Contacts of the strand formed by residues 6226 - 6235 (chain D) 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 VAL6226 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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6130D LEU* 4.8 2.2 - - + -
6132D MET* 3.5 28.7 - - + -
6178D PHE* 3.6 32.3 - - + -
6179D THR 2.8 10.0 + - - +
6180D TYR* 2.9 24.9 - - + -
6181D THR 3.1 15.1 + - - -
6218D PRO* 3.9 13.2 - - + -
6219D ILE 3.6 4.5 - - - +
6220D MET* 3.6 21.5 - - + -
6225D ARG* 1.3 71.0 - - - +
6227D VAL* 1.3 62.3 + - - +
6228D ALA 3.6 24.7 - - - +
6229D ILE* 4.8 0.2 - - + -
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Residues in contact with VAL6227 (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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6180D TYR* 2.9 22.9 + - - -
6181D THR* 4.0 13.5 - - + -
6183D GLU 4.7 0.2 - - - +
6184D HIS* 3.6 38.1 - - + -
6189D TYR* 3.8 21.1 - - + -
6203D PHE* 3.2 34.8 - - + -
6219D ILE* 2.8 14.2 + - + +
6221D ASP* 3.9 17.3 - - + +
6226D VAL* 1.3 74.5 - - - +
6228D ALA* 1.3 63.0 + - + +
6246D THR* 3.7 3.5 - - - +
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Residues in contact with ALA6228 (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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6180D TYR* 4.3 3.4 - - - -
6203D PHE* 3.7 27.4 - - + -
6218D PRO* 3.4 5.2 - - - +
6219D ILE* 2.8 41.0 + - + -
6226D VAL* 3.6 8.3 - - - +
6227D VAL* 1.3 81.9 - - - +
6229D ILE* 1.3 63.6 + - - +
6230D VAL 4.2 0.2 - - - -
6244D VAL* 4.1 5.6 - - + -
6245D VAL 3.3 8.1 - - - +
6246D THR* 3.7 9.6 - - + -
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Residues in contact with ILE6229 (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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6130D LEU* 3.8 23.6 - - + -
6132D MET* 3.9 6.3 - - + -
6137D MET* 3.7 30.7 - - + -
6139D PRO* 4.9 1.8 - - + -
6164D MET* 3.8 27.4 - - + -
6216D GLY* 4.1 22.2 - - - +
6217D ARG 3.8 2.9 - - - -
6218D PRO* 5.2 0.2 - - + -
6226D VAL* 4.8 0.9 - - + -
6228D ALA* 1.3 77.8 - - - +
6230D VAL* 1.3 72.7 + - - +
6231D LEU* 3.7 3.1 + - + +
6244D VAL* 3.1 7.6 - - - -
6245D VAL* 2.8 44.2 + - + +
6247D TRP* 3.9 14.1 - - + -
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Residues in contact with VAL6230 (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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6191D TRP* 3.8 25.4 - - + -
6214D ASP 4.1 8.5 - - - +
6215D SER* 3.5 1.0 - - - -
6216D GLY* 2.9 30.0 + - - -
6217D ARG 3.0 18.0 + - - +
6219D ILE* 3.9 22.2 - - + -
6229D ILE* 1.3 73.3 - - - +
6231D LEU* 1.3 62.9 + - - +
6232D GLY 3.8 11.7 - - - +
6242D LEU* 4.2 14.6 - - + -
6243D SER 3.7 4.7 - - - +
6244D VAL* 4.4 1.6 - - - -
6264D TRP* 3.7 32.8 - - + -
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Residues in contact with LEU6231 (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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6139D PRO* 4.0 14.4 - - + -
6141D HIS* 3.1 25.1 - - + -
6162D TYR 4.2 1.1 - - - +
6163D ASP* 3.6 32.8 - - - +
6164D MET* 4.1 5.6 - - - -
6215D SER* 3.5 11.7 - - - -
6229D ILE* 4.2 3.4 - - + +
6230D VAL* 1.3 77.9 - - - +
6232D GLY* 1.3 59.2 + - - +
6243D SER* 2.8 24.8 + - - +
6244D VAL 4.2 4.5 - - - -
6245D VAL* 3.7 34.1 - - + -
6255D LYS* 3.6 35.7 - - + -
6263D GLU* 3.9 6.2 - - + -
6264D TRP 3.6 4.5 + - - -
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Residues in contact with GLY6232 (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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6230D VAL* 3.6 8.9 - - - +
6231D LEU* 1.3 80.2 - - - +
6233D GLY* 1.3 59.0 + - - -
6242D LEU* 3.6 5.7 - - - +
6243D SER* 2.9 26.3 + - - +
6261D THR* 4.8 0.2 - - - -
6262D GLU 3.5 13.5 - - - -
6263D GLU* 4.3 1.3 - - - -
6264D TRP* 3.7 22.7 - - - -
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Residues in contact with GLY6233 (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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6232D GLY* 1.3 75.2 - - - -
6234D ALA* 1.3 60.5 + - - -
6235D ASP 4.0 1.5 + - - -
6240D THR* 4.3 3.8 - - - -
6241D ALA 3.2 11.0 - - - -
6242D LEU* 4.1 2.0 - - - -
6243D SER 4.2 1.8 - - - -
6260D GLY 3.9 0.5 - - - +
6261D THR* 3.9 7.2 - - - +
6262D GLU* 2.8 33.7 + - - +
6264D TRP* 3.6 21.7 - - - +
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Residues in contact with ALA6234 (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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6233D GLY* 1.3 72.3 - - - -
6235D ASP* 1.3 66.1 + - - +
6236D GLU* 3.1 10.3 + - + +
6240D THR* 4.0 2.6 - - - +
6241D ALA* 2.6 40.0 + - + +
6258D PRO* 3.9 9.4 - - + -
6259D GLU 3.4 25.8 - - - +
6260D GLY* 3.5 16.2 - - - -
6261D THR* 3.6 9.2 - - - +
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Residues in contact with ASP6235 (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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6207D ARG* 2.7 57.4 + - + +
6233D GLY 4.0 2.4 + - - -
6234D ALA* 1.3 71.2 - - - +
6236D GLU* 1.3 58.6 + - - +
6237D GLY 3.0 4.2 + - - -
6240D THR* 3.9 16.2 - - + +
6260D GLY* 4.5 4.5 + - - +
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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