Contacts of the strand formed by residues 175 - 185 (chain A) in PDB entry 5NXR
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 GLY 175 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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126A MET* 4.0 4.5 - - - -
154A TYR* 3.4 12.4 - - - -
155A GLN* 2.8 36.1 + - - +
173A GLY 3.6 0.8 + - - -
174A ASP* 1.3 77.6 - - - +
176A TYR* 1.3 65.4 + - - -
196A SER 3.3 11.9 - - - -
197A SER* 3.4 11.7 - - - -
415A CL 4.6 0.7 - - - -
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Residues in contact with TYR 176 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
126A MET* 3.7 7.7 - - - +
153A GLN 3.2 12.8 - - - +
154A TYR* 4.1 2.9 - - + -
175A GLY* 1.3 77.1 - - - +
177A GLY* 1.3 63.0 + - - +
194A TYR* 4.7 10.3 + + - -
195A SER* 3.3 3.3 - - - -
196A SER* 2.8 58.6 + - - +
222A ARG* 3.5 23.0 + - - -
405A LDA 3.5 71.2 - - + +
415A CL 4.1 6.3 - - + -
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Residues in contact with GLY 177 (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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100A VAL* 3.6 11.7 - - - -
126A MET* 4.1 1.9 - - - -
152A LEU* 3.7 1.7 - - - +
153A GLN 2.9 31.4 + - - +
176A TYR* 1.3 83.3 - - - +
178A PHE* 1.3 66.0 - - - +
194A TYR* 3.1 13.5 - - - -
195A SER* 3.8 5.8 - - - -
405A LDA 6.0 0.2 - - - +
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Residues in contact with PHE 178 (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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100A VAL* 3.5 8.2 - - - +
150A PHE* 5.9 1.8 - - + -
151A ALA 3.1 14.6 - - - +
152A LEU* 4.1 16.2 - - + -
177A GLY* 1.3 75.9 - - - +
179A SER* 1.3 71.0 + - - +
180A THR* 4.3 20.6 - - + -
192A GLY 5.5 1.6 - - - -
193A GLY* 3.2 2.7 - - - -
194A TYR* 2.8 68.0 + + + +
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Residues in contact with SER 179 (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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100A VAL* 3.5 25.3 - - - +
103A ASP* 2.7 27.3 + - - +
104A THR* 5.2 0.4 - - - -
137A ARG* 4.7 0.3 + - - -
150A PHE* 3.2 5.4 - - - +
151A ALA* 2.8 37.7 + - - +
178A PHE* 1.3 81.7 - - - +
180A THR* 1.3 67.1 + - - +
192A GLY 3.3 12.8 - - - -
193A GLY* 3.9 1.3 - - - -
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Residues in contact with THR 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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104A THR* 4.7 1.2 + - - -
107A TRP* 5.1 0.2 - - - -
148A LEU* 3.5 20.6 - - - +
149A SER 3.0 14.6 + - - -
150A PHE* 4.1 8.2 - - - +
178A PHE* 4.3 16.6 - - + -
179A SER* 1.3 77.9 - - - +
181A ALA* 1.3 65.0 + - - +
191A GLY* 3.1 3.3 - - - -
192A GLY* 2.9 42.4 + - - +
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Residues in contact with ALA 181 (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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107A TRP* 3.9 23.8 - - + -
147A GLY 3.7 0.8 - - - +
148A LEU* 3.5 5.3 - - - +
149A SER* 2.8 45.7 + - - +
180A THR* 1.3 75.0 + - - +
182A TYR* 1.3 61.0 + - - +
189A THR* 4.2 5.6 - - + -
190A LEU 3.3 11.2 - - - +
191A GLY* 4.1 0.4 - - - -
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Residues in contact with TYR 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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145A VAL* 4.7 12.8 - - + +
147A GLY* 3.5 28.5 - - - -
148A LEU* 3.7 22.7 - - + -
181A ALA* 1.3 75.8 - - - +
183A GLU* 1.3 81.9 + - - +
184A LEU* 3.8 27.3 + - + +
189A THR* 3.3 5.9 - - - -
190A LEU* 2.8 37.2 + - + +
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Residues in contact with GLU 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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147A GLY* 3.1 28.8 + - - +
182A TYR* 1.3 90.9 + - - +
184A LEU* 1.3 62.5 + - - +
185A GLY* 4.4 4.5 - - - +
188A VAL 3.5 10.1 - - - +
189A THR* 4.0 12.3 + - + +
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Residues in contact with LEU 184 (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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182A TYR* 4.0 30.5 + - + +
183A GLU* 1.3 74.1 - - - +
185A GLY* 1.3 62.4 + - - +
186A TRP* 5.8 11.8 - - + -
188A VAL* 3.0 29.9 + - + +
190A LEU* 3.7 36.1 - - + +
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Residues in contact with GLY 185 (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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183A GLU* 3.4 6.9 - - - +
184A LEU* 1.3 79.2 - - - +
186A TRP* 1.3 69.0 + - - +
187A GLY 3.0 5.8 - - - -
188A VAL* 2.9 26.9 + - - +
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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