Contacts of the helix formed by residues 1118 - 1132 (chain A) in PDB entry 5XA0
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 ASP1118 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1114A GLN 4.6 1.1 + - - +
1115A ILE* 3.3 13.4 + - - +
1116A LYS 3.2 0.6 - - - -
1117A GLN* 1.3 77.9 - - + +
1119A LEU* 1.3 55.1 + - - +
1120A ASP 3.4 1.8 - - - -
1121A GLN* 3.8 14.4 - - + -
1122A LEU* 2.7 37.6 + - + +
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Residues in contact with LEU1119 (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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1115A ILE 3.0 11.0 + - - +
1116A LYS* 3.4 16.3 + - - +
1118A ASP* 1.3 74.4 - - - +
1120A ASP* 1.3 57.3 + - - +
1122A LEU* 2.7 27.1 + - - +
1123A ARG* 2.8 13.4 + - - +
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Residues in contact with ASP1120 (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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1116A LYS 4.9 0.4 + - - -
1117A GLN 4.5 5.9 + - - +
1118A ASP 3.4 0.6 - - - -
1119A LEU* 1.3 77.0 - - - +
1121A GLN* 1.3 62.1 + - - +
1123A ARG* 3.1 12.0 + - - +
1124A SER* 3.0 20.1 + - - -
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Residues in contact with GLN1121 (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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1117A GLN 4.9 1.7 + - - +
1118A ASP* 3.4 19.8 + - + +
1119A LEU 3.2 0.4 - - - -
1120A ASP* 1.3 79.2 - - - +
1122A LEU* 1.3 57.9 + - - +
1124A SER* 3.2 8.2 + - - +
1125A ILE* 2.9 30.0 + - - +
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Residues in contact with LEU1122 (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 ASP* 2.7 25.3 + - + +
1119A LEU* 2.7 9.9 + - - +
1121A GLN* 1.3 71.4 - - - +
1123A ARG* 1.3 58.8 + - - +
1125A ILE* 4.0 5.5 - - - +
1126A VAL* 2.9 27.6 + - - +
1183A LEU* 5.9 0.2 - - - +
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Residues in contact with ARG1123 (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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1119A LEU 2.8 9.9 + - - +
1120A ASP* 3.3 13.9 - - - +
1122A LEU* 1.3 76.5 - - - +
1124A SER* 1.3 60.0 + - - +
1126A VAL* 3.5 5.9 - - - +
1127A GLU* 2.7 28.2 + - - +
1205A LEU* 6.2 4.7 - - + -
1206A ARG* 6.0 3.1 - - + +
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Residues in contact with SER1124 (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 ASP 3.0 12.3 + - - -
1121A GLN* 3.2 10.3 + - - -
1123A ARG* 1.3 73.6 - - - +
1125A ILE* 1.3 59.2 + - - +
1127A GLU* 3.0 7.9 + - - +
1128A LYS* 2.9 30.7 + - - +
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Residues in contact with ILE1125 (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 16.3 + - - +
1122A LEU* 4.4 6.1 - - - +
1124A SER* 1.3 71.5 - - - +
1126A VAL* 1.3 54.3 + - - +
1128A LYS* 5.0 3.1 - - - -
1129A SER* 2.5 43.6 + - - +
1179A ILE* 4.7 2.2 - - + +
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Residues in contact with VAL1126 (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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1122A LEU 2.9 23.4 + - - +
1123A ARG* 3.5 9.4 - - - +
1124A SER 3.2 0.2 - - - -
1125A ILE* 1.3 73.3 - - - +
1127A GLU* 1.3 65.4 + - - +
1129A SER* 2.8 1.0 - - - -
1130A GLU* 1.9 58.5 + - + +
1179A ILE* 5.7 1.3 - - - -
1183A LEU* 4.9 10.5 - - + -
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Residues in contact with GLU1127 (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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1123A ARG 2.7 20.1 + - - +
1124A SER* 3.0 10.1 + - - +
1126A VAL* 1.3 71.8 - - - +
1128A LYS* 1.3 57.0 + - - +
1130A GLU* 4.8 0.2 - - - -
1131A LEU* 2.5 38.2 - - - +
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Residues in contact with LYS1128 (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 SER 2.9 16.8 + - - +
1125A ILE* 4.7 3.1 - - - +
1127A GLU* 1.3 76.3 - - - +
1129A SER* 1.3 62.2 + - - +
1131A LEU* 4.3 1.1 - - - +
1132A TRP* 4.1 10.6 + - - +
1133A VAL 4.5 1.7 + - - -
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Residues in contact with SER1129 (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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1090A ARG* 6.0 0.4 - - - -
1125A ILE* 2.5 28.6 + - - -
1126A VAL* 2.8 1.1 - - - -
1128A LYS* 1.3 71.9 - - - +
1130A GLU* 1.3 59.2 + - - -
1131A LEU 3.0 2.0 + - - -
1132A TRP 3.1 0.3 + - - -
1133A VAL* 2.5 43.7 + - - +
1179A ILE* 3.3 30.1 - - - -
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Residues in contact with GLU1130 (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 VAL* 1.9 50.6 + - + +
1127A GLU* 4.8 0.2 - - - -
1129A SER* 1.3 71.7 - - - +
1131A LEU* 1.3 62.2 + - - +
1132A TRP* 4.4 2.9 - - - +
1179A ILE* 5.0 0.6 - - - +
1180A LEU* 4.6 16.0 - - - +
1183A LEU* 4.8 12.1 - - + -
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Residues in contact with LEU1131 (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 VAL 2.8 9.9 + - - -
1127A GLU* 2.5 25.0 + - - +
1128A LYS 4.3 2.5 - - - +
1129A SER 3.0 0.8 + - - -
1130A GLU* 1.3 74.4 - - - +
1132A TRP* 1.3 60.2 + - + +
1213A VAL* 5.5 11.6 - - + +
1214A VAL* 5.2 15.5 - - - +
1217A LEU* 5.3 8.8 - - - +
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Residues in contact with TRP1132 (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 LYS 4.1 5.7 + - - +
1129A SER 3.1 3.6 + - - -
1130A GLU 4.4 2.5 - - - +
1131A LEU* 1.3 81.6 - - + +
1133A VAL* 1.3 72.2 + - - +
1134A TYR 3.2 10.2 + - - -
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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