Contacts of the helix formed by residues 1221 - 1232 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1102D GLU* 2.7 35.6 + - - -
1220D VAL* 1.3 75.2 - - - +
1222D LYS* 1.3 64.4 + - - +
1223D GLU* 3.8 13.5 + - - -
1224D LEU* 3.4 14.7 + - - +
1225D MET* 3.2 18.4 + - - +
1250D TRP* 3.9 5.5 - - - -
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Residues in contact with LYS1222 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1220D VAL 3.6 2.1 + - - -
1221D SER* 1.3 72.4 - - - +
1223D GLU* 1.3 66.3 + - - +
1224D LEU 3.4 0.2 - - - -
1225D MET* 3.5 10.4 + - - +
1226D SER* 3.0 27.9 + - - -
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Residues in contact with GLU1223 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1221D SER* 3.1 17.9 - - - +
1222D LYS* 1.3 83.9 + - - +
1224D LEU* 1.3 62.4 + - - +
1226D SER* 3.0 19.3 + - - +
1227D LEU* 3.2 13.9 + - - +
1248D ASP* 4.6 2.1 - - - +
1249D PRO* 5.4 11.2 - - + -
1250D TRP* 4.3 21.7 - - + +
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Residues in contact with LEU1224 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1102D GLU* 3.9 9.9 - - + +
1193D LEU* 3.8 26.0 - - + -
1197D VAL* 4.1 24.9 - - + -
1198D PHE* 4.9 1.6 - - + -
1220D VAL* 4.0 22.7 - - + -
1221D SER* 3.3 14.4 + - - +
1223D GLU* 1.3 77.0 - - - +
1225D MET* 1.3 58.1 + - - +
1227D LEU* 3.0 5.8 + - + +
1228D VAL* 3.0 36.8 + - + +
1250D TRP* 3.7 57.7 - - + +
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Residues in contact with MET1225 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1198D PHE* 4.1 6.1 - - - -
1214D ILE* 3.8 27.6 - - + +
1216D PRO* 3.5 35.9 - - + -
1218D TYR 5.8 0.2 - - - +
1220D VAL* 3.8 27.1 - - + +
1221D SER 3.2 13.2 + - - +
1222D LYS* 3.7 11.7 - - - +
1223D GLU 3.4 0.2 - - - -
1224D LEU* 1.3 78.1 - - - +
1226D SER* 1.3 51.9 + - - +
1228D VAL* 3.3 10.6 - - + +
1229D SER* 2.7 36.5 + - - +
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Residues in contact with SER1226 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1222D LYS 3.0 14.2 + - - -
1223D GLU* 3.0 20.1 + - - +
1225D MET* 1.3 75.0 - - - +
1227D LEU* 1.3 62.1 + - - +
1229D SER* 3.7 6.5 - - - -
1230D GLY* 3.2 18.7 + - - -
1240D THR* 5.4 0.2 + - - -
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Residues in contact with LEU1227 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1109D PHE* 4.9 0.9 - - + -
1193D LEU* 3.7 19.1 - - + -
1223D GLU 3.2 13.2 + - - +
1224D LEU* 3.0 9.8 + - + +
1226D SER* 1.3 74.7 + - - +
1228D VAL* 1.3 63.8 + - - +
1230D GLY* 3.6 1.7 + - - -
1231D LEU* 3.2 37.5 + - + +
1240D THR* 4.6 6.8 + - + -
1245D LEU* 3.7 26.9 - - + -
1248D ASP* 3.5 34.3 + - - +
1250D TRP* 3.4 36.6 - - + -
1251D VAL* 4.0 8.7 - - + -
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Residues in contact with VAL1228 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1190D GLY 4.5 8.1 - - - +
1193D LEU* 3.6 34.1 - - + -
1194D TYR* 4.6 17.5 - - + +
1197D VAL* 5.6 0.2 - - + -
1198D PHE* 5.1 5.6 - - + -
1214D ILE* 4.2 15.0 - - + -
1224D LEU* 3.0 27.6 + - + +
1225D MET* 3.3 26.7 - - + +
1227D LEU* 1.3 75.2 - - - +
1229D SER* 1.3 56.5 + - - +
1231D LEU* 3.8 4.8 - - - -
1232D LEU* 2.9 43.9 + - + +
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Residues in contact with SER1229 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1214D ILE* 3.6 19.0 - - - +
1225D MET* 2.7 25.0 + - - +
1226D SER* 3.7 8.5 - - - -
1227D LEU 3.3 0.4 - - - -
1228D VAL* 1.3 74.5 - - - +
1230D GLY* 1.3 63.0 + - - +
1232D LEU* 3.4 4.9 - - - +
1233D GLN* 3.2 24.1 + - - +
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Residues in contact with GLY1230 (chain D).
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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1226D SER 3.2 12.6 + - - -
1227D LEU 4.1 0.2 - - - -
1229D SER* 1.3 77.7 - - - +
1231D LEU* 1.3 60.5 + - - +
1233D GLN* 3.5 8.0 - - - +
1238D ARG 5.4 2.2 - - - -
1239D ARG* 3.4 9.9 - - - +
1240D THR* 2.8 40.3 + - - -
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Residues in contact with LEU1231 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1109D PHE* 4.4 7.6 - - + -
1186D MET* 3.5 32.7 - - + +
1187D TRP* 3.6 15.4 - - - -
1189D LEU* 5.2 0.2 - - + -
1190D GLY* 3.7 28.5 - - - +
1193D LEU* 4.3 10.8 - - + -
1227D LEU* 3.2 39.4 + - + +
1228D VAL* 3.9 3.1 - - - +
1230D GLY* 1.3 78.6 - - - +
1232D LEU* 1.3 56.7 + - - +
1233D GLN 3.4 0.9 - - - -
1239D ARG* 3.5 21.1 - - - -
1240D THR* 3.6 28.7 - - + +
1245D LEU* 4.1 11.4 - - + -
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Residues in contact with LEU1232 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1187D TRP* 3.5 42.8 - - + +
1190D GLY 3.9 16.4 - - - +
1191D VAL* 3.9 25.4 - - + +
1194D TYR* 4.2 8.5 - - + -
1202D PRO* 3.9 25.1 - - + -
1203D PHE* 4.5 5.6 - - + -
1212D ALA* 3.4 23.3 - - + +
1214D ILE* 4.1 17.9 - - + -
1228D VAL* 2.9 22.2 + - + +
1229D SER* 3.4 7.5 - - - +
1231D LEU* 1.3 76.8 - - - +
1233D GLN* 1.3 60.5 + - - +
1234D PRO* 3.5 0.9 - - - +
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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