Contacts of the strand formed by residues 145 - 152 (chain A) in PDB entry 2QN4
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 145 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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98A VAL* 5.4 2.1 - - - +
107A ARG 5.9 0.5 + - - -
138A VAL* 3.4 2.0 - - - -
139A SER* 2.8 44.6 + - - +
141A ARG* 3.7 21.9 + - - -
143A SER* 3.7 17.2 + - - +
144A CYS* 1.3 79.1 - - - +
146A ASP* 1.3 64.2 + - - +
147A LEU* 4.1 0.3 - - - +
160A ALA* 3.9 29.2 - - + +
162A GLN* 6.0 0.9 - - - +
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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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136A LYS* 3.0 43.5 + - + +
137A LEU 3.9 4.9 - - - -
138A VAL* 3.6 7.4 - - - +
144A CYS* 4.3 2.1 + - - +
145A GLN* 1.3 73.8 - - - +
147A LEU* 1.3 60.6 + - - +
160A ALA* 3.5 5.0 - - - -
161A SER 3.2 29.5 + - - +
162A GLN* 3.9 22.3 + - - +
164A PRO* 3.8 26.5 - - + +
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Residues in contact with LEU 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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96A TRP* 4.7 2.9 - - + -
98A VAL* 5.1 1.3 - - + -
109A VAL* 4.1 11.2 - - + -
126A PHE* 3.9 26.9 - - + -
137A LEU* 3.0 41.2 + - + +
139A SER* 3.9 26.0 - - - +
145A GLN 4.1 0.4 - - - +
146A ASP* 1.3 75.8 - - - +
148A GLY* 1.3 59.8 + - - +
158A LEU* 3.9 30.2 - - + +
159A GLY 3.2 21.3 - - - +
160A ALA* 3.8 6.7 - - + +
161A SER 4.2 1.6 - - - -
164A PRO* 3.5 4.9 - - - +
165A HIS* 3.0 22.7 + - - +
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Residues in contact with GLY 148 (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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147A LEU* 1.3 73.3 - - - +
149A VAL* 1.3 63.9 + - - -
150A SER 4.2 0.2 + - - -
157A TRP 3.7 0.3 - - - +
158A LEU* 3.5 4.3 - - - -
159A GLY 2.8 30.8 + - - +
161A SER* 3.4 18.7 + - - -
163A PRO 3.5 18.6 - - - -
165A HIS* 3.8 6.5 - - - -
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Residues in contact with VAL 149 (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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32A LEU* 5.3 0.4 - - + -
47A GLN* 3.5 35.7 - - + +
148A GLY* 1.3 77.7 - - - +
150A SER* 1.3 65.8 + - - +
156A ALA* 3.7 26.0 - - + -
157A TRP 3.3 7.4 - - - +
158A LEU* 3.9 13.2 - - + -
161A SER* 4.0 3.0 + - - -
163A PRO* 4.6 4.4 + - - +
165A HIS* 3.8 26.0 - - + +
66B ALA* 3.3 38.1 - - + +
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Residues in contact with SER 150 (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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148A GLY 5.2 0.2 + - - -
149A VAL* 1.3 74.6 + - - +
151A ARG* 1.3 66.1 + - - +
152A ASP* 3.5 4.9 + - - +
156A ALA* 3.4 1.7 - - - -
157A TRP* 2.9 40.1 + - - +
161A SER* 4.1 15.6 + - - -
66B ALA 4.7 0.4 - - - -
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Residues in contact with ARG 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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49A THR* 3.4 18.3 + - - +
150A SER* 1.3 74.8 - - - +
152A ASP* 1.3 58.7 + - - +
153A GLY 2.7 24.7 + - - +
154A ALA* 3.9 13.6 + - - +
155A ARG 3.4 15.8 + - - -
156A ALA* 4.0 4.3 - - - +
66B ALA 3.4 21.2 + - - +
67B ALA 2.8 33.1 + - - -
68B ALA 3.2 16.4 - - - +
69B PRO* 3.2 32.8 - - - +
70B GLU* 3.8 31.7 - - + +
72B ARG* 3.7 6.7 - - - +
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Residues in contact with ASP 152 (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 ARG* 2.4 41.9 + - - -
108A ARG* 4.2 2.6 + - - -
150A SER* 3.5 2.9 + - - +
151A ARG* 1.3 74.3 - - - +
153A GLY* 1.3 62.9 + - - +
154A ALA 3.2 4.0 + - - -
155A ARG* 2.7 20.3 + - - +
157A TRP* 3.5 23.1 + - + -
70B GLU* 3.6 3.1 - - - +
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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