Contacts of the strand formed by residues 177 - 181 (chain C) in PDB entry 3MX0
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 GLY 177 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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85C TRP* 3.1 22.6 - - - -
86C VAL 2.7 13.7 - - - -
88C ARG* 3.9 4.0 - - - -
125C GLU* 3.4 4.7 - - - +
126C SER 2.6 32.1 + - - -
175C ARG* 3.2 5.0 + - - +
176C LYS* 1.3 80.6 - - - +
178C PHE* 1.3 57.5 + - - -
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Residues in contact with PHE 178 (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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31C LEU* 4.0 17.0 - - + -
32C LEU* 5.5 0.2 - - + -
83C THR* 4.6 0.8 + - - -
85C TRP* 3.6 2.9 - - - -
86C VAL* 2.6 72.9 + - + -
88C ARG* 4.5 10.5 - - + -
94C ILE* 4.3 9.4 - - + -
123C TYR* 5.5 4.3 - - + -
124C ALA 2.8 17.0 - - - +
125C GLU* 4.2 9.6 - - + -
173C LEU* 3.5 32.5 - - + -
177C GLY* 1.3 76.6 - - - +
179C TYR* 1.3 75.7 + - - +
180C LEU* 4.2 25.8 - - + -
196C VAL* 4.1 17.5 - - + -
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Residues in contact with TYR 179 (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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82C ARG* 3.3 26.5 + - + -
83C THR* 3.1 28.0 - - - +
85C TRP* 3.1 44.4 - + - -
123C TYR* 2.7 18.2 - - - +
124C ALA* 2.5 45.5 + - + +
126C SER* 4.3 12.3 - - - -
129C ASP* 2.4 29.2 + - - -
130C TYR* 3.1 27.4 + + + +
139C PHE* 3.4 24.0 - + + -
178C PHE* 1.3 76.4 - - - +
180C LEU* 1.3 58.0 + - - +
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Residues in contact with LEU 180 (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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32C LEU* 5.1 1.1 - - + -
82C ARG* 3.5 2.1 - - - +
83C THR* 2.6 51.6 + - + +
94C ILE* 5.1 4.5 - - + -
96C ILE* 3.9 29.4 - - + -
121C LEU* 5.0 3.1 - - + -
122C TYR 3.2 10.1 - - - +
123C TYR* 4.2 9.0 - - + -
139C PHE* 4.0 0.9 - - - -
142C ILE* 5.1 0.2 - - + -
178C PHE* 4.2 21.3 - - + -
179C TYR* 1.3 83.1 - - - +
181C ALA* 1.3 61.9 + - - +
182C PHE* 4.6 9.2 - - + -
194C VAL* 4.0 16.8 - - + -
196C VAL* 3.6 29.8 - - + -
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Residues in contact with ALA 181 (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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80C TRP* 3.8 17.3 - - + -
81C LEU 3.3 11.0 - - - +
82C ARG* 4.2 4.7 - - + -
120C ASN 3.4 0.3 - - - +
121C LEU* 3.1 23.9 - - - +
122C TYR* 3.1 17.4 + - + -
139C PHE* 2.8 38.8 - - + -
180C LEU* 1.3 72.4 - - - +
182C PHE* 1.3 65.0 + - - +
183C GLN 4.1 0.2 - - - -
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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