Contacts of the strand formed by residues 124 - 130 (chain B) 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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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124A LEU* 5.6 13.7 - - + -
175A GLY 5.2 8.3 - - - +
177A GLY 5.8 0.7 - - - +
97B ALA 3.1 7.4 + - - +
98B ASN* 3.7 20.7 - - - +
99B VAL* 2.8 30.3 + - - +
121B GLN* 5.7 11.0 - - + +
122B LYS* 3.7 19.1 - - + +
123B ILE* 1.3 75.5 - - - +
125B TYR* 1.3 60.1 + - - +
175B GLY* 3.7 24.0 - - - +
177B GLY* 4.0 17.7 - - - +
178B GLN* 3.9 20.2 - - - -
179B ASN* 4.1 6.5 - - + +
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Residues in contact with TYR 125 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84B LEU* 3.8 19.8 - - + +
87B ILE* 3.6 20.3 - - + +
99B VAL* 3.3 33.7 - - + -
101B THR* 5.6 1.8 - - + -
113B ALA* 3.6 18.4 - - + -
114B LEU* 2.6 45.2 + - - +
123B ILE* 3.5 24.9 - - + +
124B LEU* 1.3 74.4 - - - +
126B THR* 1.3 63.1 + - - +
127B SER* 6.0 0.2 - - - -
143B LEU* 4.0 14.6 - - + -
146B ALA* 3.4 19.1 - - + -
147B ARG 3.1 14.9 + - - -
177B GLY* 3.4 2.2 - - - -
178B GLN 3.0 26.6 + - - +
179B ASN* 3.5 5.2 - - - -
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Residues in contact with THR 126 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99B VAL* 2.9 6.7 + - - +
100B VAL* 3.2 17.1 - - + +
101B THR* 3.0 25.5 + - - +
125B TYR* 1.3 71.4 - - - +
127B SER* 1.3 60.1 + - - +
128B ILE* 4.0 22.9 - - + -
147B ARG* 3.4 26.0 + - - +
149B VAL* 4.5 6.5 - - + -
168B LEU* 4.5 12.8 - - + +
172B GLY* 3.7 11.4 - - - -
176B GLY 4.3 0.9 - - - -
177B GLY* 3.2 24.4 - - - -
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Residues in contact with SER 127 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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101B THR* 3.3 17.1 + - - -
106B ASN* 3.7 2.4 + - - -
125B TYR* 4.1 1.2 - - - -
126B THR* 1.3 71.9 - - - +
128B ILE* 1.3 57.1 + - - +
129B TYR* 3.5 8.3 - - - -
141B SER* 2.7 31.0 + - - -
143B LEU* 4.9 4.7 - - - -
146B ALA* 4.9 5.6 - - - -
147B ARG 2.9 9.1 + - - +
148B ASN* 3.5 20.4 - - - -
149B VAL 2.8 32.1 + - - +
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Residues in contact with ILE 128 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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100B VAL* 3.9 13.7 - - + -
101B THR 3.0 10.0 + - - +
102B LEU* 3.5 24.1 - - + -
103B GLY 2.7 32.2 + - - -
126B THR* 4.0 13.7 - - + +
127B SER* 1.3 75.1 + - - +
129B TYR* 1.3 58.8 + - - +
141B SER* 5.0 0.2 - - - -
149B VAL* 3.4 8.7 - - + +
151B ILE* 4.1 21.5 - - + -
159B LEU* 5.0 3.7 - - + +
165B VAL* 4.2 15.0 - - + +
168B LEU* 3.4 49.6 - - + -
169B ILE 4.3 2.0 - - - +
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Residues in contact with TYR 129 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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103B GLY* 4.4 7.6 - - - +
127B SER* 3.5 25.1 - - - -
128B ILE* 1.3 76.0 - - - +
130B SER* 1.3 58.9 + - - +
136B VAL 6.0 0.2 - - - +
138B ASN* 3.6 26.5 - - + +
141B SER* 3.6 33.2 - - - +
142B ARG* 3.4 41.0 + - + -
148B ASN* 3.3 32.1 + - + +
149B VAL 3.0 9.9 + - - -
150B GLN* 3.3 25.3 + - + +
151B ILE* 2.9 28.0 + - - -
159B LEU* 5.0 2.0 - - - -
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Residues in contact with SER 130 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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129B TYR* 1.3 75.9 - - - +
131B SER* 1.3 58.5 + - - +
132B ALA* 2.9 9.3 + - - +
133B ASP* 2.9 29.7 + - - +
138B ASN* 3.0 16.1 + - - +
151B ILE* 3.3 22.1 + - - -
153B GLY 3.9 1.2 + - - -
154B VAL* 2.7 44.1 + - - -
159B LEU* 4.4 7.9 - - - +
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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