Contacts of the strand formed by residues 68 - 73 (chain H) in PDB entry 2YMX
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 ALA 68 (chain H).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48H ILE* 3.8 29.2 - - + -
60H TYR* 3.6 20.6 - - + -
64H PHE* 2.9 20.1 + - + +
65H LYS 4.0 8.5 - - - +
67H LYS* 1.3 73.7 - - - +
69H THR* 1.3 66.6 + - - +
70H LEU* 5.0 0.7 - - + -
81H MET* 4.4 6.3 - - + -
82H GLN 3.3 5.2 - - - +
83H LEU* 3.8 15.0 - - + -
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Residues in contact with THR 69 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60H TYR* 3.4 8.3 - - - +
67H LYS 5.1 0.9 + - - -
68H ALA* 1.3 76.5 + - - +
70H LEU* 1.3 70.0 + - - +
71H THR* 3.9 12.6 + - + +
81H MET* 3.4 2.6 - - - -
82H GLN* 3.0 52.6 + - - +
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Residues in contact with LEU 70 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36H TRP* 3.5 36.1 - - + +
48H ILE* 5.0 2.5 - - + -
49H GLY* 3.9 4.5 - - - -
50H GLU 3.6 40.4 - - - +
51H MET* 3.8 21.6 - - + +
58H THR* 4.5 6.6 + - + -
60H TYR* 2.8 34.3 + - + +
68H ALA* 5.0 1.8 - - + -
69H THR* 1.3 78.1 - - - +
71H THR* 1.3 66.8 + - - +
80H TYR 3.5 3.8 - - - +
81H MET* 3.6 28.9 - - + -
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Residues in contact with THR 71 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19H LYS* 4.5 13.7 + - - +
51H MET* 3.2 15.0 - - - +
69H THR* 4.7 13.7 + - + +
70H LEU* 1.3 78.5 - - - +
72H VAL* 1.3 60.3 + - - +
80H TYR* 2.7 57.8 + - - +
82H GLN* 5.5 1.0 + - - +
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Residues in contact with VAL 72 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29H PHE* 3.8 28.5 - - + -
51H MET* 4.0 13.0 - - + -
53H PRO* 3.9 29.4 - - + +
56H GLY* 5.2 11.4 - - - +
71H THR* 1.3 78.6 - - - +
73H ASP* 1.3 73.8 + - - +
74H GLN* 4.2 6.5 - - + +
78H THR 3.6 6.5 - - - +
80H TYR* 4.3 6.0 - - - -
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Residues in contact with ASP 73 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29H PHE* 4.1 0.2 - - - -
72H VAL* 1.3 78.2 - - - +
74H GLN* 1.3 62.9 + - - +
75H SER* 2.8 26.9 + - - -
76H SER* 2.7 24.0 + - - +
77H SER* 3.3 3.3 + - - -
78H THR 2.8 31.6 + - - +
80H TYR* 3.8 21.6 + - + -
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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