Contacts of the strand formed by residues 124 - 130 (chain C) in PDB entry 2QXU
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 LEU 124 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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97C ALA 2.9 8.2 + - - +
98C ASN* 3.6 23.9 - - - +
99C VAL* 2.8 31.5 + - - +
122C LYS* 3.7 14.6 - - + +
123C ILE* 1.3 74.3 - - - +
125C TYR* 1.3 60.3 + - - +
175C GLY* 3.9 24.7 - - - +
177C GLY* 4.0 15.3 - - - +
178C GLN* 3.8 23.8 - - - -
179C ASN* 4.1 6.5 - - + +
124D LEU* 6.5 1.1 - - + -
175D GLY 5.2 2.5 - - - +
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Residues in contact with TYR 125 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84C LEU* 3.8 20.9 - - + +
87C ILE* 3.6 19.9 - - + +
99C VAL* 3.4 32.5 - - + -
101C THR* 5.7 1.3 - - + -
113C ALA* 3.5 18.8 - - + -
114C LEU* 2.6 44.9 + - - +
123C ILE* 3.5 26.8 - - + +
124C LEU* 1.3 75.1 - - - +
126C THR* 1.3 63.4 + - - +
127C SER* 6.0 0.4 - - - -
143C LEU* 4.2 14.8 - - + -
146C ALA* 3.5 18.8 - - + -
147C ARG* 3.0 22.7 + - - +
178C GLN 3.0 20.7 + - - +
179C ASN* 3.6 5.2 - - - -
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Residues in contact with THR 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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99C VAL 3.0 10.5 + - - -
100C VAL* 3.3 15.3 - - + +
101C THR* 3.0 24.2 + - - -
125C TYR* 1.3 71.1 - - - +
127C SER* 1.3 59.3 + - - +
128C ILE* 4.0 22.7 - - + -
147C ARG* 3.3 26.9 - - - +
149C VAL* 4.5 7.0 - - + -
168C LEU* 4.8 9.9 - - + +
172C GLY* 3.9 9.1 - - - -
176C GLY 4.1 2.4 + - - -
177C GLY* 3.2 26.5 + - - -
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Residues in contact with SER 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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101C THR* 3.2 18.4 + - - -
106C ASN* 3.6 2.1 + - - -
125C TYR* 4.1 1.0 - - - -
126C THR* 1.3 71.3 - - - +
128C ILE* 1.3 60.4 + - - +
129C TYR* 3.4 11.2 - - - -
141C SER* 2.6 30.9 + - - -
143C LEU* 4.9 5.2 - - - -
146C ALA* 5.1 5.4 - - - -
147C ARG 2.8 9.1 + - - -
148C ASN* 3.5 20.6 - - - -
149C VAL 2.9 26.5 + - - -
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Residues in contact with ILE 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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100C VAL* 3.8 13.9 - - + -
101C THR 2.9 12.1 + - - +
102C LEU* 3.5 22.2 - - + -
103C GLY 2.7 31.7 + - - -
104C GLY 4.6 0.9 + - - -
126C THR* 4.0 15.5 - - + -
127C SER* 1.3 73.5 + - - +
129C TYR* 1.3 59.5 + - - +
149C VAL* 3.5 9.4 - - + +
151C ILE* 4.2 21.5 - - + -
159C LEU* 4.8 4.2 - - + +
165C VAL* 4.3 15.7 - - + +
168C LEU* 3.5 46.0 - - + -
169C ILE 4.3 2.5 - - - +
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Residues in contact with TYR 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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103C GLY* 4.3 8.3 - - - +
127C SER* 3.4 25.6 - - - -
128C ILE* 1.3 77.7 - - - +
130C SER* 1.3 59.4 + - - +
133C ASP* 5.9 0.7 - - - +
138C ASN* 3.5 32.5 - - + +
141C SER* 3.8 30.3 - - - +
142C ARG* 3.1 33.7 - - + -
148C ASN* 3.4 25.0 + - + +
149C VAL 3.1 8.6 + - - -
150C GLN* 3.3 39.4 - - + +
151C ILE* 2.9 26.9 + - - +
159C LEU* 4.9 2.2 - - - -
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Residues in contact with SER 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 TYR* 1.3 76.6 - - - +
131C SER* 1.3 64.8 + - - +
132C ALA 3.0 7.0 + - - -
133C ASP* 3.0 22.6 + - - +
138C ASN* 3.0 18.5 + - - +
151C ILE* 3.3 23.7 + - - -
152C HIS 3.7 12.0 - - - -
154C VAL* 2.6 34.1 + - - -
159C LEU* 4.5 7.5 - - - +
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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