Contacts of the helix formed by residues 1217 - 1227 (chain D) in PDB entry 3LW0
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 SER1217 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1177D ARG* 3.9 2.7 - - - +
1215D GLY 4.1 1.0 + - - -
1216D LEU* 1.3 75.8 - - - +
1218D ASN* 1.3 65.2 + - - +
1219D GLU* 3.6 6.8 + - - +
1220D GLN* 2.9 38.5 + - - +
1221D VAL* 2.9 20.8 + - - +
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Residues in contact with ASN1218 (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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1163D THR 4.9 7.5 + - - +
1164D ASP 6.1 0.5 - - - -
1165D TYR 4.5 5.8 + - - +
1166D TYR* 3.5 54.6 - - + +
1176D VAL* 3.6 20.8 - - + +
1177D ARG* 3.4 22.6 + - - +
1217D SER* 1.3 73.2 - - - +
1219D GLU* 1.3 63.9 + - - +
1221D VAL* 3.2 6.1 + - - +
1222D LEU* 3.0 22.2 + - - +
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Residues in contact with GLU1219 (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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1166D TYR* 2.7 35.9 + - + +
1168D LYS* 3.3 19.2 - - - +
1217D SER* 3.3 6.7 + - - +
1218D ASN* 1.3 79.6 - - - +
1220D GLN* 1.3 62.4 + - + +
1222D LEU* 3.4 19.3 + - - +
1223D ARG* 3.2 22.0 + - - +
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Residues in contact with GLN1220 (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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1215D GLY 4.0 4.2 - - - +
1216D LEU* 3.3 29.0 - - + +
1217D SER* 2.9 40.1 + - - +
1219D GLU* 1.3 73.2 - - + +
1221D VAL* 1.3 60.0 + - - +
1223D ARG* 3.5 5.9 + - - +
1224D PHE* 2.9 30.7 + - - +
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Residues in contact with VAL1221 (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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1176D VAL* 4.1 21.8 - - + +
1177D ARG* 3.6 35.2 - - + +
1184D LEU* 5.5 0.7 - - + -
1213D TYR* 3.7 34.5 - - + -
1216D LEU* 3.9 6.7 - - + -
1217D SER 2.9 19.5 + - - +
1218D ASN* 3.2 9.2 + - - +
1220D GLN* 1.3 73.4 - - - +
1222D LEU* 1.3 68.0 + - - +
1224D PHE* 3.2 5.5 + - - -
1225D VAL* 3.0 35.5 + - + +
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Residues in contact with LEU1222 (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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1166D TYR* 4.2 15.5 - - + -
1168D LYS* 4.6 11.4 - - - +
1176D VAL* 5.2 3.7 - - + +
1184D LEU* 3.7 43.3 - - + +
1218D ASN 3.0 10.4 + - - +
1219D GLU* 3.4 39.0 - - - +
1221D VAL* 1.3 75.7 - - - +
1223D ARG* 1.3 57.8 + - - +
1226D MET* 3.0 71.7 + - + +
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Residues in contact with ARG1223 (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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1219D GLU 3.2 10.3 + - - +
1220D GLN* 3.9 8.3 - - - +
1221D VAL 3.3 0.2 - - - -
1222D LEU* 1.3 77.5 - - - +
1224D PHE* 1.3 61.3 + - - +
1226D MET* 3.8 8.4 - - + +
1227D GLU* 2.9 67.7 + - + +
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Residues in contact with PHE1224 (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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1213D TYR* 3.8 32.5 - + - -
1216D LEU* 4.0 18.2 - - + -
1220D GLN 2.9 18.2 + - - +
1221D VAL 3.7 2.9 - - - +
1223D ARG* 1.3 79.3 - - - +
1225D VAL* 1.3 56.9 + - - +
1227D GLU* 3.4 5.3 + - - +
1228D GLY 3.4 3.5 + - - -
1229D GLY* 2.8 58.1 + - - -
1230D LEU 3.5 20.9 - - - -
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Residues in contact with VAL1225 (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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1176D VAL 5.7 0.7 - - - +
1179D MET 4.0 6.5 - - - +
1181D PRO* 3.9 12.8 - - + +
1184D LEU* 3.8 21.5 - - + -
1196D TRP* 3.8 26.8 - - + -
1213D TYR* 3.5 38.8 - - + +
1221D VAL* 3.0 24.0 + - + +
1224D PHE* 1.3 73.5 - - + +
1226D MET* 1.3 66.8 + - - +
1228D GLY* 3.1 14.2 + - - -
1229D GLY 4.0 9.0 - - - +
1251D TYR* 3.7 8.3 - - - -
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Residues in contact with MET1226 (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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1181D PRO* 3.8 18.6 - - - +
1184D LEU* 3.8 10.3 - - + +
1185D LYS* 3.9 30.1 - - + -
1222D LEU* 3.0 51.4 + - + +
1223D ARG* 4.0 7.2 - - + +
1225D VAL* 1.3 76.5 - - - +
1227D GLU* 1.3 65.8 + - + +
1228D GLY 3.2 0.2 - - - -
1251D TYR* 2.6 30.1 + - - +
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Residues in contact with GLU1227 (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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1223D ARG* 2.9 57.8 + - + +
1224D PHE* 3.9 4.0 - - - +
1225D VAL 3.2 0.2 - - - -
1226D MET* 1.3 81.5 - - + +
1228D GLY* 1.3 58.6 + - - +
1229D GLY 3.5 2.4 + - - -
1251D TYR* 4.9 0.4 - - - -
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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