Contacts of the strand formed by residues 124 - 130 (chain C) in PDB entry 3MA0
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 124 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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175A LEU* 6.0 2.0 - - - -
205A GLN* 3.1 12.5 + - - +
123C GLN* 1.3 76.0 - - - +
125C ASN* 1.3 63.3 + - - +
126C TYR* 3.9 4.1 + - - -
157C LYS 2.9 10.3 + - - -
158C ILE* 3.3 3.5 - - - +
159C LYS 2.8 32.2 + - - +
190C ASP* 3.5 10.3 - - - -
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Residues in contact with ASN 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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172A GLU* 5.3 6.9 + - - +
205A GLN* 4.0 7.1 - - - +
124C GLY* 1.3 76.6 - - - +
126C TYR* 1.3 61.4 + - - +
159C LYS* 3.4 26.4 - - - +
161C VAL* 3.6 24.1 - - + +
185C ASN* 5.9 0.4 - - - +
188C LYS* 3.1 41.4 + - - +
189C ILE* 3.7 1.2 - - - -
190C ASP* 2.8 43.7 + - - +
191C ALA 3.3 6.2 + - - +
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Residues in contact with TYR 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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117C LEU* 3.3 33.0 + - + +
118C VAL* 3.4 3.3 + - - -
121C VAL* 2.6 40.1 + - + +
123C GLN 4.8 1.8 - - - -
124C GLY 4.4 2.7 - - - -
125C ASN* 1.3 81.4 - - - +
127C PHE* 1.3 59.4 + - - +
128C LEU* 4.8 7.6 - - + -
149C LEU* 4.3 21.1 - - + -
158C ILE* 3.6 38.8 - - + -
159C LYS 2.8 8.5 + - - +
160C VAL* 3.5 8.9 - - + +
161C VAL* 3.0 27.9 + - - +
162C GLY 4.0 0.3 + - - -
189C ILE* 4.6 0.2 - - - -
191C ALA* 3.3 26.9 - - + -
193C VAL* 3.7 24.0 - - + -
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Residues in contact with PHE 127 (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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126C TYR* 1.3 73.3 - - - +
128C LEU* 1.3 78.6 + - - +
129C MET* 4.0 15.5 - - + -
161C VAL* 4.7 2.9 - - + -
162C GLY* 3.4 31.2 - - - -
163C ASP 3.8 1.1 - - - -
164C GLN* 3.9 16.4 - - + -
177C ILE* 3.6 31.4 - - + -
178C MET* 4.3 17.7 - - + -
181C ALA* 3.4 27.4 - - + -
185C ASN* 5.4 0.4 - - - -
189C ILE* 3.9 25.1 - - + +
191C ALA 2.9 9.5 + - - +
192C VAL* 3.5 8.3 - - + -
193C VAL* 2.7 30.0 + - - +
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Residues in contact with LEU 128 (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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312A HIS* 3.5 40.2 - - + +
126C TYR* 4.8 4.5 - - + -
127C PHE* 1.3 79.7 - - - +
129C MET* 1.3 59.1 + - - +
142C ARG* 3.5 23.7 + - - +
145C GLN* 5.5 0.9 - - - +
146C MET* 3.8 13.7 - - - -
149C LEU* 4.1 15.7 - - + -
160C VAL* 3.8 26.2 - - + -
162C GLY 2.9 11.2 + - - +
163C ASP* 3.3 4.4 - - - +
164C GLN 3.0 27.0 + - - +
193C VAL* 3.7 28.7 - - + -
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Residues in contact with MET 129 (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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127C PHE* 3.7 18.7 + - + -
128C LEU* 1.3 72.1 - - - +
130C GLY* 1.3 58.6 + - - +
142C ARG* 4.0 1.1 - - - +
145C GLN* 5.7 0.2 - - - -
164C GLN 3.4 4.5 - - - +
166C VAL* 3.6 20.9 - - + -
174C ALA* 3.7 24.2 - - - +
177C ILE* 5.2 4.7 - - + -
178C MET* 5.5 2.2 - - - +
192C VAL* 4.3 6.3 - - + -
193C VAL 3.0 20.3 + - - +
194C ALA* 3.1 31.6 - - + -
195C SER* 3.0 20.7 + - - -
199C THR* 3.3 34.3 - - - +
203C ALA* 3.7 18.6 - - + -
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Residues in contact with GLY 130 (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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129C MET* 1.3 78.7 - - - +
131C GLY* 1.3 62.7 - - - -
138C ALA 5.6 0.4 - - - -
142C ARG* 3.3 18.5 - - - +
164C GLN 2.9 11.9 + - - -
165C TRP* 3.8 13.2 - - - -
166C VAL* 3.1 26.4 + - - +
169C TRP* 4.9 0.5 - - - -
195C SER* 3.5 11.8 - - - -
199C THR* 5.2 1.4 + - - -
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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