Contacts of the strand formed by residues 188 - 198 (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 VAL 188 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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183A GLU* 3.5 4.3 - - - +
184A LEU* 3.0 49.4 + - + -
185A GLY 2.9 13.1 + - - +
186A TRP* 4.0 10.5 - - + +
187A GLY* 1.3 80.3 - - - +
189A THR* 1.3 69.8 + - - +
190A LEU* 4.3 16.2 - - + -
231A LYS 3.4 7.6 - - - +
232A PHE* 4.0 17.0 - - + -
406A LDA 4.1 31.9 - - + -
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Residues in contact with THR 189 (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* 3.6 28.4 - - + -
181A ALA* 4.2 7.2 - - + -
182A TYR 3.3 16.6 - - - +
183A GLU* 4.0 13.2 + - + +
187A GLY 4.2 1.9 + - - -
188A VAL* 1.3 77.0 + - - +
190A LEU* 1.3 69.5 + - - +
230A GLY* 3.1 5.0 - - - -
231A LYS* 3.0 53.7 + - - -
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Residues in contact with LEU 190 (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* 3.7 3.6 - - - -
181A ALA* 3.3 3.3 - - - +
182A TYR* 2.8 38.1 + - + +
184A LEU* 3.7 34.1 - - + +
188A VAL* 4.3 11.4 - - + -
189A THR* 1.3 81.2 - - - +
191A GLY* 1.3 59.0 + - - +
229A GLY 3.6 5.4 - - - +
230A GLY* 4.1 13.2 - - - -
406A LDA 6.1 3.1 - - + -
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Residues in contact with GLY 191 (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* 3.9 5.8 - - - -
107A TRP* 3.6 11.3 - - - -
180A THR* 3.1 14.1 - - - -
181A ALA* 4.1 0.4 - - - -
190A LEU* 1.3 76.4 - - - +
192A GLY* 1.3 59.2 + - - -
228A VAL* 3.5 4.8 - - - +
229A GLY 2.9 33.8 + - - +
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Residues in contact with GLY 192 (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* 3.3 12.8 + - - -
178A PHE* 6.0 0.9 - - - -
179A SER* 3.3 3.1 - - - -
180A THR* 2.9 39.3 + - - +
191A GLY* 1.3 75.3 - - - -
193A GLY* 1.3 57.9 + - - -
227A ASN 3.1 13.9 - - - -
228A VAL* 4.1 5.6 - - - -
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Residues in contact with GLY 193 (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 4.6 5.4 - - - -
101A VAL* 4.8 4.0 - - - -
104A THR* 4.5 1.1 - - - -
178A PHE* 3.2 13.9 - - - -
179A SER* 3.9 7.6 - - - -
192A GLY* 1.3 74.5 - - - -
194A TYR* 1.3 60.3 + - - +
226A TRP* 3.2 5.4 - - - +
227A ASN* 2.9 40.3 + - - +
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Residues in contact with TYR 194 (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* 4.3 1.6 - - - +
101A VAL* 4.0 4.5 - - - +
176A TYR* 4.7 11.8 + + - -
177A GLY* 3.1 3.5 - - - -
178A PHE* 2.8 61.5 + + + +
193A GLY* 1.3 75.6 - - - +
195A SER* 1.3 77.8 + - - +
196A SER* 3.5 19.4 + - - -
224A GLN* 3.2 39.6 + - + -
225A ALA 3.5 4.5 - - - -
226A TRP* 3.7 21.1 - + + -
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Residues in contact with SER 195 (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 VAL* 3.6 20.1 - - - +
125A PHE* 5.1 3.3 - - - +
126A MET* 3.7 27.3 + - - +
176A TYR 3.3 12.3 - - - -
177A GLY* 3.8 3.1 - - - -
194A TYR* 1.3 82.4 - - - +
196A SER* 1.3 61.6 + - - +
197A SER* 4.5 1.9 + - - -
223A ALA 5.0 0.7 + - - -
224A GLN* 3.3 12.1 - - - +
225A ALA* 2.8 38.7 + - - +
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Residues in contact with SER 196 (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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175A GLY* 3.3 1.4 - - - -
176A TYR* 2.8 61.8 + - - +
194A TYR* 3.5 25.1 + - - -
195A SER* 1.3 72.5 - - - +
197A SER* 1.3 61.6 + - - +
222A ARG* 3.1 27.3 + - - +
223A ALA 3.6 5.5 + - - -
224A GLN* 4.6 4.0 + - - +
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Residues in contact with SER 197 (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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125A PHE* 3.6 31.7 - - - -
126A MET* 3.2 30.5 - - - +
155A GLN* 4.8 0.7 + - - -
173A GLY 4.4 1.8 - - - -
174A ASP 3.4 12.8 - - - -
175A GLY* 3.4 3.6 - - - -
195A SER* 4.5 1.7 + - - -
196A SER* 1.3 74.6 + - - +
198A SER* 1.3 60.3 + - - +
222A ARG* 3.5 13.5 - - - +
223A ALA 2.8 35.8 + - - -
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Residues in contact with SER 198 (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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125A PHE* 3.7 6.9 - - - -
173A GLY* 3.0 23.3 + - - -
174A ASP* 2.8 31.1 + - - +
197A SER* 1.3 75.8 - - - +
199A ARG* 1.3 65.5 + - - +
204A LYS* 6.1 1.3 - - - -
221A LYS 3.9 8.5 - - - -
222A ARG* 3.6 20.0 - - - +
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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