Contacts of the helix formed by residues 1133 - 1147 (chain A) in PDB entry 5XRA
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 ALA1133 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1126A ILE* 4.7 18.4 - - + -
1127A ASP* 5.9 2.9 - - - +
1129A ASP 4.9 0.9 - - - +
1130A PRO* 2.7 17.7 + - + +
1132A ALA* 1.3 72.0 - - + +
1134A ARG* 1.3 53.9 + - - +
1135A ASP* 3.0 4.0 - - - -
1136A ASP* 2.6 51.0 + - + +
1137A ILE* 3.0 12.7 + - + +
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Residues in contact with ARG1134 (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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1017A TYR* 3.7 24.2 + - - +
1021A THR* 4.4 20.0 + - + +
1024A ARG* 5.7 8.9 - - - +
1130A PRO 3.3 5.7 + - - -
1131A ARG 3.7 14.8 - - - +
1132A ALA 3.3 3.8 + - - -
1133A ALA* 1.3 76.7 - - - +
1135A ASP* 1.3 60.1 + - - +
1137A ILE* 3.3 9.3 + - - +
1138A VAL* 2.9 45.2 + - + +
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Residues in contact with ASP1135 (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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1132A ALA 5.0 0.6 + - - +
1133A ALA* 3.0 1.3 - - - -
1134A ARG* 1.3 83.5 - - - +
1136A ASP* 1.3 57.6 + - - +
1138A VAL* 4.2 3.3 - - - +
1139A GLY* 2.7 33.4 + - - -
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Residues in contact with ASP1136 (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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1124A LEU* 3.9 9.8 - - + +
1126A ILE* 6.2 1.6 - - + -
1133A ALA* 2.6 34.7 + - + +
1135A ASP* 1.3 77.7 - - - +
1137A ILE* 1.3 56.7 + - + +
1139A GLY* 3.8 0.8 - - - -
1140A TRP* 2.9 28.6 + - - +
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Residues in contact with ILE1137 (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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1017A TYR* 4.6 7.9 - - + -
1018A THR* 3.9 18.6 - - + +
1021A THR* 3.9 18.4 - - + -
1022A ILE* 3.7 27.9 - - + +
1124A LEU* 4.4 5.4 - - + -
1126A ILE* 3.7 32.1 - - + -
1130A PRO* 3.8 28.0 - - + +
1133A ALA* 3.0 10.7 + - + +
1134A ARG* 3.6 9.9 - - - +
1136A ASP* 1.3 76.8 - - - +
1138A VAL* 1.3 63.9 + - - +
1140A TRP* 3.0 17.6 + - - +
1141A ALA* 3.0 12.6 + - - +
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Residues in contact with VAL1138 (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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1021A THR* 3.9 26.5 - - + +
1022A ILE* 6.5 0.2 - - - +
1025A GLU* 3.7 22.9 - - + +
1134A ARG* 2.9 36.9 + - + +
1135A ASP* 4.2 3.1 - - - +
1137A ILE* 1.3 74.4 - - - +
1139A GLY* 1.3 61.5 + - - +
1141A ALA* 3.5 7.9 + - - +
1142A HIS* 3.2 20.8 + - - +
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Residues in contact with GLY1139 (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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1135A ASP 2.7 22.7 + - - -
1136A ASP* 3.8 2.0 - - - -
1138A VAL* 1.3 73.4 - - - +
1140A TRP* 1.3 60.5 + - - +
1142A HIS* 3.3 8.4 + - - +
1143A ASP* 3.2 28.3 + - - +
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Residues in contact with TRP1140 (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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1022A ILE* 3.9 24.9 - - + -
1054A LEU* 4.5 12.6 - - + -
1089A ALA* 3.6 24.5 - - + -
1090A CYS 3.3 31.4 - - - -
1091A PHE* 4.1 9.9 - + + -
1121A GLN* 3.8 15.6 - - - +
1122A ASP 3.4 21.0 + - - -
1123A GLY 4.3 1.3 + - - -
1124A LEU* 3.5 40.1 - - + +
1136A ASP 2.9 16.2 + - - +
1137A ILE 3.0 8.9 + - - +
1139A GLY* 1.3 73.3 - - - +
1141A ALA* 1.3 73.6 + - - +
1143A ASP* 3.0 7.8 + - + +
1144A VAL* 2.9 46.8 + - + +
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Residues in contact with ALA1141 (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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1022A ILE* 4.7 11.9 - - + +
1025A GLU* 3.6 31.2 - - + +
1026A LEU* 4.0 14.8 - - + +
1137A ILE 3.0 11.3 + - - +
1138A VAL* 3.7 9.4 - - - +
1140A TRP* 1.3 82.6 - - - +
1142A HIS* 1.3 54.2 + - - +
1144A VAL* 4.8 2.5 - - - -
1145A ARG* 2.6 41.1 + - - +
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Residues in contact with HIS1142 (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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1025A GLU* 4.3 15.2 + - - +
1138A VAL 3.2 10.1 + - - +
1139A GLY* 3.5 11.9 - - - +
1140A TRP 3.1 0.4 - - - -
1141A ALA* 1.3 79.0 - - - +
1143A ASP* 1.3 58.7 + - - +
1145A ARG* 3.5 14.7 + - - +
1146A GLY* 2.7 33.9 + - - -
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Residues in contact with ASP1143 (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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1121A GLN* 2.9 30.4 + - - +
1139A GLY 3.2 14.2 + - - +
1140A TRP* 3.0 8.7 + - - +
1142A HIS* 1.3 81.1 + - - +
1144A VAL* 1.3 58.3 + - - +
1146A GLY* 2.8 17.1 + - - -
1147A ALA* 3.1 10.2 + - - +
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Residues in contact with VAL1144 (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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1052A LEU* 4.5 22.6 - - + +
1054A LEU* 4.6 5.6 - - + -
1089A ALA* 4.0 19.1 - - + -
1120A VAL* 3.9 16.7 - - + +
1121A GLN* 3.0 27.8 + - + +
1140A TRP* 2.9 56.4 + - + +
1141A ALA* 4.0 3.8 - - - +
1143A ASP* 1.3 71.7 - - - +
1145A ARG* 1.3 62.6 + - - +
1146A GLY 3.4 0.2 + - - -
1147A ALA 3.2 16.5 + - - +
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Residues in contact with ARG1145 (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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1025A GLU* 3.1 35.0 + - - -
1026A LEU* 4.5 8.1 - - + -
1029A ALA* 3.5 29.7 - - + +
1031A TYR* 3.5 37.7 + - + +
1052A LEU* 5.8 4.5 - - - -
1141A ALA 2.6 20.3 + - - +
1142A HIS* 3.5 12.6 - - - +
1144A VAL* 1.3 75.2 - - - +
1146A GLY* 1.3 63.4 + - - +
1147A ALA 3.5 5.4 + - - +
1148A ILE* 4.5 4.5 - - - +
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Residues in contact with GLY1146 (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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1142A HIS* 2.7 22.1 + - - -
1143A ASP* 2.8 7.3 + - - -
1145A ARG* 1.3 75.7 - - - +
1147A ALA* 1.3 60.0 + - - -
1148A ILE* 3.3 6.6 + - - +
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Residues in contact with ALA1147 (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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1120A VAL* 3.5 37.3 - - + +
1121A GLN* 4.6 4.5 - - - +
1143A ASP 3.1 10.9 + - - +
1144A VAL 3.2 11.8 - - - +
1145A ARG 3.4 2.6 - - - +
1146A GLY* 1.3 74.5 - - - +
1148A ILE* 1.3 62.2 + - - +
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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