Contacts of the helix formed by residues 1226 - 1235 (chain A) in PDB entry 3DKC
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 ALA1226 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1089A PHE* 3.5 31.0 - - + -
1202A HIS 5.4 0.2 - - - +
1203A ARG* 4.7 4.5 - - + -
1204A ASP* 3.9 13.9 - - + -
1222A ASP 4.5 0.8 + - - -
1224A GLY 3.2 1.8 - - - -
1225A LEU* 1.3 76.6 - - - +
1227A ARG* 1.3 64.7 + - - +
1228A ASP 3.4 1.1 - - - -
1229A MET* 3.3 4.8 + - - +
1230A TYR* 3.0 54.3 + - + -
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Residues in contact with ARG1227 (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* 5.9 0.6 - - - +
1120A GLU* 5.7 1.0 + - - +
1123A GLN* 3.3 30.6 - - - +
1124A PHE* 4.1 6.5 - - - +
1127A GLU* 2.7 43.7 + - - -
1203A ARG* 4.0 42.4 - - - +
1224A GLY 3.3 14.7 + - - +
1225A LEU 3.2 2.6 - - - -
1226A ALA* 1.3 77.5 - - - +
1228A ASP* 1.3 86.7 + - - +
1230A TYR* 3.3 4.7 + - - +
1231A ASP* 3.0 46.8 + - - +
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Residues in contact with ASP1228 (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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1114A ARG* 3.8 19.7 - - + +
1115A ILE* 3.4 27.8 - - + +
1120A GLU* 3.5 32.4 - - - +
1225A LEU 4.6 2.9 + - - +
1226A ALA 3.4 0.6 - - - -
1227A ARG* 1.3 104.6 + - - +
1229A MET* 1.3 65.1 + - - +
1231A ASP* 3.3 11.0 + - - +
1232A LYS* 2.9 32.7 + - - +
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Residues in contact with MET1229 (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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1088A HIS* 3.3 43.3 - - + +
1089A PHE* 3.5 22.4 - - + -
1114A ARG* 3.7 30.7 - - + +
1225A LEU 5.3 0.6 + - - +
1226A ALA 3.3 6.4 + - - +
1228A ASP* 1.3 79.9 - - - +
1230A TYR* 1.3 78.7 + - - +
1232A LYS* 3.8 2.3 - - - +
1233A GLU* 2.9 53.3 + - + +
1244A LYS* 3.2 29.4 - - + +
1245A LEU* 4.2 3.4 - - + -
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Residues in contact with TYR1230 (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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1088A HIS* 5.9 0.7 - - + -
1089A PHE* 5.6 0.4 - + - -
1203A ARG* 2.7 43.5 + - + +
1204A ASP* 3.6 10.7 + - - +
1226A ALA* 3.0 29.5 + - + -
1227A ARG* 3.5 7.9 - - - +
1229A MET* 1.3 85.7 - - - +
1231A ASP* 1.3 64.7 + - - +
1233A GLU* 4.2 0.2 - - - +
1234A PHE* 2.9 42.0 + + + -
1245A LEU* 3.5 19.3 - - + -
1246A PRO* 3.3 39.8 - - + +
1250A MET* 5.3 5.0 - - - +
1260A PHE* 3.4 38.6 - + + -
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Residues in contact with ASP1231 (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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1203A ARG* 5.6 2.3 + - - -
1227A ARG* 3.0 35.2 + - - +
1228A ASP* 3.5 19.4 - - - +
1230A TYR* 1.3 78.8 - - - +
1232A LYS* 1.3 65.2 + - + +
1234A PHE* 4.1 4.8 - - - +
1235A ASP* 3.5 21.5 + - - +
1258A GLN* 5.6 2.2 + - - +
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Residues in contact with LYS1232 (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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1114A ARG* 2.7 60.1 + - - +
1116A THR* 2.8 27.7 + - - +
1120A GLU* 3.0 27.1 + - - -
1228A ASP* 2.9 20.9 + - - +
1229A MET 3.8 1.6 - - - +
1231A ASP* 1.3 81.2 - - + +
1233A GLU* 1.3 60.0 + - - +
1235A ASP* 3.3 5.7 - - - +
1236A SER* 3.2 27.0 + - - -
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Residues in contact with GLU1233 (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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1114A ARG* 2.7 35.0 + - - +
1229A MET* 2.9 36.1 + - + +
1232A LYS* 1.3 74.1 - - - +
1234A PHE* 1.3 64.9 + - - +
1235A ASP 3.2 0.4 - - - -
1236A SER* 3.7 11.7 + - - -
1239A ASN* 3.0 61.2 + - - +
1244A LYS* 3.4 27.8 + - + +
1245A LEU* 3.8 13.5 - - + -
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Residues in contact with PHE1234 (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 TYR* 2.9 34.3 + + + +
1231A ASP* 4.1 6.3 - - - +
1233A GLU* 1.3 78.8 - - - +
1235A ASP* 1.3 57.6 + - - +
1236A SER 3.6 3.1 + - - +
1239A ASN 5.3 1.7 - - - +
1240A LYS* 6.2 0.2 - - - -
1245A LEU* 3.8 12.6 - - + -
1250A MET* 3.4 28.3 - - + -
1254A SER 4.1 8.5 - - - -
1255A LEU 4.7 4.9 - - - -
1258A GLN* 3.5 50.5 - - + +
1260A PHE* 3.8 27.1 - + - -
1290A PHE* 3.5 39.5 - + - -
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Residues in contact with ASP1235 (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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1231A ASP 3.5 13.5 + - - +
1232A LYS* 3.3 9.1 + - - +
1233A GLU 3.2 0.6 - - - -
1234A PHE* 1.3 78.0 - - + +
1236A SER* 1.3 56.7 + - - +
1237A VAL 4.4 0.2 + - - -
1258A GLN* 5.7 3.4 - - - +
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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