Contacts of the strand formed by residues 82 - 86 (chain C) in PDB entry 5I75
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 82 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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57C GLN* 5.0 7.6 - - - -
67C LEU* 4.1 15.7 - - + -
68C ILE* 4.1 3.8 - - + +
74C ARG* 3.0 29.8 + - - +
78C VAL* 3.9 13.9 - - + -
79C PRO* 3.7 37.4 - - + +
80C ASP 3.2 0.6 - - - -
81C ARG* 1.3 101.3 - - + +
83C THR* 1.3 59.1 + - - +
93C PHE* 3.5 30.1 - + + -
94C THR 3.8 3.1 - - - -
95C ILE* 3.7 26.7 - - + -
102C ASP* 3.4 25.1 - - - -
106C TYR* 4.0 8.7 - - - -
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Residues in contact with THR 83 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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68C ILE* 4.2 7.4 - - - -
72C SER 5.5 0.2 - - - -
74C ARG* 3.4 29.2 - - - +
80C ASP 4.1 7.2 - - - +
81C ARG 4.5 3.6 - - - +
82C PHE* 1.3 75.9 - - - +
84C GLY* 1.3 60.9 + - - +
93C PHE* 3.3 13.2 - - - -
94C THR* 2.9 53.5 + - - +
96C SER* 6.6 0.2 - - - -
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Residues in contact with GLY 84 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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55C TRP* 5.2 1.1 - - - -
68C ILE* 4.5 9.3 - - - +
71C ALA 3.4 19.3 - - - -
72C SER* 3.3 25.2 + - - -
83C THR* 1.3 78.8 - - - +
85C SER* 1.3 61.9 + - - -
92C THR 3.6 8.1 - - - -
93C PHE* 4.6 1.8 - - - -
94C THR* 5.6 0.7 - - - -
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Residues in contact with SER 85 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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55C TRP* 5.2 0.9 + - - -
71C ALA* 3.7 6.7 + - - +
72C SER* 5.1 2.7 - - - -
84C GLY* 1.3 74.9 - - - -
86C GLY* 1.3 61.7 + - - +
91C PHE* 3.7 6.6 - - - +
92C THR* 2.9 46.8 + - - +
94C THR* 4.6 4.9 + - - -
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Residues in contact with GLY 86 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50C SER 4.7 0.2 - - - +
51C THR* 4.9 0.7 - - - +
71C ALA* 3.6 14.9 - - - +
85C SER* 1.3 78.0 - - - +
87C SER* 1.3 63.2 + - - -
90C ASP 3.9 10.1 - - - -
91C PHE* 3.3 22.9 - - - -
92C THR* 5.8 0.4 - - - -
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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