Contacts of the strand formed by residues 124 - 130 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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124C LEU* 6.5 0.9 - - + -
175C GLY 5.5 5.4 - - - +
97D ALA 3.0 8.1 + - - +
98D ASN* 3.6 24.2 - - + +
99D VAL* 2.7 35.4 + - - +
122D LYS* 3.7 17.5 - - + +
123D ILE* 1.3 75.1 - - - +
125D TYR* 1.3 57.7 + - - +
172D GLY 5.7 0.4 - - - +
175D GLY* 4.8 13.9 - - - +
177D GLY* 3.9 17.0 - - - +
178D GLN* 3.9 26.9 - - - +
179D ASN* 4.0 7.6 - - + +
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Residues in contact with TYR 125 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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84D LEU* 3.6 22.7 - - + +
87D ILE* 3.5 20.3 - - + +
99D VAL* 3.3 33.2 - - + -
101D THR* 5.6 1.3 - - + -
113D ALA* 3.6 22.2 - - + -
114D LEU* 2.7 44.3 + - - +
123D ILE* 3.4 26.9 - - + +
124D LEU* 1.3 75.7 - - - +
126D THR* 1.3 64.8 + - - +
143D LEU* 4.1 15.7 - - + -
146D ALA* 3.5 19.5 - - + -
147D ARG* 3.2 14.4 + - - +
177D GLY* 3.7 0.4 - - - -
178D GLN 3.0 26.5 + - - +
179D ASN* 3.9 1.3 - - - -
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Residues in contact with THR 126 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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99D VAL 2.9 10.9 + - - -
100D VAL* 3.2 6.9 - - + +
101D THR* 2.9 25.4 + - - +
125D TYR* 1.3 70.6 + - - +
127D SER* 1.3 59.4 + - - +
128D ILE* 4.0 24.2 - - + -
147D ARG* 3.3 24.1 - - - +
149D VAL* 4.5 6.5 - - + -
168D LEU* 4.6 11.0 - - + +
172D GLY* 3.5 17.6 + - - -
176D GLY 3.9 3.1 + - - -
177D GLY* 3.3 24.9 + - - -
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Residues in contact with SER 127 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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101D THR* 3.3 18.2 + - - -
104D GLY 5.5 0.2 + - - -
106D ASN* 3.7 2.5 + - - -
125D TYR 4.2 0.8 - - - -
126D THR* 1.3 71.6 - - - +
128D ILE* 1.3 61.0 + - - +
129D TYR* 3.6 9.7 - - - -
141D SER* 2.7 30.6 + - - -
143D LEU* 4.9 9.4 - - - -
146D ALA* 5.1 1.8 - - - +
147D ARG 2.9 9.1 + - - -
148D ASN* 3.5 19.9 - - - -
149D VAL 2.9 26.4 + - - -
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Residues in contact with ILE 128 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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100D VAL* 4.1 21.5 - - + -
101D THR 2.8 13.6 + - - +
102D LEU* 3.5 12.7 - - + -
103D GLY 2.7 31.9 + - - -
104D GLY 4.6 0.2 + - - -
126D THR* 4.0 14.6 - - + -
127D SER* 1.3 75.9 + - - +
129D TYR* 1.3 60.1 + - - +
149D VAL* 3.5 9.9 - - + +
151D ILE* 4.0 21.1 - - + -
159D LEU* 4.9 3.5 - - + +
165D VAL* 4.2 14.4 - - + +
168D LEU* 3.3 52.3 - - + -
169D ILE 4.2 1.8 - - - +
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Residues in contact with TYR 129 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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103D GLY* 4.4 8.3 - - - +
127D SER* 3.6 23.6 - - - -
128D ILE* 1.3 78.3 - - - +
130D SER* 1.3 58.7 + - - +
133D ASP* 6.0 0.4 - - + +
138D ASN* 3.6 30.5 - - + +
141D SER* 3.7 31.6 - - - +
142D ARG* 3.3 39.7 + - + +
148D ASN* 3.8 16.6 + - + +
149D VAL 3.1 5.8 + - - -
150D GLN* 3.2 39.6 + - + +
151D ILE* 2.8 29.8 + - - +
159D LEU* 5.0 2.0 - - - -
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Residues in contact with SER 130 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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129D TYR* 1.3 73.4 - - - +
131D SER* 1.3 65.1 + - - +
132D ALA* 3.0 12.2 + - - +
133D ASP* 3.1 21.5 + - - +
138D ASN* 2.9 19.0 - - - +
151D ILE* 3.2 8.9 - - - +
152D HIS 3.6 11.4 - - - -
154D VAL* 2.7 45.1 + - - -
159D LEU* 4.5 8.1 - - - +
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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