Contacts of the helix formed by residues 1127 - 1139 (chain A) in PDB entry 5OT2
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 ASP1127 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1120A LEU* 4.7 0.2 - - - +
1123A GLY 5.4 0.4 - - - +
1124A HIS* 3.4 34.1 + - + +
1126A ALA* 1.3 74.0 - - - +
1128A GLN* 1.3 59.7 + - - +
1129A GLU* 3.3 12.5 + - - +
1130A GLN* 3.2 34.8 + - + +
1131A ALA* 3.2 18.4 + - - +
1304A TRP* 4.3 2.0 - - - -
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Residues in contact with GLN1128 (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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1126A ALA 2.7 8.6 + - - +
1127A ASP* 1.3 71.7 + - - +
1129A GLU* 1.3 73.7 + - - +
1131A ALA* 3.2 5.4 + - + +
1132A LYS* 2.9 34.5 + - - +
1284A MET* 4.8 11.7 - - - +
1304A TRP* 3.6 50.3 - - + +
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Residues in contact with GLU1129 (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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1127A ASP* 3.3 9.5 + - - +
1128A GLN* 1.3 89.5 - - - +
1130A GLN* 1.3 56.9 + - - +
1132A LYS* 3.2 35.7 + - - +
1133A LEU* 2.9 48.6 + - + +
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Residues in contact with GLN1130 (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 LEU* 4.2 13.3 - - + +
1121A GLU* 5.1 6.9 + - - +
1124A HIS* 3.7 43.7 + - + +
1127A ASP* 3.2 34.7 + - + +
1128A GLN 3.3 0.2 - - - -
1129A GLU* 1.3 76.5 - - - +
1131A ALA* 1.3 56.9 + - - +
1133A LEU* 3.1 19.1 + - - +
1134A ILE* 2.9 45.8 + - + +
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Residues in contact with ALA1131 (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 LEU* 4.1 13.4 - - + +
1127A ASP 3.2 5.1 + - - +
1128A GLN* 3.2 11.8 + - - +
1130A GLN* 1.3 79.0 - - - +
1132A LYS* 1.3 57.8 + - - +
1134A ILE* 3.2 5.6 + - - +
1135A ARG* 2.9 28.2 + - - +
1284A MET* 4.2 14.8 - - + -
1304A TRP* 4.0 27.8 - - + -
1306A LEU* 4.1 16.0 - - + +
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Residues in contact with LYS1132 (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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1128A GLN* 2.9 19.1 + - - +
1129A GLU* 3.2 37.9 + - - +
1131A ALA* 1.3 75.0 - - - +
1133A LEU* 1.3 64.0 + - + +
1135A ARG* 3.0 38.8 + - - +
1136A SER* 3.0 28.3 + - - -
1206A ASP* 5.8 3.9 + - - -
1284A MET* 4.0 19.4 - - + +
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Residues in contact with LEU1133 (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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1129A GLU* 2.9 38.7 + - + +
1130A GLN* 3.1 23.7 + - - +
1132A LYS* 1.3 78.6 - - + +
1134A ILE* 1.3 61.6 + - + +
1136A SER* 3.5 7.2 + - - -
1137A ALA* 2.9 27.6 + - - +
1206A ASP* 6.0 2.0 - - - +
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Residues in contact with ILE1134 (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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1118A VAL* 5.7 2.2 - - + -
1120A LEU* 5.3 11.4 - - + -
1130A GLN* 2.9 39.7 + - + +
1131A ALA* 3.2 6.2 + - - +
1133A LEU* 1.3 76.1 - - + +
1135A ARG* 1.3 67.6 + - - +
1137A ALA* 2.9 17.9 + - + +
1138A ILE* 3.0 30.4 + - + +
1306A LEU* 3.6 21.3 - - + -
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Residues in contact with ARG1135 (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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706A HIS* 4.1 28.0 + - - -
1131A ALA 2.9 14.6 + - - +
1132A LYS* 3.0 59.8 + - - +
1134A ILE* 1.3 75.8 - - - +
1136A SER* 1.3 75.0 + - - +
1139A GLU* 3.0 44.6 + - - +
1204A ASP 3.9 18.4 + - - -
1205A LYS* 5.7 1.2 - - - +
1282A VAL* 3.6 46.9 - - + +
1284A MET* 4.1 21.3 - - + +
1306A LEU* 4.0 6.4 - - + +
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Residues in contact with SER1136 (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 LYS* 3.0 16.4 + - - -
1133A LEU* 4.0 5.8 - - - -
1135A ARG* 1.3 94.6 + - - +
1137A ALA* 1.3 60.2 + - - +
1138A ILE 3.6 0.3 + - - -
1139A GLU* 4.4 3.5 + - - +
1204A ASP 5.4 0.9 + - - -
1205A LYS* 4.2 11.6 + - - +
1206A ASP* 5.1 7.4 + - - -
1274A ARG* 3.6 49.9 + - - +
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Residues in contact with ALA1137 (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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1133A LEU 2.9 17.9 + - - +
1134A ILE* 2.9 20.8 + - + +
1136A SER* 1.3 78.7 - - - +
1138A ILE* 1.3 63.1 + - + +
1274A ARG* 5.5 1.0 - - - +
1275A GLY* 3.9 13.1 + - - -
1276A VAL* 4.8 2.1 - - - +
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Residues in contact with ILE1138 (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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1118A VAL* 4.5 17.3 - - + -
1134A ILE* 3.0 26.4 + - + +
1135A ARG* 3.9 2.9 - - - +
1137A ALA* 1.3 84.1 - - + +
1139A GLU* 1.3 68.2 + - - +
1140A HIS 3.1 1.4 + - - -
1275A GLY* 3.5 3.1 - - - -
1276A VAL* 2.7 45.9 + - + +
1279A ILE* 3.9 14.1 - - + +
1282A VAL* 4.3 17.7 - - + -
1306A LEU* 4.4 18.8 - - + -
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Residues in contact with GLU1139 (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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706A HIS* 2.9 35.4 + - - -
1135A ARG* 3.0 29.9 + - - +
1136A SER* 4.4 1.9 + - - +
1138A ILE* 1.3 75.4 - - - +
1140A HIS* 1.3 70.2 + - - +
1141A THR* 5.3 1.3 - - - -
1205A LYS* 3.1 41.3 + - - +
1274A ARG 3.2 7.1 - - - +
1275A GLY* 3.6 1.0 - - - -
1279A ILE* 4.7 1.1 - - - -
1280A GLU 3.4 18.8 - - - +
1281A ARG* 4.3 1.6 - - - -
1282A VAL* 3.6 32.9 + - + +
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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