Contacts of the helix formed by residues 1301 - 1310 (chain A) in PDB entry 5Y36
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 PRO1301 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1243A GLU* 4.3 11.0 - - - +
1299A ASP 4.6 1.3 - - - +
1300A LYS* 1.3 90.6 - - + +
1302A ILE* 1.4 64.9 + - - +
1303A ARG* 5.2 3.6 - - - +
1304A GLU* 3.6 36.7 - - + +
1305A GLN* 3.3 23.6 + - - +
1327A PHE* 4.1 7.2 - - + -
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Residues in contact with ILE1302 (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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1239A ALA* 3.5 44.0 - - + +
1240A SER 4.0 0.9 - - - +
1243A GLU* 3.5 14.9 + - + +
1259A VAL* 5.5 8.1 - - + -
1263A LYS* 5.4 14.1 - - - +
1300A LYS 3.5 3.7 + - - +
1301A PRO* 1.4 71.2 - - - +
1303A ARG* 1.3 61.8 + - - +
1305A GLN* 3.5 7.7 + - - +
1306A ALA* 3.0 23.0 + - + +
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Residues in contact with ARG1303 (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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884A ARG* 5.5 2.8 - - - +
888A ASN* 5.2 10.7 + - - +
913A LYS* 5.6 0.2 - - - +
916A PHE* 5.5 10.8 - - + -
917A ILE* 5.5 9.0 - - - -
1240A SER* 3.6 32.6 + - - +
1243A GLU* 2.9 38.6 + - - +
1301A PRO* 5.2 3.6 - - - +
1302A ILE* 1.3 72.8 - - - +
1304A GLU* 1.3 84.8 + - - +
1306A ALA* 2.9 5.4 + - - +
1307A GLU* 2.7 70.4 + - + +
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Residues in contact with GLU1304 (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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884A ARG* 3.3 25.7 + - - +
1301A PRO* 3.6 28.6 + - + +
1303A ARG* 1.3 107.8 + - - +
1305A GLN* 1.3 61.4 + - - +
1307A GLU* 3.7 24.3 - - - +
1308A ASN* 4.1 12.1 + - - -
1326A TYR 4.5 3.5 - - - +
1327A PHE* 3.4 30.7 - - + -
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Residues in contact with GLN1305 (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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1266A LEU* 5.7 5.2 - - - +
1294A TYR* 5.5 2.6 - - - -
1297A HIS* 3.1 31.5 + - - +
1298A ARG* 5.0 2.5 + - - +
1300A LYS* 3.1 25.9 + - - -
1301A PRO 3.3 11.3 + - - +
1302A ILE* 3.8 6.2 - - - +
1303A ARG 3.2 0.4 - - - -
1304A GLU* 1.3 76.0 - - - +
1306A ALA* 1.3 60.7 + - - +
1307A GLU 3.5 0.2 + - - -
1308A ASN* 3.6 2.8 + - - +
1309A ILE* 3.3 22.1 + - - +
1326A TYR* 2.7 53.8 + - + +
1327A PHE* 4.3 15.7 - - + -
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Residues in contact with ALA1306 (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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916A PHE* 5.2 7.9 - - + -
1236A LEU* 4.2 17.3 - - + +
1239A ALA* 6.0 0.7 - - + -
1240A SER* 3.8 24.7 - - - +
1302A ILE* 3.0 19.0 + - + +
1303A ARG 2.9 8.2 + - - +
1305A GLN* 1.3 70.5 - - - +
1307A GLU* 1.3 61.9 + - - +
1308A ASN 3.4 0.2 - - - -
1309A ILE* 3.3 28.5 + - + +
1310A ILE* 4.1 7.8 - - - +
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Residues in contact with GLU1307 (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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910A GLU* 5.0 3.3 - - - +
913A LYS* 3.1 46.1 + - + +
916A PHE* 5.7 7.2 - - + -
1240A SER* 5.4 1.3 - - - +
1303A ARG* 2.7 59.1 + - + +
1304A GLU* 3.7 19.6 - - - +
1305A GLN 3.3 0.4 - - - -
1306A ALA* 1.3 72.6 - - - +
1308A ASN* 1.3 66.1 + - - +
1310A ILE* 3.7 21.7 - - - +
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Residues in contact with ASN1308 (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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905A ARG* 4.4 10.1 + - - +
910A GLU* 3.8 17.5 - - - +
1304A GLU 4.1 6.6 + - - +
1305A GLN 3.6 5.5 + - - +
1306A ALA 3.4 0.2 - - - -
1307A GLU* 1.3 82.2 - - - +
1309A ILE* 1.4 64.1 + - - +
1310A ILE 3.2 4.5 + - - -
1311A HIS* 3.3 24.7 + - + -
1324A PHE* 3.4 15.1 - - + -
1325A LYS* 3.0 23.7 + - - +
1326A TYR* 2.9 30.3 + - + +
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Residues in contact with ILE1309 (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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978A ILE* 5.8 0.4 - - + -
1236A LEU* 3.8 46.2 - - + -
1266A LEU* 4.4 13.2 - - + -
1269A ILE* 5.4 7.2 - - + -
1294A TYR* 4.8 8.1 - - + +
1305A GLN 3.3 14.6 + - - +
1306A ALA* 3.3 24.9 + - + +
1308A ASN* 1.4 76.4 - - - +
1310A ILE* 1.3 62.3 + - + +
1311A HIS 3.0 0.4 - - - -
1312A LEU* 2.9 45.1 + - + +
1313A PHE* 3.5 10.7 - - + -
1324A PHE* 5.1 0.2 - - - -
1326A TYR* 4.7 16.2 - - + +
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Residues in contact with ILE1310 (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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909A SER 4.2 5.4 - - - +
910A GLU* 3.9 27.1 - - + -
916A PHE* 5.9 6.5 - - + -
977A GLU* 3.2 53.5 - - + +
978A ILE* 3.8 19.5 - - + -
1306A ALA 4.1 13.7 - - - +
1307A GLU 3.7 19.5 - - - +
1308A ASN 4.0 3.1 - - - +
1309A ILE* 1.3 77.8 - - + +
1311A HIS* 1.3 69.0 + - + +
1312A LEU 3.3 0.4 - - - -
1313A PHE* 3.4 19.7 + - - +
36D G 3.7 6.6 + - - +
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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