Contacts of the strand formed by residues 146 - 151 (chain C) in PDB entry 2Q41
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 GLN 146 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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122C LYS 3.3 2.8 + - - -
123C LYS* 2.9 33.3 + - + +
124C VAL 3.3 25.8 + - - +
144C ILE* 3.7 2.0 - - - +
145C GLU* 1.3 84.8 - - + +
147C ILE* 1.3 67.7 + - - +
148C ASP* 2.5 35.7 + - - +
175C ARG* 3.4 12.1 - - - +
177C ASN* 4.7 8.1 - - + +
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Residues in contact with ILE 147 (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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124C VAL* 3.8 3.8 - - + -
126C VAL* 4.5 8.5 - - + -
135C LEU* 3.2 35.7 - - + +
138C VAL* 3.2 36.1 - - + -
139C ALA* 3.9 18.2 - - + +
144C ILE* 3.4 24.9 - - + -
146C GLN* 1.3 71.7 - - - +
148C ASP* 1.3 78.0 + - - +
173C ASP* 5.1 0.9 - - - -
175C ARG* 2.6 23.2 + - + +
176C VAL* 2.9 18.2 - - + -
177C ASN 2.9 17.8 + - - -
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Residues in contact with ASP 148 (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 LYS* 4.1 0.3 + - - -
124C VAL 3.6 8.0 + - - +
125C LEU* 3.1 16.4 - - + +
126C VAL* 2.6 37.7 + - - +
146C GLN* 2.5 30.7 + - - +
147C ILE* 1.3 94.3 - - - +
149C MSE 1.3 58.9 + - - +
150C CYS* 5.3 0.2 - - - -
177C ASN* 2.8 40.3 + - - +
179C VAL* 5.2 1.1 - - + -
186C PHE* 5.0 7.3 - - + -
195C TYR* 3.2 18.7 + - - +
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Residues in contact with MSE 149 (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 VAL* 2.9 39.9 - - + +
127C ILE 3.4 0.4 - - - -
128C GLY 2.9 37.2 - - - +
129C GLY* 2.9 42.6 - - - +
132C GLY* 6.0 0.2 - - - -
134C VAL* 5.2 7.0 - - + -
135C LEU* 4.1 31.7 - - + +
147C ILE 4.4 0.2 - - - -
148C ASP* 1.3 71.7 - - - +
150C CYS* 1.3 73.0 + - - +
151C GLU* 3.9 4.7 - - + +
171C TYR* 4.9 5.8 - - + -
176C VAL* 4.9 1.6 - - + +
177C ASN 3.8 5.5 + - - +
178C LEU* 3.7 13.8 - - + +
179C VAL 2.9 26.3 + - - +
201C ASP* 4.5 4.7 - - + +
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Residues in contact with CYS 150 (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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125C LEU* 3.8 24.7 - - - -
126C VAL 3.0 8.6 + - - +
127C ILE* 4.2 9.8 - - + +
128C GLY* 3.1 18.8 + - - -
148C ASP 4.8 0.7 - - - -
149C MSE 1.3 82.2 - - - +
151C GLU* 1.3 61.8 + - - +
152C ILE* 3.6 3.3 + - - +
179C VAL* 3.1 18.8 - - - +
181C GLY 4.1 11.9 - - - +
183C GLY* 4.4 13.7 + - - -
186C PHE* 4.0 29.6 - - - -
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Residues in contact with GLU 151 (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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76C GLN* 4.2 4.1 + - - -
92C LEU* 5.8 3.0 - - - +
128C GLY* 3.5 6.4 - - - -
129C GLY* 2.9 41.0 + - - +
130C GLY 3.5 4.7 + - - -
149C MSE 3.9 3.9 - - + +
150C CYS* 1.3 71.8 - - - +
152C ILE* 1.3 65.3 + - - +
153C ASP* 2.5 62.3 + - - +
156C VAL* 4.2 11.9 - - + +
157C VAL* 3.3 23.1 - - + -
178C LEU* 4.6 2.5 - - + +
179C VAL 3.9 2.8 + - - -
180C ILE* 3.3 15.0 - - - +
181C GLY 3.3 12.0 + - - -
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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