Contacts of the strand formed by residues 122 - 128 (chain A) in PDB entry 1QAQ
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 GLU 122 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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27A ARG* 4.1 5.4 - - - +
96A TYR 4.3 1.4 + - - -
97A LYS* 3.1 40.2 + - + +
98A ILE 2.8 24.1 + - - +
120A ALA 3.2 0.8 + - - -
121A ASP* 1.3 94.1 + - - +
123A ILE* 1.3 63.7 + - - +
124A TYR* 3.9 28.0 + - + -
175A ARG* 3.5 15.7 + - - -
176A LEU 3.5 3.1 - - - -
177A ASN* 3.1 25.3 - - - +
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Residues in contact with ILE 123 (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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98A ILE* 3.3 16.4 - - + -
114A ILE* 3.4 60.6 - - + +
115A VAL* 4.3 11.2 - - + -
120A ALA* 4.1 15.9 - - + +
122A GLU* 1.3 79.2 - - - +
124A TYR* 1.3 64.3 + - - +
125A LEU* 3.8 19.9 + - + -
150A VAL* 5.8 2.2 - - + -
174A ILE 3.8 0.5 - - - +
175A ARG* 3.3 5.8 - - - +
176A LEU* 2.7 53.1 + - + +
178A ARG* 4.6 6.3 - - - +
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Residues in contact with TYR 124 (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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25A ASN 4.2 0.6 + - - -
26A ILE* 3.8 25.4 - - + -
27A ARG* 3.2 32.1 + - - +
28A LEU* 3.7 29.4 - - + -
98A ILE 2.6 16.6 + - - +
99A PHE* 3.0 20.7 - - + -
100A GLY 2.9 24.8 + - - -
122A GLU* 3.9 22.2 + - + -
123A ILE* 1.3 75.1 - - - +
125A LEU* 1.3 63.7 + - - +
155A LEU* 3.7 16.8 - - + -
173A LEU* 4.1 14.6 - - + -
174A ILE 3.4 7.6 - - - -
175A ARG* 3.5 33.4 + - + -
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Residues in contact with LEU 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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37A ILE* 4.4 7.9 - - + -
98A ILE* 4.9 0.2 - - + -
99A PHE 4.6 1.1 - - - -
100A GLY* 3.1 22.0 - - - +
102A ILE* 4.1 23.8 - - + -
111A ILE* 4.3 24.7 - - + -
114A ILE* 3.9 23.3 - - + -
123A ILE* 3.8 20.1 - - + +
124A TYR* 1.3 82.1 - - - +
126A ILE* 1.3 63.3 + - - +
127A VAL* 4.0 9.9 - - + -
173A LEU* 3.4 4.4 - - - +
174A ILE* 2.7 53.9 + - + +
176A LEU* 4.6 5.6 - - + -
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Residues in contact with ILE 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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13A ILE* 4.4 2.7 - - + -
22A ILE* 4.1 23.1 - - + -
44A PHE* 3.8 33.4 - - + -
99A PHE* 4.5 8.3 - - + -
100A GLY 2.8 10.4 + - - +
101A ASN* 3.7 23.5 - - + +
102A ILE 3.5 23.6 + - - +
125A LEU* 1.3 75.9 - - - +
127A VAL* 1.3 68.0 + - - +
158A VAL* 4.0 17.0 - - + -
163A PHE* 4.0 15.3 - - + -
171A SER* 4.0 5.6 - - - -
172A SER 3.3 8.7 - - - +
173A LEU* 4.2 15.0 - - + -
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Residues in contact with VAL 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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102A ILE* 4.0 28.0 - - + -
107A SER* 4.2 7.0 - - - +
125A LEU* 4.3 11.9 - - + -
126A ILE* 1.3 80.4 - - - +
128A GLU* 1.3 63.9 + - - +
131A PHE* 3.8 32.1 - - + -
132A ALA* 4.0 18.2 - - + -
171A SER* 2.8 8.9 - - - -
172A SER 2.7 35.8 + - - +
174A ILE* 4.2 15.9 - - + -
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Residues in contact with GLU 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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104A TYR* 2.8 64.7 - - + +
107A SER* 5.6 0.8 + - - -
127A VAL* 1.3 75.3 - - - +
129A TYR* 1.3 67.7 + - - +
130A GLY* 4.5 1.8 - - - +
131A PHE* 2.9 25.2 + - + +
132A ALA* 2.9 11.3 + - - +
167A PRO* 5.5 5.4 - - - +
169A VAL* 3.8 25.7 - - + +
170A ASN 3.7 9.0 - - - +
171A SER* 3.9 6.7 - - - +
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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