Contacts of the strand formed by residues 70 - 73 (chain C) in PDB entry 1H9D
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 PHE 70 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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64C ARG* 4.2 0.2 - - - -
65C THR* 3.0 38.7 + - + +
67C SER* 3.3 24.1 + - - +
68C PRO 3.6 0.6 - - - -
69C ASN* 1.3 103.2 - - + +
71C LEU* 1.3 71.9 + - - +
91C VAL* 4.1 12.3 - - + -
92C VAL 3.3 6.7 - - - +
93C ALA* 3.8 26.2 - - + -
94C LEU* 4.3 2.9 - - - +
97C VAL* 4.6 1.6 - - + -
124C MET* 4.4 0.9 - - + -
150C ILE* 5.8 1.3 - - + -
152C VAL* 3.4 39.3 - - + -
158C GLN* 3.6 41.5 - - + -
159C VAL 5.2 0.4 - - - -
160C ALA* 4.1 11.4 - - + -
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Residues in contact with LEU 71 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62C LEU* 4.0 28.3 - - + -
63C VAL 3.3 9.4 - - - +
64C ARG* 3.6 38.1 - - + +
65C THR* 3.8 2.8 - - - +
70C PHE* 1.3 82.4 - - - +
72C CYS* 1.3 65.4 + - - +
91C VAL* 3.6 5.0 - - - +
92C VAL* 2.8 40.4 + - + +
94C LEU* 4.1 31.4 - - + -
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Residues in contact with CYS 72 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62C LEU* 3.3 8.0 - - - -
63C VAL* 2.8 39.4 + - - +
65C THR* 3.9 18.4 - - + +
71C LEU* 1.3 77.1 - - - +
73C SER* 1.3 69.8 + - - +
89C PHE* 3.8 16.2 - - + -
90C LYS 3.2 12.8 - - - +
91C VAL* 4.5 2.0 - - - -
150C ILE* 4.1 9.4 - - + -
162C TYR* 3.4 34.5 - - - -
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Residues in contact with SER 73 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59C PRO 4.9 1.0 + - - -
61C GLU 3.4 10.8 - - - -
62C LEU* 3.8 5.2 - - - +
63C VAL* 4.2 0.8 - - - +
72C CYS* 1.3 88.5 - - - +
74C VAL* 1.3 68.9 + - - +
75C LEU 3.7 1.2 + - - -
87C ILE* 4.1 17.0 - - - -
88C ALA 3.5 3.1 + - - -
89C PHE* 3.5 13.2 - - - -
90C LYS* 2.5 49.7 + - - +
162C TYR* 4.0 4.2 - - - -
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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