Contacts of the helix formed by residues 1230 - 1242 (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 SER1230 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1087A LEU* 5.0 15.4 - - - +
1088A SER* 4.8 20.5 - - - -
1228A LEU 3.7 2.5 + - - -
1229A PRO* 1.4 71.0 - - - +
1231A LYS* 1.4 62.2 + - - +
1232A TYR 3.2 3.6 + - - -
1233A VAL* 3.3 20.6 + - - +
1234A ASN* 3.6 21.2 + - - -
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Residues in contact with LYS1231 (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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1229A PRO* 4.1 19.2 - - + +
1230A SER* 1.4 79.5 + - - +
1232A TYR* 1.3 91.4 + - + +
1234A ASN* 4.6 5.5 - - - +
1235A PHE* 3.7 18.7 + - - +
1258A PHE* 4.4 5.7 - - + -
1264A HIS* 6.1 0.2 + - - -
1265A TYR* 3.9 32.6 - - + +
1268A GLU* 3.5 17.1 + - - -
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Residues in contact with TYR1232 (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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1228A LEU* 4.0 21.3 - - + -
1229A PRO* 3.4 46.2 + - + +
1230A SER 3.2 0.8 - - - -
1231A LYS* 1.3 89.8 + - - +
1233A VAL* 1.4 63.0 - - + +
1235A PHE* 3.7 4.9 + - - +
1236A LEU* 3.5 30.2 + - + +
1265A TYR* 3.8 20.0 - + - -
1268A GLU* 2.7 48.3 + - + +
1269A ILE* 3.6 30.6 - - + +
1272A GLN* 4.0 26.2 + - + +
1313A PHE* 5.9 1.3 - - + -
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Residues in contact with VAL1233 (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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973A TYR* 4.5 11.9 - - + +
978A ILE* 3.9 33.4 - - + +
979A ASN* 6.0 5.2 - - + +
1228A LEU* 5.5 7.2 - - + +
1229A PRO 4.8 6.7 - - - +
1230A SER* 3.7 13.9 - - - +
1232A TYR* 1.4 77.2 - - + +
1234A ASN* 1.3 71.4 + - - +
1235A PHE 3.5 0.2 + - - -
1236A LEU* 3.8 1.9 + - - +
1237A TYR* 3.6 19.2 + - - +
1313A PHE* 4.4 23.0 - - + -
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Residues in contact with ASN1234 (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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971A GLN* 4.6 12.8 + - - +
973A TYR* 3.3 38.3 + - + +
1087A LEU* 6.2 2.2 - - - +
1230A SER* 3.6 18.7 + - - +
1231A LYS* 4.9 4.6 - - - +
1232A TYR 3.5 0.2 - - - -
1233A VAL* 1.3 81.9 - - - +
1235A PHE* 1.4 63.6 + - - +
1237A TYR* 3.7 2.5 + - - +
1238A LEU* 3.3 34.2 + - + +
1258A PHE* 5.0 5.8 - - + -
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Residues in contact with PHE1235 (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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1231A LYS 3.7 18.8 + - - +
1232A TYR 3.7 4.7 + - - +
1233A VAL 3.4 0.4 - - - -
1234A ASN* 1.4 77.4 - - - +
1236A LEU* 1.4 80.6 + - + +
1238A LEU* 3.7 1.5 - - - +
1239A ALA* 2.8 41.3 + - + +
1258A PHE* 3.9 23.9 - + + -
1259A VAL* 4.0 28.3 - - + +
1262A HIS 3.1 23.6 - - - -
1263A LYS* 4.3 13.7 - - + -
1265A TYR* 3.6 34.5 - + + -
1266A LEU* 4.2 18.4 - - + -
1269A ILE* 5.2 1.1 - - + -
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Residues in contact with LEU1236 (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* 5.0 0.9 - - - -
978A ILE* 6.4 1.1 - - + -
1232A TYR* 3.5 17.0 + - + +
1233A VAL 4.3 3.1 - - - +
1234A ASN 3.6 0.2 - - - -
1235A PHE* 1.4 91.1 - - + +
1237A TYR* 1.4 64.1 + - - +
1239A ALA* 3.9 5.1 - - + +
1240A SER* 3.5 20.4 + - - -
1266A LEU* 3.8 28.5 - - + -
1269A ILE* 4.0 15.3 - - + -
1306A ALA* 4.2 13.5 - - + +
1309A ILE* 3.8 33.0 - - + -
1313A PHE* 3.8 30.1 - - + -
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Residues in contact with TYR1237 (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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915A GLY* 3.7 15.9 + - - -
916A PHE* 3.1 51.7 - + - -
919A ARG* 3.5 22.3 + - - -
973A TYR* 3.5 47.1 - + + -
975A VAL* 4.1 25.6 - - + -
978A ILE* 4.8 14.5 - - + +
1233A VAL 3.6 15.1 + - - +
1234A ASN 4.0 3.8 - - - +
1235A PHE 3.4 0.4 - - - -
1236A LEU* 1.4 78.8 - - - +
1238A LEU* 1.3 70.7 + - + +
1240A SER 3.6 0.2 + - - -
1241A HIS* 3.2 20.3 + + + +
31D T 5.5 1.7 + - - -
32D T 3.7 7.5 + - - -
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Residues in contact with LEU1238 (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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973A TYR* 3.5 34.1 - - + +
1234A ASN* 3.3 24.4 + - + +
1235A PHE* 4.1 2.0 - - - +
1237A TYR* 1.3 90.1 - - + +
1239A ALA* 1.3 58.8 + - - +
1241A HIS* 4.0 8.3 - - + -
1242A TYR* 2.9 56.9 + - + +
1255A LYS* 3.8 31.6 - - + +
1258A PHE* 5.4 6.7 - - + -
1259A VAL* 4.0 13.9 - - + -
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Residues in contact with ALA1239 (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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1235A PHE* 2.8 36.4 + - + +
1236A LEU* 3.9 9.4 - - + +
1238A LEU* 1.3 72.7 - - - +
1240A SER* 1.4 61.4 + - - +
1242A TYR* 3.8 2.1 + - - +
1243A GLU* 3.6 13.7 + - - +
1259A VAL* 3.7 27.9 - - + +
1302A ILE* 3.5 27.8 - - + +
1306A ALA* 6.0 0.4 - - + -
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Residues in contact with SER1240 (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* 3.6 28.5 - - - +
1236A LEU 3.5 5.0 + - - -
1237A TYR 3.8 7.4 - - - -
1238A LEU 3.4 0.4 - - - -
1239A ALA* 1.4 76.0 - - - +
1241A HIS* 1.4 66.7 + - - +
1243A GLU* 3.4 17.4 + - - +
1302A ILE* 4.0 2.7 - - - +
1303A ARG* 3.6 36.1 + - - +
1306A ALA* 3.8 23.8 - - - +
1307A GLU* 5.4 0.7 - - - +
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Residues in contact with HIS1241 (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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915A GLY 4.6 13.1 + - - -
916A PHE* 4.1 18.5 + - + +
1237A TYR* 3.2 22.2 + + + +
1238A LEU* 3.2 18.6 + - + +
1240A SER* 1.4 78.2 - - - +
1242A TYR* 1.3 89.7 + + - +
1243A GLU 3.3 3.6 + - - -
1244A LYS 4.3 1.4 + - - -
1245A LEU* 3.4 51.2 + - + +
30D G 5.1 12.1 - - - -
31D T 5.2 11.0 - - - -
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Residues in contact with TYR1242 (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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1238A LEU* 2.9 48.6 + - + +
1239A ALA* 4.1 4.0 - - - +
1240A SER 3.4 0.2 - - - -
1241A HIS* 1.3 90.7 + + - +
1243A GLU* 1.4 62.7 + - - +
1244A LYS 3.5 0.9 - - - -
1245A LEU* 3.5 29.7 - - + +
1246A LYS 4.9 1.6 - - - -
1247A GLY* 4.6 12.6 - - - -
1252A ASN* 3.1 46.1 + - + -
1255A LYS* 3.6 26.9 - - + +
1256A GLN* 4.0 32.4 - - + +
1259A VAL* 4.9 6.7 - - + -
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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