Contacts of the helix formed by residues 1221 - 1232 (chain A) in PDB entry 3DLS
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 SER1221 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1102A GLU* 2.6 34.5 + - - -
1220A VAL* 1.3 82.2 - - - +
1222A LYS* 1.3 63.3 + - - +
1223A GLU* 3.7 17.0 + - - +
1224A LEU 3.4 11.8 + - - -
1225A MET* 3.3 19.1 + - - +
1250A TRP* 4.2 1.9 - - - -
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Residues in contact with LYS1222 (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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1221A SER* 1.3 74.3 - - - +
1223A GLU* 1.3 66.2 + - - +
1225A MET* 3.9 7.3 - - - +
1226A SER* 3.3 28.9 + - - -
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Residues in contact with GLU1223 (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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1221A SER* 3.2 18.9 - - - +
1222A LYS* 1.3 85.5 + - - +
1224A LEU* 1.3 62.8 + - - +
1226A SER* 3.6 7.5 + - - -
1227A LEU* 3.3 20.6 + - - +
1248A ASP* 4.6 1.9 - - - +
1249A PRO* 5.2 13.7 - - + -
1250A TRP* 4.0 22.7 - - + +
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Residues in contact with LEU1224 (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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1102A GLU* 3.7 24.5 - - + +
1193A LEU* 4.2 6.1 - - + -
1197A VAL* 3.7 29.2 - - + -
1198A PHE* 4.8 0.4 - - + -
1220A VAL* 3.8 24.9 - - + -
1221A SER* 3.4 9.4 + - - +
1222A LYS 3.4 0.2 - - - -
1223A GLU* 1.3 76.8 - - - +
1225A MET* 1.3 62.1 + - + +
1227A LEU* 3.0 11.0 + - + +
1228A VAL* 2.8 52.8 + - + +
1250A TRP* 3.7 40.1 - - + +
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Residues in contact with MET1225 (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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1198A PHE* 3.6 27.1 - - + -
1214A ILE* 4.3 3.1 - - + -
1216A PRO* 3.6 25.8 - - + -
1218A TYR 5.7 0.4 - - - +
1220A VAL* 3.7 18.8 - - + +
1221A SER 3.3 12.8 + - - +
1222A LYS* 3.9 8.1 - - - +
1223A GLU 3.4 0.2 - - - -
1224A LEU* 1.3 79.7 - - + +
1226A SER* 1.3 54.0 + - - +
1228A VAL* 3.4 23.3 - - + +
1229A SER* 2.8 41.1 + - - +
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Residues in contact with SER1226 (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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1222A LYS 3.3 15.8 + - - -
1223A GLU* 3.6 9.5 + - - -
1225A MET* 1.3 76.5 - - - +
1227A LEU* 1.3 61.1 + - - +
1229A SER* 3.9 5.5 - - - -
1230A GLY* 3.0 24.4 + - - -
1240A THR* 5.4 0.2 + - - -
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Residues in contact with LEU1227 (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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1109A PHE* 4.5 0.4 - - + -
1193A LEU* 3.6 20.4 - - + -
1223A GLU 3.3 12.3 + - - +
1224A LEU* 3.0 10.2 + - + +
1226A SER* 1.3 79.9 + - - +
1228A VAL* 1.3 64.0 + - - +
1230A GLY* 4.0 0.7 - - - -
1231A LEU* 3.3 25.4 + - + +
1240A THR* 4.8 5.3 + - + -
1245A LEU* 3.5 28.7 - - + -
1248A ASP* 3.4 27.1 - - - +
1250A TRP* 3.4 42.4 - - + -
1251A VAL* 4.2 8.1 - - + -
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Residues in contact with VAL1228 (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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1190A GLY 5.1 3.1 - - - +
1193A LEU* 3.7 22.7 - - + -
1194A TYR* 4.7 11.4 - - + +
1197A VAL* 6.1 0.4 - - + -
1198A PHE* 5.1 5.6 - - + -
1214A ILE* 3.7 17.0 - - + -
1224A LEU* 2.8 42.3 + - + +
1225A MET* 3.4 33.7 - - + +
1227A LEU* 1.3 72.6 - - - +
1229A SER* 1.3 60.6 + - - +
1231A LEU* 3.4 4.0 + - - +
1232A LEU* 2.9 41.8 + - + +
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Residues in contact with SER1229 (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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1214A ILE* 4.2 16.4 - - - +
1225A MET* 2.8 27.4 + - - +
1226A SER* 4.0 6.5 - - - -
1228A VAL* 1.3 73.8 - - - +
1230A GLY* 1.3 63.6 + - - +
1232A LEU* 3.6 7.1 - - - +
1233A GLN* 3.5 22.3 + - - +
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Residues in contact with GLY1230 (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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1226A SER 3.0 18.8 + - - -
1227A LEU 3.5 0.9 + - - -
1228A VAL 3.4 0.2 - - - -
1229A SER* 1.3 76.9 - - - +
1231A LEU* 1.3 59.2 + - - +
1233A GLN* 3.6 6.7 - - - +
1238A ARG 4.5 1.9 - - - +
1239A ARG* 3.5 9.2 - - - +
1240A THR* 2.9 37.6 + - - -
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Residues in contact with LEU1231 (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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1109A PHE* 4.3 3.4 - - + -
1186A MET* 3.5 40.6 - - + +
1187A TRP* 3.6 13.7 - - - -
1189A LEU* 4.3 4.5 - - + -
1190A GLY* 3.8 24.9 - - - +
1193A LEU* 3.8 25.6 - - + -
1227A LEU* 3.3 19.8 + - + +
1228A VAL* 3.8 2.0 - - - +
1230A GLY* 1.3 74.8 - - - +
1232A LEU* 1.3 59.1 + - - +
1233A GLN 3.3 2.5 - - - -
1239A ARG* 3.4 24.7 + - - -
1240A THR* 3.9 18.8 - - + +
1245A LEU* 4.1 21.5 - - + -
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Residues in contact with LEU1232 (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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1187A TRP* 3.5 51.8 - - + +
1190A GLY* 3.8 19.3 - - - +
1191A VAL* 3.7 14.8 - - + +
1194A TYR* 4.3 12.1 - - + -
1202A PRO* 4.2 23.8 - - + -
1203A PHE* 4.4 6.7 - - + -
1212A ALA* 3.5 24.0 - - + +
1214A ILE* 4.4 13.0 - - + -
1228A VAL* 2.9 23.2 + - + +
1229A SER* 3.6 8.7 - - - +
1230A GLY 3.4 0.4 - - - -
1231A LEU* 1.3 74.4 - - - +
1233A GLN* 1.3 57.5 + - - +
1234A PRO* 3.9 0.5 - - - +
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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