Contacts of the helix formed by residues 1235 - 1246 (chain A) in PDB entry 1I44
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 PRO1235 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1106A LEU* 3.5 33.7 - - + -
1109A MET* 4.2 17.3 - - + -
1203A THR* 4.4 6.7 - - + -
1233A ASN 3.5 5.8 - - - +
1234A CYS* 1.3 88.7 - - - +
1236A GLU* 1.3 67.0 + - - +
1237A ARG 3.2 2.0 - - - +
1238A VAL* 3.0 37.3 + - + +
1239A THR* 3.2 9.2 + - - -
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Residues in contact with GLU1236 (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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1234A CYS 3.2 5.3 + - - -
1235A PRO* 1.3 69.8 - - - +
1237A ARG* 1.3 67.3 + - - +
1239A THR* 3.0 20.4 + - + -
1240A ASP* 3.0 33.9 + - - +
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Residues in contact with ARG1237 (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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1106A LEU* 5.0 19.3 - - + -
1110A ILE* 4.3 21.1 - - + +
1235A PRO* 3.2 1.2 - - - +
1236A GLU* 1.3 85.9 + - - +
1238A VAL* 1.3 62.7 + - + +
1240A ASP* 3.4 8.6 + - - +
1241A LEU* 3.4 24.7 + - + +
1262A LEU 3.3 23.2 + - - -
1263A LEU* 3.8 20.3 - - + +
1266A ASP* 2.8 39.3 + - - +
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Residues in contact with VAL1238 (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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1106A LEU* 4.1 12.8 - - + -
1109A MET* 4.9 10.1 - - + -
1110A ILE* 4.7 10.8 - - + -
1199A LEU* 4.1 22.0 - - + -
1203A THR* 3.7 15.3 - - + -
1234A CYS* 4.3 1.1 - - - -
1235A PRO* 3.0 31.9 + - + +
1237A ARG* 1.3 74.8 - - - +
1239A THR* 1.3 66.2 + - - +
1241A LEU* 3.2 10.3 + - + +
1242A MET* 3.0 42.4 + - + +
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Residues in contact with THR1239 (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* 3.1 47.6 + - + +
1234A CYS* 3.6 15.6 + - - +
1235A PRO 3.2 6.2 + - - -
1236A GLU* 3.0 16.0 + - + -
1238A VAL* 1.3 78.6 - - - +
1240A ASP* 1.3 63.8 + - - +
1242A MET* 3.3 4.4 + - - +
1243A ARG* 2.9 30.6 + - + +
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Residues in contact with ASP1240 (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 GLU* 3.0 36.3 + - - +
1237A ARG* 3.7 9.9 - - - +
1239A THR* 1.3 80.4 - - - +
1241A LEU* 1.3 63.3 + - + +
1243A ARG* 3.3 6.7 + - - +
1244A MET* 3.0 32.7 + - + +
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Residues in contact with LEU1241 (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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1110A ILE* 4.9 7.0 - - + -
1113A ALA* 4.9 7.6 - - + -
1199A LEU* 3.6 22.0 - - + -
1237A ARG* 3.4 16.1 + - + +
1238A VAL* 3.2 14.5 + - + +
1240A ASP* 1.3 77.2 - - + +
1242A MET* 1.3 63.5 + - - +
1244A MET* 3.2 12.6 + - - +
1245A CYS* 3.1 29.3 + - - -
1259A ILE* 4.2 26.4 - - + +
1262A LEU* 4.3 19.3 - - + -
1263A LEU* 4.1 34.5 - - + -
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Residues in contact with MET1242 (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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1196A GLY* 3.7 16.8 - - - +
1199A LEU* 3.9 8.3 - - + +
1200A TRP* 3.8 19.5 - - - +
1203A THR* 3.5 23.1 - - - +
1230A GLN* 3.3 28.3 - - - +
1231A PRO* 4.4 0.9 - - + -
1234A CYS* 3.7 5.4 - - - -
1238A VAL* 3.0 38.3 + - + +
1239A THR 3.4 7.6 - - - +
1241A LEU* 1.3 77.8 - - - +
1243A ARG* 1.3 62.4 - - - +
1245A CYS* 3.1 10.1 + - - +
1246A TRP* 3.1 56.3 + - + -
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Residues in contact with ARG1243 (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 TYR* 5.9 6.5 - - + -
1230A GLN* 5.2 2.2 - - - +
1239A THR* 2.9 20.2 + - + +
1240A ASP* 3.6 8.5 - - - +
1241A LEU 3.3 0.2 - - - -
1242A MET* 1.3 75.7 - - - +
1244A MET* 1.3 63.7 + - + +
1246A TRP* 3.0 21.2 + - - +
1247A GLN* 3.6 11.8 + - - +
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Residues in contact with MET1244 (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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1240A ASP* 3.0 24.1 + - + +
1241A LEU* 3.2 17.7 + - - +
1243A ARG* 1.3 76.4 - - + +
1245A CYS* 1.3 60.1 + - - +
1247A GLN* 3.0 39.7 + - - +
1253A ARG* 3.7 6.9 - - - +
1254A PRO* 3.9 31.2 - - + -
1262A LEU* 4.2 28.7 - - + -
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Residues in contact with CYS1245 (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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1192A MET* 3.4 51.4 - - - +
1193A TRP* 3.5 12.3 - - - -
1195A PHE* 3.8 15.7 - - - -
1196A GLY* 3.8 16.6 - - - -
1199A LEU* 4.9 0.4 - - - -
1241A LEU 3.1 21.8 + - - -
1242A MET 3.1 9.9 + - - +
1244A MET* 1.3 78.1 - - - +
1246A TRP* 1.3 60.4 + - + +
1247A GLN 3.5 0.2 - - - -
1253A ARG* 3.3 23.1 + - - -
1254A PRO* 5.0 0.7 - - - -
1259A ILE* 4.9 4.7 - - - -
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Residues in contact with TRP1246 (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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1193A TRP* 3.3 59.6 + + + -
1196A GLY* 3.5 23.8 - - - -
1197A VAL* 3.7 11.6 - - + +
1200A TRP* 4.0 2.5 - + + -
1210A TYR* 5.9 0.4 - - - -
1227A TYR* 3.7 41.7 - + + -
1228A LEU* 3.6 50.9 - - + -
1230A GLN* 4.0 9.4 - - - -
1242A MET* 3.1 44.6 + - + +
1243A ARG* 3.0 12.4 + - - +
1245A CYS* 1.3 86.2 - - + +
1247A GLN* 1.3 65.5 + - - +
1248A PHE* 3.3 2.8 + - - -
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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