Contacts of the strand formed by residues 119 - 126 (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 PHE 119 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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52C TRP* 5.1 7.0 - + + -
98C LEU* 4.8 6.3 - - + -
100C PHE* 3.0 48.7 - + + -
102C VAL* 5.2 2.2 - - + -
117C GLU 5.5 0.2 - - - -
118C THR* 1.3 77.2 - - - +
120C ASN* 1.3 83.8 + - - +
144C THR* 3.8 1.4 - - - +
145C ILE* 3.1 49.7 + - + +
146C ALA* 6.0 0.2 - - - -
182C PHE* 3.9 29.4 - + + -
183C GLN 4.0 11.7 - - - +
184C ASP* 4.3 16.6 - - + +
185C ILE* 5.0 1.1 - - - -
187C ALA* 6.3 0.9 - - + -
189C VAL* 3.2 26.7 - - + -
191C LEU* 5.4 6.7 - - + -
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Residues in contact with ASN 120 (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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118C THR* 4.5 3.1 + - - -
119C PHE* 1.3 102.1 - - - +
121C LEU* 1.3 60.0 + - - +
122C TYR* 3.0 39.6 + - + -
141C LYS* 3.6 20.3 + - - +
143C ASP 4.1 1.6 - - - -
144C THR* 3.9 13.7 + - - +
145C ILE* 4.6 0.7 - - - -
181C ALA 3.4 0.7 - - - +
182C PHE* 3.4 24.8 - - - -
183C GLN* 3.1 23.6 + - - +
185C ILE* 4.6 12.6 - - - +
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Residues in contact with LEU 121 (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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96C ILE* 4.3 20.6 - - + -
98C LEU* 3.2 31.0 - - + -
120C ASN* 1.3 69.8 - - - +
122C TYR* 1.3 71.4 + - - +
141C LYS* 3.7 1.9 - - - +
142C ILE* 2.9 41.7 + - + -
143C ASP 2.9 27.8 + - - +
145C ILE* 3.7 11.7 - - + -
168C ARG* 5.1 7.6 - - + -
180C LEU* 5.0 5.6 - - + -
181C ALA 3.1 20.9 - - - +
182C PHE* 3.5 24.7 - - + -
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Residues in contact with TYR 122 (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* 3.7 23.1 - + - -
120C ASN* 3.0 40.4 + - + -
121C LEU* 1.3 86.5 - - - +
123C TYR* 1.3 64.8 + - - +
136C LYS 5.8 0.9 - - - -
139C PHE* 2.5 53.4 - - + +
140C THR 3.3 4.7 - - - -
141C LYS* 3.9 23.5 - - + +
142C ILE* 4.2 4.7 - - - +
180C LEU* 3.2 9.0 - - - +
181C ALA* 3.1 28.8 + - + -
183C GLN* 2.8 25.9 + - + -
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Residues in contact with TYR 123 (chain C).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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94C ILE* 6.1 2.7 - - + -
122C TYR* 1.3 76.5 - - - +
124C ALA* 1.3 72.2 + - - +
125C GLU* 4.0 30.5 + - + -
138C LEU 3.7 0.5 - - - +
139C PHE* 3.3 3.9 - - - -
140C THR* 2.9 54.1 + - + +
142C ILE* 3.4 31.0 - - + -
170C VAL* 3.6 35.8 - - + +
173C LEU* 5.2 7.1 - - + +
178C PHE* 5.5 4.3 - - + -
179C TYR 2.7 11.2 - - - +
180C LEU* 4.2 7.4 - - + -
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Residues in contact with ALA 124 (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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123C TYR* 1.3 77.7 - - - +
125C GLU* 1.3 64.5 + - - +
126C SER* 3.7 0.6 + - - -
138C LEU* 3.5 14.6 - - + +
139C PHE* 3.2 37.5 - - + -
178C PHE* 2.8 7.5 - - - -
179C TYR* 2.5 44.5 + - + +
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Residues in contact with GLU 125 (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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123C TYR* 4.0 28.5 + - + -
124C ALA* 1.3 74.8 - - - +
126C SER* 1.3 60.5 + - - +
172C PRO 3.8 3.1 - - - +
173C LEU* 3.5 26.4 - - + +
174C THR* 2.6 39.6 + - - +
175C ARG* 3.2 32.4 + - + +
177C GLY 3.4 6.7 - - - +
178C PHE* 4.0 7.9 - - + +
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Residues in contact with SER 126 (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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85C TRP* 2.9 34.7 - - - -
124C ALA* 3.7 1.1 + - - -
125C GLU* 1.3 76.3 - - - +
127C ASP* 1.3 61.8 + - - +
128C LEU 2.9 20.9 + - - -
130C TYR* 3.4 30.5 + - - -
175C ARG* 4.4 2.5 - - - +
177C GLY 2.6 17.0 + - - +
179C TYR* 4.3 12.8 - - - -
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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