Contacts of the strand formed by residues 142 - 147 (chain A) in PDB entry 1QP4
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 MET 142 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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108A LEU* 6.0 0.2 - - + -
119A LEU* 3.2 30.1 - - + +
121A VAL* 4.1 15.7 - - + -
134A LEU* 3.4 57.9 - - + +
137A TYR* 4.8 7.2 - - - +
138A ARG* 5.3 0.7 - - - -
140A ILE 3.4 10.8 + - - +
141A PRO* 1.3 76.3 - - - +
143A VAL* 1.3 66.0 + - - +
144A VAL* 5.1 2.0 - - + -
154A PHE* 4.6 13.6 + - + +
155A THR* 2.8 40.3 - - + +
156A ASP* 3.1 11.3 + - - +
305A LEU* 3.8 2.9 - - - +
308A ARG* 4.7 10.0 + - - +
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Residues in contact with VAL 143 (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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119A LEU 2.9 5.0 + - - +
120A LEU* 3.5 22.8 - - + +
121A VAL* 2.8 25.5 + - - -
142A MET* 1.3 79.1 - - - +
144A VAL* 1.3 76.0 + - - +
145A MET* 3.8 2.2 + - + +
155A THR* 4.1 0.2 - - - -
156A ASP* 3.5 24.9 - - + +
157A ALA 4.5 0.9 - - - +
158A VAL* 4.2 13.9 - - + +
301A ALA* 3.7 29.4 - - + +
304A MET* 4.8 3.8 - - + -
305A LEU* 3.8 17.9 - - + +
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Residues in contact with VAL 144 (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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121A VAL* 3.3 16.8 - - + +
126A TYR* 3.6 12.8 - - + +
134A LEU* 5.3 2.2 - - + -
142A MET* 5.1 5.4 - - + -
143A VAL* 1.3 75.4 - - - +
145A MET* 1.3 64.0 + - - +
146A ASP* 3.3 25.8 - - - +
147A TRP* 3.7 54.9 + - + +
155A THR* 3.9 17.7 - - + +
156A ASP 3.2 6.6 + - - +
157A ALA* 3.5 3.5 - - + +
158A VAL 3.2 22.7 + - - +
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Residues in contact with MET 145 (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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64A LEU* 4.8 1.8 - - - -
77A ILE* 3.8 26.9 - - + +
81A VAL* 4.6 6.1 - - + -
120A LEU* 4.1 25.8 - - + -
121A VAL 2.8 13.4 + - - +
122A MET* 4.3 22.7 - - + -
143A VAL* 4.1 7.9 - - + +
144A VAL* 1.3 76.9 - - - +
146A ASP* 1.3 59.7 + - - +
147A TRP 3.9 1.6 - - - -
158A VAL* 3.3 21.8 - - + +
297A LEU* 3.4 47.0 - - + +
298A GLY* 4.4 4.0 - - - -
301A ALA* 4.1 16.8 - - + -
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Residues in contact with ASP 146 (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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73A TYR* 6.0 2.0 - - - +
74A PHE* 5.6 0.7 - - - -
122A MET* 3.0 31.8 - - + +
124A SER* 2.8 34.2 + - - +
126A TYR* 2.5 35.1 + - - -
144A VAL* 3.3 3.6 - - - +
145A MET* 1.3 82.4 - - - +
147A TRP* 1.3 64.1 + - - +
160A ASP* 6.0 0.9 - - - -
191A ASN* 3.8 17.3 + - - +
192A THR* 6.5 0.9 - - + -
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Residues in contact with TRP 147 (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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126A TYR* 3.4 46.0 - + - -
131A LEU* 4.5 11.2 - - + -
134A LEU* 5.2 4.5 - - + -
144A VAL* 3.7 40.3 + - + +
145A MET 3.9 1.8 - - - -
146A ASP* 1.3 79.7 - - - +
148A GLY* 1.3 64.4 + - - +
149A GLU 3.2 15.3 - - - +
150A ALA* 3.8 7.2 - - + -
151A LYS* 3.0 63.3 - - + +
152A ALA* 3.5 25.6 - - + -
154A PHE* 5.7 0.9 - + - -
155A THR* 4.3 8.3 - - - -
157A ALA* 4.5 12.3 - - + -
158A VAL 3.9 15.0 + - - +
159A ILE* 4.0 8.2 - - + +
160A ASP* 4.4 2.6 + - - +
191A ASN* 3.6 11.2 + - - -
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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