Contacts of the strand formed by residues 124 - 130 (chain A) 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 A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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97A ALA 3.0 8.6 + - - +
98A ASN* 3.6 20.6 - - + +
99A VAL* 2.8 29.5 + - - +
121A GLN* 5.7 5.2 - - + -
122A LYS* 3.7 17.3 - - + +
123A ILE* 1.3 74.2 - - - +
125A TYR* 1.3 61.5 + - - +
175A GLY* 3.7 24.9 - - - +
177A GLY* 4.0 17.3 - - - +
178A GLN* 4.0 20.9 - - - -
179A ASN* 4.1 7.0 - - + +
121B GLN* 5.9 2.7 - - - +
124B LEU* 5.6 14.6 - - + -
175B GLY 5.2 8.1 - - - +
177B GLY 5.7 0.9 - - - +
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Residues in contact with TYR 125 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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84A LEU* 3.7 21.6 - - + +
87A ILE* 3.6 19.8 - - + +
99A VAL* 3.3 33.4 - - + -
101A THR* 5.5 2.5 - - + -
113A ALA* 3.6 18.8 - - + -
114A LEU* 2.5 44.9 + - - +
123A ILE* 3.4 26.4 - - + +
124A LEU* 1.3 75.6 - - - +
126A THR* 1.3 65.3 + - - +
127A SER* 6.0 0.2 - - - -
143A LEU* 4.1 15.3 - - + -
146A ALA* 3.5 18.8 - - + -
147A ARG 3.1 14.6 + - - -
177A GLY* 3.5 0.3 - - - -
178A GLN 3.0 27.8 + - - +
179A ASN* 3.6 5.4 - - - -
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Residues in contact with THR 126 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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99A VAL 2.9 6.9 + - - -
100A VAL* 3.3 17.5 - - + +
101A THR* 3.0 24.6 + - - +
125A TYR* 1.3 74.0 - - - +
127A SER* 1.3 59.8 + - - +
128A ILE* 3.7 23.9 + - + -
147A ARG* 3.4 28.6 - - - +
149A VAL* 4.6 5.6 - - + -
168A LEU* 4.6 10.3 - - + +
172A GLY* 3.7 12.0 - - - -
176A GLY 4.2 1.6 + - - -
177A GLY* 3.2 24.3 - - - -
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Residues in contact with SER 127 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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101A THR* 3.4 17.8 + - - -
106A ASN* 3.8 1.9 + - - -
125A TYR* 4.1 0.8 - - - -
126A THR* 1.3 72.0 - - - +
128A ILE* 1.3 61.1 + - - +
129A TYR* 3.6 8.8 - - - -
141A SER* 2.7 32.0 + - - -
143A LEU* 4.9 5.2 - - - -
146A ALA* 4.9 5.6 - - - +
147A ARG 2.9 8.7 + - - -
148A ASN* 3.5 21.6 - - - -
149A VAL 2.9 27.9 + - - +
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Residues in contact with ILE 128 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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100A VAL* 3.8 14.1 - - + -
101A THR 2.9 13.5 + - - +
102A LEU* 3.5 23.2 - - + -
103A GLY 2.8 24.9 + - - -
104A GLY 4.6 0.2 + - - -
126A THR* 4.0 15.0 - - + -
127A SER* 1.3 74.4 + - - +
129A TYR* 1.3 63.8 + - - +
149A VAL* 3.4 9.2 - - + +
151A ILE* 4.4 10.5 - - + -
159A LEU* 5.1 3.3 - - + +
165A VAL* 4.0 29.2 - - + +
168A LEU* 3.5 46.4 - - + -
169A ILE 4.1 2.2 - - - +
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Residues in contact with TYR 129 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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103A GLY* 4.4 8.1 - - - +
127A SER* 3.6 31.4 - - - -
128A ILE* 1.3 75.1 - - - +
130A SER* 1.3 58.7 + - - +
133A ASP* 6.2 0.4 - - + -
138A ASN* 3.6 29.6 - - + +
141A SER* 3.8 23.3 - - - +
142A ARG* 3.3 39.4 + - + +
148A ASN* 3.5 23.2 + - + +
149A VAL 3.1 5.4 + - - -
150A GLN* 3.2 44.3 + - + +
151A ILE* 2.9 28.0 + - - +
159A LEU* 5.0 1.8 - - - -
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Residues in contact with SER 130 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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129A TYR* 1.3 74.8 - - - +
131A SER* 1.3 59.7 + - - +
132A ALA* 2.9 8.6 + - - +
133A ASP* 2.9 27.6 + - - +
138A ASN* 3.1 16.5 + - - +
151A ILE* 3.3 22.6 + - - -
152A HIS 4.1 0.9 - - - -
154A VAL* 2.6 45.0 + - - -
159A LEU* 4.2 10.1 - - - +
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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