Contacts of the strand formed by residues 65 - 68 (chain D) in PDB entry 1YPH
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 VAL 65 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32D SER 3.6 0.7 - - - +
33D LEU* 3.5 5.9 - - - -
34D GLN* 2.8 45.4 + - + +
35D ASP 5.2 4.3 - - - +
36D LYS* 6.0 1.1 - - - -
63D SER 4.4 7.0 - - - +
64D ASP* 1.3 80.5 - - - +
66D VAL* 1.3 76.0 + - - +
67D VAL* 4.3 6.0 - - + +
82D LYS* 3.9 18.2 - - + -
83D LEU 3.7 20.6 - - - +
84D LYS* 5.3 11.2 - - + -
85D ILE* 4.8 1.3 - - - -
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Residues in contact with VAL 66 (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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31D VAL* 3.8 30.7 - - + -
32D SER 3.8 2.7 - - - -
33D LEU* 3.7 19.1 - - + -
46D LEU* 5.4 0.2 - - + -
52D VAL* 4.0 12.8 - - + -
65D VAL* 1.3 71.7 - - - +
67D VAL* 1.3 61.2 + - - +
68D ALA 3.9 0.2 + - - -
81D GLN 3.3 2.8 - - - +
82D LYS* 3.5 1.2 - - - -
83D LEU* 2.8 57.6 + - + +
85D ILE* 3.9 16.4 - - + -
106D LEU* 4.0 10.1 - - + -
108D LEU* 3.9 21.5 - - + -
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Residues in contact with VAL 67 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30D GLN 4.5 0.3 - - - +
31D VAL* 3.3 7.1 - - - -
32D SER* 2.8 40.0 + - - +
34D GLN* 3.5 35.2 - - + +
65D VAL* 4.3 7.2 - - + +
66D VAL* 1.3 75.3 - - - +
68D ALA* 1.3 59.8 + - - +
70D GLU* 3.7 30.9 - - + +
80D ILE* 3.4 30.3 - - + -
81D GLN 3.4 2.9 - - - +
82D LYS* 4.3 16.8 - - + -
141D TRP* 5.5 0.2 - - - -
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Residues in contact with ALA 68 (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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31D VAL* 4.0 19.7 - - + +
46D LEU* 4.3 3.1 - - + -
66D VAL 3.9 0.4 + - - -
67D VAL* 1.3 72.1 - - - +
69D GLY* 1.3 64.1 + - - +
70D GLU 3.4 2.5 - - - -
79D LYS 4.7 0.2 - - - +
80D ILE* 3.5 4.3 - - - +
81D GLN* 2.9 35.3 + - + +
83D LEU* 4.1 23.3 - - + -
118D VAL* 4.0 24.1 - - + +
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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