Contacts of the strand formed by residues 1107 - 1110 (chain M) in PDB entry 1LD4
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 TYR1107 (chain M).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1053M THR* 3.8 3.1 - - - +
1054M VAL* 2.8 41.8 + - + +
1056M PRO* 5.8 4.3 - - + -
1069M GLN 5.5 1.9 + - - -
1073M HIS* 3.8 27.0 - + + -
1074M ALA* 3.5 13.9 - - + +
1075M ASP* 3.4 15.5 - - - -
1076M TYR* 3.3 40.7 + + - -
1078M CYS* 4.6 10.7 - - - -
1105M GLU* 4.3 26.3 + - + +
1106M ALA* 1.3 88.3 - - - +
1108M VAL* 1.3 71.3 + - - +
1109M GLU* 4.4 4.5 - - + -
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Residues in contact with VAL1108 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1051M PHE* 3.6 24.0 - - + -
1052M THR 3.8 12.6 - - - +
1053M THR* 4.2 17.0 - - + +
1074M ALA* 3.4 26.9 + - - +
1075M ASP* 3.9 17.2 - - - +
1107M TYR* 1.3 83.5 - - - +
1109M GLU* 1.3 63.4 + - - +
1203M ILE* 3.5 30.6 - - + +
1213M LEU* 4.7 1.4 - - - +
1217M THR* 5.9 1.6 - - - +
1219M ILE* 4.0 16.2 - - + -
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Residues in contact with GLU1109 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1051M PHE* 3.9 5.4 - - - +
1052M THR* 3.5 25.2 + - - +
1054M VAL* 4.0 25.4 - - + +
1073M HIS* 5.6 5.7 + - - -
1074M ALA* 5.8 3.1 - - + -
1107M TYR* 5.8 3.6 - - + -
1108M VAL* 1.3 78.6 - - - +
1110M LEU* 1.3 69.7 + - - +
1111M SER* 3.4 2.3 + - - -
1203M ILE* 5.8 0.2 - - - -
1213M LEU* 5.0 6.1 - - + -
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Residues in contact with LEU1110 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1048M THR* 6.5 0.7 - - - -
1050M LYS 5.2 0.4 - - - +
1051M PHE* 3.7 29.4 - - + -
1109M GLU* 1.3 76.4 - - - +
1111M SER* 1.3 70.3 + - - +
1114M CYS* 5.1 11.2 - - + -
1118M HIS* 5.7 5.4 - - + -
1203M ILE* 4.4 3.6 - - + +
1205M ALA* 5.0 5.4 - - + -
1210M SER* 4.6 15.7 - - - +
1213M LEU* 3.9 37.9 - - + +
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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