Contacts of the strand formed by residues 6164 - 6168 (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 MET6164 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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6137D MET* 3.6 39.5 - - + -
6138D LYS* 3.4 19.1 - - - +
6139D PRO* 3.9 9.0 - - - -
6140D LEU* 4.0 6.9 - - - +
6158D LYS* 3.8 1.9 - - - +
6159D SER* 2.8 44.8 + - - +
6160D SER 4.0 0.3 + - - -
6162D TYR* 3.1 18.5 - - + +
6163D ASP* 1.3 85.1 - - - +
6165D GLU* 1.3 58.8 + - - +
6166D PHE* 5.6 2.0 - - + -
6229D ILE* 3.8 20.6 - - + -
6231D LEU* 4.1 6.1 - - - -
6245D VAL* 3.8 26.9 - - + -
6247D TRP* 5.3 3.8 - - + -
6253D THR* 5.6 1.6 - - + -
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Residues in contact with GLU6165 (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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6137D MET* 3.2 4.0 - - - +
6138D LYS* 2.8 65.6 + - + +
6140D LEU* 3.6 27.6 - - + +
6143D LYS* 5.4 1.1 + - - -
6156D PHE* 3.3 36.3 - - + +
6157D THR 3.6 12.6 - - - +
6158D LYS* 3.7 14.9 + - - +
6164D MET* 1.3 75.1 - - - +
6166D PHE* 1.3 61.4 + - - +
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Residues in contact with PHE6166 (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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6135D LYS* 3.8 30.7 - - + -
6136D VAL 3.2 11.9 - - - +
6137D MET* 4.3 8.3 - - + -
6155D LYS 4.3 0.3 - - - +
6156D PHE* 3.4 6.6 - - - -
6157D THR* 2.9 71.0 + - + -
6158D LYS 4.3 1.3 - - - -
6159D SER* 3.8 26.5 - - - -
6164D MET* 5.1 2.2 - - + -
6165D GLU* 1.3 79.3 - - - +
6167D ALA* 1.3 63.8 + - - +
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Residues in contact with ALA6167 (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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6135D LYS* 2.8 9.2 - - - +
6136D VAL* 2.8 33.8 + - + -
6154D LEU* 4.0 21.8 - - + -
6155D LYS 4.0 16.2 - - - +
6156D PHE* 3.8 24.4 - - + -
6166D PHE* 1.3 79.3 - - - +
6168D GLN* 1.3 58.4 + - - +
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Residues in contact with GLN6168 (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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6134D GLY 3.8 12.1 - - - +
6135D LYS* 4.1 2.9 - - - -
6136D VAL* 4.4 0.2 - - - -
6154D LEU* 3.7 19.8 - - - +
6167D ALA* 1.3 74.5 - - - +
6169D LEU* 1.3 75.0 + - - +
6170D PRO* 3.7 0.7 - - - +
6174D ARG* 3.2 30.0 + - - +
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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