Contacts of the strand formed by residues 179 - 183 (chain A) in PDB entry 1QRW
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 SER 179 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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132A THR 3.7 0.7 - - - +
133A GLN* 3.4 3.0 - - - +
134A SER* 2.8 38.0 + - - -
136A ALA 2.6 29.6 + - - -
138A MET* 3.4 16.1 - - - +
147A TRP* 4.1 16.5 - - - -
158A MET* 4.3 1.3 - - - -
160A GLY 3.7 3.8 - - - -
161A GLY* 4.2 1.1 - - - -
169A ASN* 3.2 19.2 + - - -
177A ARG* 4.8 0.5 - - - +
178A SER* 1.3 70.5 + - - +
180A LEU* 1.3 60.4 + - - +
181A PHE* 5.1 0.2 - - - -
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Residues in contact with LEU 180 (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 VAL* 4.0 23.6 - - + -
120A THR 5.2 0.2 - - - +
121A ALA* 3.7 31.4 - - + -
123A TYR* 4.4 4.3 - - + +
131A LEU* 3.9 17.5 - - + -
132A THR 3.3 3.8 - - - +
133A GLN* 3.6 31.0 - - + -
158A MET* 3.0 9.2 - - - +
159A SER* 2.9 22.7 + - - -
160A GLY 2.8 23.0 + - - +
161A GLY* 5.2 2.2 - - - +
178A SER* 3.6 21.5 - - - +
179A SER* 1.3 73.5 - - - +
181A PHE* 1.3 61.4 + - - +
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Residues in contact with PHE 181 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93A GLU* 6.6 0.4 - - + -
100A VAL* 5.0 0.9 - - + -
114A ILE* 4.6 16.8 - - + -
131A LEU* 3.6 8.6 - - - -
132A THR* 2.9 73.8 + - + -
134A SER* 4.9 4.0 - - - -
147A TRP* 3.5 54.7 - + + +
155A GLN* 3.6 37.5 - - + -
156A GLY* 3.9 7.0 - - - -
157A VAL 3.3 13.5 - - - +
159A SER 4.0 0.2 - - - +
179A SER 5.1 0.2 - - - -
180A LEU* 1.3 74.5 - - - +
182A GLU* 1.3 72.1 + - - +
183A ARG* 3.7 5.7 + - + -
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Residues in contact with GLU 182 (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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62A ASN* 3.4 2.4 - - - +
63A ASP* 3.0 45.4 + - + +
64A ARG* 2.8 38.5 + - - -
129A ARG 4.5 7.6 - - - +
130A GLY 4.8 3.3 - - - +
131A LEU* 3.7 19.1 - - + +
156A GLY* 3.0 2.6 - - - -
157A VAL* 2.8 38.4 + - + +
159A SER* 4.3 2.4 - - - -
181A PHE* 1.3 72.9 - - - +
183A ARG* 1.3 75.5 + - - +
186A PRO* 5.4 0.4 - - - +
187A ILE* 3.8 12.6 - - + -
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Residues in contact with ARG 183 (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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93A GLU* 3.0 40.5 + - - +
117A LYS* 5.9 2.2 - - - -
118A ASN 6.3 0.2 - - - +
130A GLY 4.1 18.0 + - - +
132A THR* 3.7 22.0 - - - +
155A GLN 3.7 7.2 - - - +
181A PHE* 3.7 7.1 + - + +
182A GLU* 1.3 77.8 + - - +
184A LEU* 1.3 64.8 + - - +
185A GLN* 3.7 12.2 + - - +
186A PRO* 3.3 35.4 - - + +
187A ILE* 3.4 11.4 - - - +
204A SO4 2.9 41.8 + - - -
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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