Contacts of the helix formed by residues 1221 - 1232 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1102B GLU* 2.8 28.8 + - - -
1220B VAL* 1.3 82.7 - - - +
1222B LYS* 1.3 62.3 + - - +
1223B GLU* 3.3 20.0 + - - +
1224B LEU 2.9 21.0 + - - -
1225B MET* 3.2 19.0 + - - +
1250B TRP* 4.0 1.4 - - - -
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Residues in contact with LYS1222 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1221B SER* 1.3 74.8 - - - +
1223B GLU* 1.3 68.2 + - - +
1225B MET* 3.4 7.5 + - - +
1226B SER* 3.0 30.8 + - - -
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Residues in contact with GLU1223 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1221B SER* 3.1 19.9 - - - +
1222B LYS* 1.3 83.1 + - - +
1224B LEU* 1.3 64.6 + - - +
1226B SER* 3.3 17.7 + - - -
1227B LEU* 3.3 12.5 + - - +
1248B ASP* 4.7 2.8 - - - +
1249B PRO* 5.2 14.8 - - + -
1250B TRP* 4.2 22.4 - - + +
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Residues in contact with LEU1224 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1102B GLU* 3.7 17.3 - - + +
1193B LEU* 4.2 7.0 - - + -
1197B VAL* 4.0 21.5 - - + -
1198B PHE* 4.9 1.8 - - + -
1220B VAL* 4.0 22.2 - - + -
1221B SER* 2.9 16.0 + - - +
1223B GLU* 1.3 74.4 - - - +
1225B MET* 1.3 60.3 + - - +
1227B LEU* 3.1 13.9 + - + +
1228B VAL* 2.9 50.5 + - + +
1250B TRP* 3.6 52.1 - - + +
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Residues in contact with MET1225 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1198B PHE* 4.5 2.7 - - - -
1214B ILE* 4.0 20.0 - - + +
1216B PRO* 3.6 35.0 - - + -
1220B VAL* 3.9 19.1 - - + +
1221B SER 3.2 16.3 + - - +
1222B LYS* 3.4 11.2 + - - +
1224B LEU* 1.3 77.8 - - - +
1226B SER* 1.3 57.2 + - - +
1228B VAL* 3.2 10.4 - - - +
1229B SER* 2.8 43.3 + - - +
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Residues in contact with SER1226 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1222B LYS 3.0 16.1 + - - -
1223B GLU* 3.3 13.5 + - - -
1225B MET* 1.3 75.4 - - - +
1227B LEU* 1.3 59.9 + - - +
1229B SER* 4.1 4.7 - - - -
1230B GLY* 3.0 25.3 + - - -
1248B ASP* 5.0 4.0 + - - -
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Residues in contact with LEU1227 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1109B PHE* 4.6 0.4 - - + -
1193B LEU* 3.6 20.2 - - + -
1223B GLU 3.3 10.0 + - - +
1224B LEU* 3.1 9.8 + - + +
1226B SER* 1.3 79.2 + - - +
1228B VAL* 1.3 65.7 + - - +
1230B GLY* 3.4 2.1 + - - -
1231B LEU* 3.3 28.0 + - + +
1240B THR* 4.7 5.5 + - + -
1245B LEU* 3.5 31.2 - - + -
1248B ASP* 3.9 27.4 - - + +
1250B TRP* 3.4 38.1 - - + -
1251B VAL* 4.2 5.8 - - + -
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Residues in contact with VAL1228 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1190B GLY* 5.4 1.8 - - - +
1193B LEU* 3.7 29.2 - - + -
1194B TYR* 4.9 9.6 - - + +
1197B VAL* 5.2 0.2 - - + -
1198B PHE* 4.7 14.6 - - + -
1214B ILE* 3.8 24.2 - - + -
1224B LEU* 2.9 33.9 + - + +
1225B MET* 3.2 24.0 - - - +
1227B LEU* 1.3 72.5 - - - +
1229B SER* 1.3 60.2 + - - +
1231B LEU* 3.5 3.4 + - - +
1232B LEU* 2.9 43.5 + - + +
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Residues in contact with SER1229 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1214B ILE* 4.3 9.4 - - - +
1225B MET* 2.8 32.6 + - - +
1226B SER* 4.1 5.4 - - - -
1228B VAL* 1.3 77.9 - - - +
1230B GLY* 1.3 65.9 + - - +
1232B LEU* 3.4 7.1 - - - +
1233B GLN* 3.2 24.1 + - - +
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Residues in contact with GLY1230 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1226B SER 3.0 18.3 + - - -
1227B LEU 3.9 0.4 - - - -
1228B VAL 3.4 0.2 - - - -
1229B SER* 1.3 76.7 - - - +
1231B LEU* 1.3 60.0 + - - +
1233B GLN* 3.3 17.6 - - - +
1238B ARG 4.6 1.5 - - - +
1239B ARG* 3.6 0.5 - - - -
1240B THR* 3.1 35.9 + - - -
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Residues in contact with LEU1231 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1109B PHE* 4.4 3.1 - - + -
1186B MET* 3.4 49.8 - - + +
1187B TRP* 3.5 13.9 - - - -
1189B LEU* 4.4 4.0 - - + -
1190B GLY* 3.8 23.3 - - - +
1193B LEU* 4.1 12.8 - - + -
1227B LEU* 3.3 37.4 + - + +
1228B VAL* 4.1 1.3 - - - +
1230B GLY* 1.3 74.7 - - - +
1232B LEU* 1.3 58.5 + - - +
1233B GLN 3.3 1.6 - - - -
1239B ARG* 3.4 25.9 + - - -
1240B THR* 3.5 15.5 + - + -
1245B LEU* 4.1 13.2 - - + -
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Residues in contact with LEU1232 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1187B TRP* 3.5 56.0 - - + +
1190B GLY* 3.9 16.6 - - - +
1191B VAL* 3.8 15.0 - - + +
1194B TYR* 4.4 9.4 - - + -
1202B PRO* 4.3 18.2 - - + -
1203B PHE* 4.4 5.6 - - + -
1212B ALA* 3.5 11.1 - - + +
1214B ILE* 4.3 22.4 - - + -
1228B VAL* 2.9 25.9 + - + +
1229B SER* 3.4 8.6 - - - +
1230B GLY 3.3 0.2 - - - -
1231B LEU* 1.3 77.4 - - - +
1233B GLN* 1.3 61.1 + - - +
1234B PRO* 3.4 8.1 - - - +
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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