Contacts of the helix formed by residues 261 - 275 (chain A) in PDB entry 3DAN
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 PRO 261 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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106A TYR* 5.1 5.2 - - - +
118A ARG* 3.5 22.7 - - - +
256A GLU* 5.5 1.8 - - + -
259A GLY 3.8 3.8 - - - +
260A VAL* 1.3 87.4 - - + +
262A LYS* 1.3 67.0 + - - +
263A ASP* 4.5 3.8 - - + +
264A GLU* 3.2 20.5 + - + +
265A ALA* 2.9 18.7 + - - +
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Residues in contact with LYS 262 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
249A THR* 5.9 2.8 - - - +
252A MET* 4.0 39.1 - - + +
253A GLU* 4.8 12.2 + - - +
256A GLU* 3.2 47.9 + - + +
260A VAL 3.6 1.2 + - - -
261A PRO* 1.3 72.4 - - - +
263A ASP* 1.3 63.2 + - - +
265A ALA* 3.1 9.5 + - - +
266A VAL* 2.9 29.0 + - - +
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Residues in contact with ASP 263 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
104A GLY 5.0 0.9 - - - +
106A TYR* 3.2 29.5 + - - +
241A TYR* 2.5 31.5 + - - +
261A PRO* 3.3 4.1 - - + +
262A LYS* 1.3 77.1 - - - +
264A GLU* 1.3 62.5 + - - +
266A VAL* 3.2 12.0 + - - +
267A HIS* 3.2 34.2 + - - -
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Residues in contact with GLU 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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106A TYR* 3.7 49.7 + - + +
107A ARG 5.2 3.8 - - - +
118A ARG* 2.9 49.7 + - - +
122A LEU* 4.4 6.4 - - - +
260A VAL* 4.0 8.7 - - + -
261A PRO* 3.2 18.2 + - + +
263A ASP* 1.3 79.2 - - - +
265A ALA* 1.3 63.4 + - - +
267A HIS* 3.4 2.4 + - - +
268A ASN* 3.0 41.2 + - - +
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Residues in contact with ALA 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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125A LEU* 4.3 10.3 - - + +
252A MET* 4.5 9.6 - - - -
255A ALA* 3.5 33.0 - - + -
260A VAL* 4.0 6.2 - - + +
261A PRO 2.9 10.7 + - - +
262A LYS* 3.1 11.9 + - - +
264A GLU* 1.3 78.4 - - - +
266A VAL* 1.3 57.7 + - - +
268A ASN* 3.2 5.5 + - - +
269A ILE* 2.9 36.3 + - + +
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Residues in contact with VAL 266 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
241A TYR* 3.3 41.5 - - + +
244A PHE* 4.0 11.0 - - + -
245A GLN* 3.8 25.8 - - + +
248A ALA* 6.2 0.2 - - + -
252A MET* 3.5 35.7 - - + -
262A LYS 2.9 16.0 + - - +
263A ASP 3.2 2.2 + - - +
265A ALA* 1.3 76.5 - - - +
267A HIS* 1.3 56.5 + - - +
269A ILE* 3.2 8.3 + - + +
270A LEU* 2.8 28.9 + - + +
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Residues in contact with HIS 267 (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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103A THR* 4.1 11.2 - - - +
104A GLY* 3.4 26.2 + - - -
106A TYR* 3.6 24.2 - + + -
108A VAL* 4.3 7.0 - - + +
237A TYR* 2.7 35.4 + + - +
241A TYR* 3.3 22.6 - + - -
263A ASP* 3.2 42.8 + - - -
264A GLU 3.8 5.8 - - - +
265A ALA 3.3 0.2 - - - -
266A VAL* 1.3 76.1 - - - +
268A ASN* 1.3 57.6 + - - +
270A LEU* 3.7 3.9 - - - +
271A PHE* 3.0 27.5 + - - +
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Residues in contact with ASN 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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106A TYR* 5.1 3.0 - - - +
107A ARG 5.2 0.4 + - - -
108A VAL* 3.4 15.7 - - - +
109A LEU* 3.0 33.4 + - - +
122A LEU* 3.5 30.7 - - + +
125A LEU* 5.6 2.7 - - + -
126A LEU* 4.7 7.6 - - + +
264A GLU* 3.0 42.6 + - - +
265A ALA* 3.6 4.7 - - - +
266A VAL 3.2 0.2 - - - -
267A HIS* 1.3 77.9 - - - +
269A ILE* 1.3 60.7 + - + +
271A PHE* 3.4 5.1 + - - +
272A ALA* 2.9 29.6 + - - +
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Residues in contact with ILE 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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125A LEU* 5.0 6.1 - - + -
126A LEU* 4.9 6.1 - - + -
129A MET* 4.3 8.3 - - - -
181A PHE* 3.7 29.8 - - + -
244A PHE* 4.0 11.7 - - + -
248A ALA* 3.8 15.7 - - + -
251A VAL* 3.5 37.2 - - + -
252A MET* 4.2 10.8 - - + +
265A ALA* 2.9 29.3 + - + +
266A VAL* 3.6 6.1 - - - +
268A ASN* 1.3 73.4 - - - +
270A LEU* 1.3 67.2 + - - +
272A ALA* 3.3 5.4 + - - +
273A VAL* 3.0 32.9 + - + +
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Residues in contact with LEU 270 (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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201A TRP* 3.7 23.6 - - + -
237A TYR* 3.6 43.3 - - + +
240A LEU* 3.9 10.5 - - + -
241A TYR* 3.7 35.9 - - + +
244A PHE* 3.8 28.9 - - + -
266A VAL 2.8 17.2 + - - +
267A HIS 3.7 4.3 - - - +
269A ILE* 1.3 76.3 - - - +
271A PHE* 1.3 59.9 + - + +
274A CYS* 2.8 35.4 + - - +
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Residues in contact with PHE 271 (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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92A PHE* 3.9 12.8 - + - -
103A THR* 3.8 20.0 - - + -
108A VAL* 3.8 26.0 - - + -
110A SER* 3.7 21.8 - - - -
111A TYR* 4.0 19.7 - + - -
201A TRP* 3.7 19.1 - + + -
205A ASN* 5.0 2.2 - - - -
267A HIS 3.0 19.2 + - - +
268A ASN* 3.7 7.2 - - - +
270A LEU* 1.3 82.1 - - + +
272A ALA* 1.3 56.9 + - - +
275A PHE* 2.8 75.5 + + + +
276A ASN* 3.2 14.0 + - - -
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Residues in contact with ALA 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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126A LEU* 3.8 33.4 - - + -
129A MET* 4.9 0.4 - - + -
268A ASN 2.9 18.8 + - - +
269A ILE* 3.3 3.6 + - - +
271A PHE* 1.3 75.5 - - - +
273A VAL* 1.3 59.1 + - + +
276A ASN* 3.2 19.2 - - - +
277A THR* 2.8 32.8 + - - -
600A HEM 3.7 14.4 - - + +
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Residues in contact with VAL 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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129A MET* 4.1 11.4 - - + -
173A PHE* 4.3 10.3 - - + -
176A LEU* 4.0 14.8 - - + +
177A GLY* 5.9 0.4 - - - +
180A TYR* 3.8 34.3 - - + -
181A PHE* 4.2 9.0 - - + -
244A PHE* 3.8 33.0 - - + -
269A ILE* 3.0 17.7 + - + +
272A ALA* 1.3 76.5 - - - +
274A CYS* 1.3 58.2 + - - +
277A THR* 3.3 6.1 - - - -
278A PHE* 2.8 29.8 + - - +
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Residues in contact with CYS 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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173A PHE* 4.2 2.9 - - - -
198A ILE* 3.6 43.9 - - + +
201A TRP* 4.0 16.8 - - + -
202A VAL* 4.8 1.2 - - - +
240A LEU* 4.4 6.5 - - - -
244A PHE* 3.4 36.3 - - - -
270A LEU* 2.8 24.0 + - - +
273A VAL* 1.3 73.7 - - - +
275A PHE* 1.3 63.5 + - - +
278A PHE* 3.4 21.3 - - - +
279A GLY* 3.5 3.8 + - - -
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Residues in contact with PHE 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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92A PHE* 3.3 32.3 - + - -
93A THR* 4.8 4.0 - - + -
111A TYR* 5.0 1.8 - - - -
201A TRP* 4.0 19.3 - + + -
202A VAL* 4.3 19.7 - - + -
205A ASN* 4.2 22.4 - - + -
206A LEU* 3.9 31.4 - - + -
271A PHE* 2.8 56.1 + + + +
274A CYS* 1.3 74.2 - - - +
276A ASN* 1.3 67.9 + - - +
279A GLY* 3.3 20.1 + - - -
280A GLY 4.2 0.3 + - - -
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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