Contacts of the strand formed by residues 150 - 158 (chain A) in PDB entry 1NQF
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 GLN 150 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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143A GLY 3.3 4.9 - - - +
144A TRP* 5.5 0.4 - - - -
148A SER 4.4 3.3 + - - +
149A TYR* 1.3 79.9 - - - +
151A ASN* 1.3 61.6 + - - +
152A TYR* 3.8 31.6 + - + +
172A TYR* 3.7 17.1 - - + +
173A ALA* 3.7 1.7 - - - -
174A HIS* 3.0 50.4 + - + +
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Residues in contact with ASN 151 (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 ILE* 6.3 1.2 - - - +
141A SER* 4.6 1.0 + - - -
142A ALA* 2.9 10.0 + - - -
143A GLY* 2.5 42.1 + - - +
149A TYR* 2.8 36.0 + - + +
150A GLN* 1.3 73.9 - - - +
152A TYR* 1.3 78.0 + - - +
153A ASP* 4.3 3.1 + - - +
171A ASP* 3.1 27.9 + - - -
172A TYR 3.4 5.1 + - - +
173A ALA* 4.3 5.8 - - + +
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Residues in contact with TYR 152 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
141A SER 3.5 6.1 - - - +
142A ALA* 3.8 16.6 - - + -
143A GLY 4.2 6.3 - - - -
150A GLN* 3.8 32.3 + - + +
151A ASN* 1.3 107.2 + - - +
153A ASP* 1.3 61.5 + - - +
154A VAL* 5.7 0.7 - - + -
170A GLY 4.3 0.2 - - - +
171A ASP* 3.3 2.8 - - - +
172A TYR* 2.9 48.5 + + + +
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Residues in contact with ASP 153 (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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31A ARG* 4.9 8.1 + - - -
102A ALA* 4.3 6.6 - - - +
139A GLU 3.8 0.6 - - - +
141A SER* 2.5 57.0 + - - +
151A ASN* 4.7 4.0 - - - +
152A TYR* 1.3 72.2 - - - +
154A VAL* 1.3 106.5 + - - +
155A SER* 3.7 4.9 + - - -
169A LEU* 4.2 12.7 - - - +
170A GLY 3.4 9.6 - - - +
171A ASP* 3.0 29.5 - - - +
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Residues in contact with VAL 154 (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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138A THR* 6.2 1.6 - - - -
139A GLU 3.2 4.3 - - - +
140A ILE* 3.7 33.9 - - + -
152A TYR* 6.4 0.4 - - + -
153A ASP* 1.3 96.8 + - - +
155A SER* 1.3 66.4 + - - +
156A THR* 5.8 3.6 - - + -
168A LEU 4.1 0.2 - - - +
169A LEU* 3.2 3.1 - - - -
170A GLY* 3.1 29.6 + - - +
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Residues in contact with SER 155 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
133A ARG* 2.6 38.6 + - - -
138A THR* 3.2 1.4 - - - -
139A GLU* 2.6 49.8 + - - +
153A ASP* 3.7 6.3 + - - -
154A VAL* 1.3 79.0 - - - +
156A THR* 1.3 74.0 + - - +
167A THR* 4.5 0.2 - - - +
168A LEU 3.5 7.1 + - - -
169A LEU* 3.8 13.2 - - - +
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Residues in contact with THR 156 (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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133A ARG* 4.3 0.9 - - - +
137A GLY 3.6 7.9 - - - -
138A THR* 3.0 28.0 - - - +
154A VAL* 5.8 4.0 - - + -
155A SER* 1.3 83.3 + - - +
157A GLN* 1.3 63.3 + - - +
158A GLN* 3.5 16.9 + - - +
166A VAL 4.4 0.4 - - - +
167A THR* 2.8 22.1 - - - +
168A LEU* 2.9 42.8 + - + +
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Residues in contact with GLN 157 (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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133A ARG* 2.8 26.5 - - - +
134A ASP* 3.9 4.9 + - - -
135A GLU 3.2 24.1 + - - +
136A PRO* 3.0 44.8 - - - +
137A GLY 3.2 22.5 + - - -
156A THR* 1.3 77.7 + - - +
158A GLN* 1.3 69.9 + - - +
159A GLN* 5.8 1.6 - - - +
165A ARG* 2.7 40.2 + - + +
166A VAL 3.2 7.0 - - - +
167A THR* 3.6 17.3 + - + +
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Residues in contact with GLN 158 (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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136A PRO* 5.3 4.7 - - + -
137A GLY* 5.0 4.8 - - - +
138A THR* 4.6 11.2 - - + +
156A THR* 3.5 19.9 + - + +
157A GLN* 1.3 82.3 - - - +
159A GLN* 1.3 69.8 + - - +
160A LEU* 3.5 9.5 - - - +
165A ARG* 4.5 0.7 - - - -
166A VAL* 3.0 25.1 + - - +
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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