Contacts of the helix formed by residues 1227 - 1240 (chain A) in PDB entry 5IYB
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 THR1227 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1221A MET* 5.2 0.4 - - - -
1225A LYS 4.7 4.3 - - - +
1226A LEU* 1.3 84.1 - - - +
1228A MET* 1.3 63.6 + - - +
1229A GLU* 3.2 28.8 + - + +
1230A GLN* 3.1 30.9 + - - +
1231A ILE* 3.4 20.6 + - - +
1250A ASP* 6.0 1.8 - - - -
226U GLU* 6.4 2.7 - - + -
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Residues in contact with MET1228 (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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1216A LEU* 3.6 16.8 - - + -
1221A MET* 3.5 30.7 - - + -
1226A LEU 4.4 0.2 + - - -
1227A THR* 1.3 73.4 - - - +
1229A GLU* 1.3 58.3 + - - +
1231A ILE* 3.3 11.2 + - - +
1232A ALA* 3.0 27.3 + - - +
1247A PHE* 4.2 26.8 - - + +
1248A ASN* 3.7 23.6 - - - +
1250A ASP* 5.1 16.3 + - + +
1255A LEU* 3.6 38.8 - - + -
1256A VAL 4.4 7.2 - - - +
1257A LEU* 5.5 3.4 - - - -
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Residues in contact with GLU1229 (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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1227A THR* 3.2 22.0 + - - +
1228A MET* 1.3 77.3 - - - +
1230A GLN* 1.3 64.8 + - + +
1232A ALA* 3.5 1.6 + - - +
1233A GLU* 3.0 31.9 + - - +
1247A PHE* 4.3 26.6 - - + -
186U LYS* 6.0 3.2 - - - +
189U ASN* 5.7 7.5 - - + +
190U ARG* 5.0 15.7 + - - -
223U MET* 5.9 3.7 - - - +
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Residues in contact with GLN1230 (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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1225A LYS 4.9 0.9 - - - +
1226A LEU* 3.1 28.9 - - + +
1227A THR* 3.1 33.5 + - - +
1228A MET 3.4 0.4 - - - -
1229A GLU* 1.3 82.1 + - + +
1231A ILE* 1.3 61.4 + - - +
1233A GLU* 3.7 10.6 - - - +
1234A LYS* 2.8 29.5 + - - +
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Residues in contact with ILE1231 (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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1166A LEU* 4.6 18.6 - - + -
1169A VAL* 5.7 0.7 - - + -
1216A LEU* 4.7 5.6 - - + -
1221A MET* 3.6 32.3 - - + -
1226A LEU* 3.6 27.1 - - + -
1227A THR 3.4 13.9 - - - +
1228A MET* 3.3 14.3 + - - +
1229A GLU 3.3 0.4 - - - -
1230A GLN* 1.3 74.6 - - - +
1232A ALA* 1.3 66.2 + - - +
1234A LYS* 3.2 5.6 + - + +
1235A ILE* 2.9 46.6 + - + +
1257A LEU* 4.8 11.7 - - + -
1298A LEU* 4.1 11.4 - - + -
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Residues in contact with ALA1232 (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 MET 3.0 17.2 + - - +
1229A GLU 3.8 4.3 - - - +
1230A GLN 3.4 0.2 - - - -
1231A ILE* 1.3 74.8 - - - +
1233A GLU* 1.3 59.4 + - - +
1235A ILE* 3.2 13.6 - - - +
1236A ASN* 3.0 31.9 + - - +
1245A CYS* 4.8 16.0 - - + +
1247A PHE* 3.8 27.6 - - + -
1257A LEU* 5.5 4.0 - - + -
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Residues in contact with GLU1233 (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 GLU 3.0 19.2 + - - +
1230A GLN* 3.8 10.9 - - - +
1232A ALA* 1.3 76.1 - - - +
1234A LYS* 1.3 58.8 + - - +
1236A ASN* 4.0 10.5 + - - +
1237A ALA* 3.0 34.3 + - + +
1E MET 5.7 0.5 - - - +
186U LYS* 4.1 26.5 + - - -
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Residues in contact with LYS1234 (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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1230A GLN 2.8 22.8 + - - +
1231A ILE* 3.2 7.8 + - - +
1233A GLU* 1.3 74.0 - - - +
1235A ILE* 1.3 58.1 + - + +
1237A ALA* 3.5 5.4 + - + +
1238A GLY* 2.9 24.8 + - - -
1296A MET* 4.0 19.6 - - + +
1297A THR* 4.3 27.5 + - - +
1298A LEU* 4.8 18.4 - - + +
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Residues in contact with ILE1235 (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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1166A LEU* 4.9 3.8 - - + -
1231A ILE* 2.9 33.6 + - + +
1232A ALA* 3.2 14.4 - - - +
1234A LYS* 1.3 74.6 - - + +
1236A ASN* 1.3 68.7 + - - +
1239A PHE* 3.0 29.8 + - - +
1243A LEU* 4.1 10.5 - - + +
1245A CYS* 3.4 29.6 - - + -
1257A LEU* 4.3 23.3 - - + -
1259A ILE* 4.7 4.5 - - + -
1292A MET* 4.4 14.6 - - + -
1296A MET* 3.6 31.0 - - + -
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Residues in contact with ASN1236 (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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1232A ALA 3.0 21.6 + - - +
1233A GLU* 4.0 9.1 + - - +
1235A ILE* 1.3 79.3 - - + +
1237A ALA* 1.3 57.9 + - - +
1240A GLY* 2.8 44.0 + - - +
1241A ASP* 3.8 11.9 + - - +
1243A LEU 4.6 12.7 - - - +
1245A CYS* 5.5 4.5 - - + +
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Residues in contact with ALA1237 (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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1233A GLU* 3.0 23.2 + - + +
1234A LYS* 3.8 6.5 - - + +
1236A ASN* 1.3 80.2 - - - +
1238A GLY* 1.3 62.9 + - - +
1240A GLY* 4.0 5.1 + - - -
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Residues in contact with GLY1238 (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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1234A LYS 2.9 16.7 + - - -
1235A ILE 3.3 1.3 + - - -
1237A ALA* 1.3 79.1 - - - +
1239A PHE* 1.3 62.4 + - - +
1296A MET* 4.1 11.0 - - - -
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Residues in contact with PHE1239 (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 ILE* 3.0 10.9 + - + +
1238A GLY* 1.3 75.3 - - - +
1240A GLY* 1.3 59.5 + - - +
1242A ASP* 5.0 7.8 - - + +
1243A LEU* 3.6 36.6 - - + -
1288A ILE* 4.3 21.3 - - + -
1291A ASN* 3.1 39.0 - - + -
1292A MET* 4.0 25.4 - - + -
1295A ASP* 5.9 1.6 - - + -
1296A MET* 3.6 26.7 - - + -
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Residues in contact with GLY1240 (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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1236A ASN* 2.8 31.5 + - - +
1237A ALA* 4.0 4.7 + - - -
1238A GLY 3.4 1.8 - - - -
1239A PHE* 1.3 76.2 - - - +
1241A ASP* 1.3 59.6 + - - -
1242A ASP* 3.0 11.9 + - - -
1243A LEU* 3.2 15.8 + - - +
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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