Contacts of the helix formed by residues 1121 - 1132 (chain A) in PDB entry 5EPG
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 THR1121 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1119A LYS 5.6 1.1 - - - +
1120A GLY* 1.3 76.6 - - - +
1122A TRP* 1.3 63.3 + - - +
1123A LYS* 3.8 11.0 + - - +
1124A ASP* 3.2 25.2 + - - +
1125A TRP* 3.1 22.6 + - - -
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Residues in contact with TRP1122 (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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1032A ILE* 3.9 27.8 - - + -
1036A GLY* 3.7 17.3 - - - +
1063A LEU* 3.1 43.8 + - + -
1064A ARG 3.8 6.0 + - - -
1065A MET* 3.2 36.6 - - + +
1066A PRO* 5.8 0.4 - - + -
1069A ASN* 4.8 4.5 - - - +
1107A LEU* 4.1 17.0 - - + -
1110A LEU* 3.4 34.1 - - + -
1114A ILE* 4.7 2.0 - - + -
1121A THR* 1.3 70.4 - - - +
1123A LYS* 1.3 59.4 + - - +
1125A TRP* 3.7 36.0 - + + +
1126A ALA* 2.8 35.0 + - - +
1136A LEU* 5.9 0.4 - - + -
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Residues in contact with LYS1123 (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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1034A LEU 3.5 8.4 - - - +
1035A ASP* 3.4 48.2 - - + +
1036A GLY* 3.8 2.0 - - - +
1121A THR* 3.2 10.7 + - - +
1122A TRP* 1.3 78.5 - - - +
1124A ASP* 1.3 56.7 + - - +
1127A GLN* 3.1 30.1 + - + +
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Residues in contact with ASP1124 (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 ASN* 4.0 23.3 + - - +
1120A GLY* 5.1 1.4 - - - -
1121A THR* 3.2 24.9 + - - +
1123A LYS* 1.3 77.3 - - - +
1125A TRP* 1.3 61.6 + - - +
1127A GLN* 3.4 4.2 + - - +
1128A THR* 3.0 43.8 + - - +
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Residues in contact with TRP1125 (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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1063A LEU 5.5 0.7 - - - -
1064A ARG* 5.5 10.5 - - + -
1110A LEU* 4.1 8.3 - - + +
1113A ILE* 3.9 26.1 - - + +
1114A ILE* 3.5 47.4 - - + +
1117A ASN* 2.9 39.4 + - - -
1118A PRO 3.8 13.5 - - - -
1120A GLY* 3.0 26.6 + - - -
1121A THR 3.1 12.1 + - - +
1122A TRP* 3.7 47.8 - + + +
1124A ASP* 1.3 74.3 - - - +
1126A ALA* 1.3 60.1 + - - +
1128A THR* 3.3 5.8 + - - -
1129A ALA* 3.0 30.2 + - - +
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Residues in contact with ALA1126 (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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1032A ILE* 4.2 12.1 - - + -
1033A TYR 3.5 25.4 - - - +
1034A LEU* 4.1 9.9 - - - +
1036A GLY* 4.2 3.8 - - - +
1110A LEU* 5.3 0.7 - - - -
1122A TRP* 2.8 20.5 + - + +
1123A LYS 4.0 3.8 - - - +
1125A TRP* 1.3 78.4 - - - +
1127A GLN* 1.3 61.9 + - - +
1129A ALA* 3.4 6.6 + - - +
1130A PHE* 3.0 20.3 + - - +
1136A LEU* 3.6 16.9 - - + +
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Residues in contact with GLN1127 (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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1034A LEU* 3.5 40.4 + - - +
1123A LYS* 3.1 20.1 + - + +
1124A ASP* 3.7 6.3 - - - +
1125A TRP 3.3 0.2 - - - -
1126A ALA* 1.3 80.2 - - - +
1128A THR* 1.3 59.8 + - + +
1130A PHE* 3.2 8.7 + - - +
1131A ASP* 2.9 59.6 + - - +
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Residues in contact with THR1128 (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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1113A ILE* 3.3 24.2 - - - +
1117A ASN* 5.9 1.6 - - - +
1124A ASP* 3.0 32.6 + - - +
1125A TRP 3.3 5.5 + - - -
1127A GLN* 1.3 77.4 - - + +
1129A ALA* 1.3 58.3 + - - +
1131A ASP* 3.2 13.7 + - - +
1132A GLU* 2.9 41.3 + - - +
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Residues in contact with ALA1129 (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 LEU* 3.8 22.2 - - + -
1113A ILE* 3.4 12.1 - - + +
1125A TRP 3.0 21.4 + - - +
1126A ALA 3.5 5.6 - - - +
1128A THR* 1.3 74.0 + - - +
1130A PHE* 1.3 65.1 + - - +
1132A GLU 3.3 2.3 + - - -
1133A SER 3.2 4.0 + - - -
1134A ILE* 2.8 41.2 + - + +
1136A LEU* 4.0 13.0 - - + -
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Residues in contact with PHE1130 (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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1034A LEU* 3.7 41.3 - - + -
1126A ALA 3.0 13.9 + - - +
1127A GLN* 3.2 9.4 + - - +
1129A ALA* 1.3 74.7 - - - +
1131A ASP* 1.3 74.1 + - - +
1133A SER* 3.0 16.4 + - - -
1134A ILE 4.5 7.0 - - - -
1136A LEU* 4.3 6.8 - - + +
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Residues in contact with ASP1131 (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 GLN* 2.9 45.0 + - - +
1128A THR* 3.2 14.8 + - - +
1130A PHE* 1.3 81.2 - - - +
1132A GLU* 1.3 62.3 + - + +
1133A SER* 3.4 2.5 + - - -
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Residues in contact with GLU1132 (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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1113A ILE* 3.6 22.7 - - - +
1128A THR* 2.9 26.1 + - - +
1129A ALA 4.1 2.7 - - - +
1130A PHE 3.1 0.8 - - - -
1131A ASP* 1.3 79.8 - - + +
1133A SER* 1.3 70.6 + - - +
1134A ILE* 3.4 16.4 + - + +
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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