Contacts of the strand formed by residues 1141 - 1143 (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 CYS1141 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1086D ASP* 3.4 7.3 - - - +
1087D LEU* 2.9 31.3 + - + -
1119D ILE* 4.1 24.9 - - - -
1136D LEU* 4.1 19.5 - - - -
1137D ALA 3.7 15.9 - - - -
1138D ALA* 3.2 10.8 + - - +
1140D ASN* 1.3 81.5 - - - +
1142D MET* 1.3 63.4 + - - +
1149D VAL* 3.9 13.9 - - + -
1150D LYS 3.3 9.2 - - - +
1151D ILE* 4.3 9.0 - - - -
1152D GLY 4.0 0.4 - - - -
1201D VAL* 5.0 1.6 - - - -
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Residues in contact with MET1142 (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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1063D VAL* 4.4 9.2 - - + -
1079D MET* 5.6 0.2 - - - -
1080D GLU 5.7 0.7 - - - +
1082D MET* 3.5 43.0 - - + +
1085D GLY* 3.4 23.3 - - - +
1086D ASP* 4.5 7.0 - - + +
1139D ARG 5.8 0.4 - - - +
1141D CYS* 1.3 76.7 - - - +
1143D VAL* 1.3 63.8 + - - +
1149D VAL* 3.3 6.5 - - - +
1150D LYS 2.8 33.3 + - - +
1152D GLY* 3.1 31.0 - - - +
1153D ASP* 4.4 5.6 - - - -
1154D PHE* 3.9 36.6 - - + -
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Residues in contact with VAL1143 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1082D MET* 3.5 10.4 - - - -
1084D ARG* 3.0 46.1 + - + +
1085D GLY 2.8 17.7 + - - +
1087D LEU* 3.9 35.2 - - + -
1090D TYR* 4.4 14.6 - - + -
1115D MET* 6.1 0.2 - - - -
1142D MET* 1.3 77.8 - - - +
1144D ALA* 1.3 70.5 + - - +
1147D PHE* 3.9 26.7 - - + +
1148D THR 3.6 2.5 - - - -
1149D VAL* 4.4 7.2 - - + -
1287D CCX 6.5 0.2 - - + -
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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
------------------------------------------------------------
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