASN* 1.3 66.9 + - - +
279A GLY 3.2 2.1 + - - -
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Residues in contact with ASN 278 (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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274A VAL* 2.9 42.5 + - - +
275A ARG* 3.0 4.0 + - - +
277A HIS* 1.3 84.8 - - - +
279A GLY* 1.3 62.5 + - - +
280A GLU* 3.2 27.3 + - - +
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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