Contacts of the helix formed by residues 302 - 314 (chain A) in PDB entry 1EXD
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 302 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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87A TRP* 4.0 2.0 - - - -
300A GLY 4.4 2.2 - - - +
301A TYR* 1.3 77.3 - - - +
303A ALA* 1.3 57.0 + - - +
304A ALA* 4.1 4.3 - - - -
305A SER* 2.5 50.0 + - - -
306A ILE* 3.1 3.9 + - - +
331A ILE* 3.6 2.2 - - + +
334A ASP* 2.5 30.3 + - - +
335A LEU* 3.7 27.1 - - + -
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Residues in contact with ALA 303 (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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87A TRP* 3.2 56.2 - - + +
88A LEU* 3.8 20.1 - - - +
302A THR* 1.3 68.4 - - - +
304A ALA* 1.3 63.6 + - - +
306A ILE* 3.0 5.3 + - - +
307A ARG* 2.9 28.5 + - - +
1396A SO4 4.2 11.8 + - - +
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Residues in contact with ALA 304 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
302A THR* 2.9 3.0 + - - +
303A ALA* 1.3 81.0 - - - +
305A SER* 1.3 56.1 + - - +
307A ARG* 3.6 21.9 + - - +
308A GLU* 3.1 25.6 + - - +
334A ASP* 4.1 13.7 - - - +
1396A SO4 3.4 20.5 + - - +
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Residues in contact with SER 305 (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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301A TYR* 3.6 16.3 - - - +
302A THR* 2.5 47.9 + - - -
304A ALA* 1.3 70.6 - - - +
306A ILE* 1.3 57.6 + - - -
308A GLU* 3.5 6.1 + - - +
309A PHE* 3.0 25.3 + - - +
327A LEU* 5.6 0.4 - - - +
330A CYS* 3.5 32.3 - - - +
331A ILE* 3.8 10.7 - - - +
334A ASP* 4.0 5.4 + - - -
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Residues in contact with ILE 306 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41A ILE* 4.3 9.6 - - + -
44A ALA* 3.6 30.5 - - + -
48A CYS* 5.5 0.7 - - - -
87A TRP* 3.8 33.2 - - + -
88A LEU* 3.8 11.9 - - + -
293A ILE* 4.7 6.3 - - + -
296A LEU* 4.0 33.7 - - + -
301A TYR* 4.5 11.2 - - + -
302A THR 4.1 3.8 - - - +
303A ALA 3.0 7.5 + - - +
305A SER* 1.3 81.3 + - - +
307A ARG* 1.3 67.3 + - - +
308A GLU 3.1 1.1 - - - -
309A PHE* 2.8 17.6 + - - +
310A CYS* 2.9 17.7 + - - -
327A LEU* 5.4 2.2 - - + -
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Residues in contact with ARG 307 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48A CYS* 4.1 15.5 - - - +
88A LEU* 2.6 31.1 + - + +
89A GLY* 4.5 3.6 + - - -
90A PHE* 3.7 27.6 - - + -
303A ALA 2.9 16.1 + - - +
304A ALA* 3.7 22.7 + - - +
306A ILE* 1.3 75.8 - - - +
308A GLU* 1.3 56.6 + - - +
310A CYS* 4.0 1.0 - - - +
311A LYS* 3.0 29.4 + - - +
1396A SO4 2.7 52.3 + - - -
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Residues in contact with GLU 308 (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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304A ALA 3.1 17.5 + - - +
305A SER* 3.6 8.7 - - - +
306A ILE 3.1 0.6 - - - -
307A ARG* 1.3 73.6 - - - +
309A PHE* 1.3 61.6 + - - +
311A LYS* 3.2 24.1 + - - +
312A ARG* 2.6 85.6 + - - +
330A CYS* 4.2 7.4 - - + +
333A GLU* 4.5 6.1 - - - +
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Residues in contact with PHE 309 (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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41A ILE* 3.4 43.5 - - + -
261A LEU* 3.9 19.7 - - + -
263A LEU* 4.7 3.4 - - + -
305A SER 3.0 14.8 + - - +
306A ILE* 2.8 9.8 + - - +
308A GLU* 1.3 75.4 - - - +
310A CYS* 1.3 69.4 + - - +
312A ARG* 3.0 6.4 + - + +
313A ILE* 2.9 57.7 + - + +
322A ILE* 3.7 25.1 - - + -
326A SER* 4.2 9.2 - - - -
327A LEU* 4.1 30.7 - - + -
330A CYS* 3.5 17.4 - - + -
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Residues in contact with CYS 310 (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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41A ILE 4.6 1.6 - - - -
44A ALA* 3.5 41.5 - - - -
45A LYS* 3.5 15.4 - - + +
48A CYS* 3.7 25.4 - - + -
306A ILE* 2.9 17.6 + - - +
307A ARG 4.0 0.7 - - - +
309A PHE* 1.3 86.7 - - - +
311A LYS* 1.3 63.6 + - - +
313A ILE* 3.2 23.8 + - - +
314A GLY* 3.8 6.1 + - - +
315A VAL* 5.6 2.6 - - - +
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Residues in contact with LYS 311 (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 CYS* 5.7 0.4 - - - +
307A ARG 3.0 20.8 + - - +
308A GLU* 3.3 25.0 + - - +
310A CYS* 1.3 77.6 - - - +
312A ARG* 1.3 61.8 + - + +
314A GLY* 3.6 8.5 + - - -
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Residues in contact with ARG 312 (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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308A GLU* 2.6 49.1 + - - +
309A PHE* 3.4 6.3 - - + +
311A LYS* 1.3 79.7 - - + +
313A ILE* 1.3 62.4 + - + +
314A GLY* 3.2 1.7 + - - -
326A SER* 4.8 6.8 + - - +
329A SER* 4.1 11.7 + - - -
330A CYS* 3.1 33.2 - - - +
333A GLU* 2.8 41.6 + - - +
912B C 4.9 5.9 + - - +
913B A 5.7 1.6 - - - +
923B G 5.2 5.0 + - - -
924B G 3.0 42.7 + - - +
925B C 4.4 6.8 + - - -
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Residues in contact with ILE 313 (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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45A LYS* 4.0 26.7 - - + -
261A LEU* 4.0 23.6 - - + -
309A PHE* 2.9 49.7 + - + +
310A CYS* 3.2 27.8 - - - +
312A ARG* 1.3 74.0 - - - +
314A GLY* 1.3 65.4 + - - +
320A ASN* 6.1 0.2 - - - -
322A ILE* 3.6 25.2 - - + +
326A SER* 4.7 5.6 - - - +
912B C 2.9 23.5 + - - +
913B A 3.4 11.6 + - - +
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Residues in contact with GLY 314 (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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45A LYS* 3.9 16.5 + - - -
310A CYS 3.8 3.0 + - - +
311A LYS 3.6 10.0 + - - -
312A ARG 3.2 5.6 - - - -
313A ILE* 1.3 86.5 - - - +
315A VAL* 1.3 69.2 + - - +
316A THR 4.3 0.2 - - - -
913B A 4.2 16.5 + - - -
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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