Contacts of the strand formed by residues 184 - 193 (chain A) in PDB entry 5ON2
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 GLU 184 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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156A VAL 3.5 1.0 - - - +
157A ASN* 3.9 2.6 - - - -
158A TRP* 3.0 57.9 + - + +
160A PRO* 3.9 25.4 - - + +
182A LYS 4.9 1.3 - - - +
183A VAL* 1.3 76.3 - - - +
185A ARG* 1.3 73.0 + - - +
186A LYS* 4.7 6.1 - - - +
286A ARG* 3.6 33.3 + - + +
287A ASN* 5.8 1.3 - - - +
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Residues in contact with ARG 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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155A ALA* 3.5 30.8 - - + +
156A VAL 3.7 6.7 - - - -
157A ASN* 5.3 1.3 - - - +
184A GLU* 1.3 80.7 - - - +
186A LYS* 1.3 59.3 + - - +
187A GLU* 4.3 4.1 + - + +
285A CYS 3.4 20.2 - - - -
286A ARG* 3.1 20.9 + - + +
288A THR* 3.2 34.9 + - - +
289A LYS 3.4 23.2 + - - -
290A VAL* 3.8 20.2 - - + +
295A MET* 5.1 6.4 - - - -
328A MET* 5.9 5.1 - - - +
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Residues in contact with LYS 186 (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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154A SER 3.7 0.3 - - - +
155A ALA* 4.6 1.6 - - - -
156A VAL* 3.0 35.0 + - + +
158A TRP* 3.7 69.6 - - + +
184A GLU* 4.7 6.5 - - - +
185A ARG* 1.3 75.4 - - - +
187A GLU* 1.3 72.5 + - - +
188A ILE* 3.5 21.1 + - + +
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Residues in contact with GLU 187 (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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153A THR* 3.5 28.4 - - + +
154A SER* 3.7 15.0 + - - -
155A ALA* 3.8 19.6 + - - +
185A ARG* 4.3 4.1 + - + +
186A LYS* 1.3 81.2 + - - +
188A ILE* 1.3 59.2 + - - +
189A PRO* 4.8 0.9 - - - +
264A GLY* 6.1 0.9 - - - -
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Residues in contact with ILE 188 (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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153A THR* 3.4 6.6 - - - +
154A SER 3.0 22.8 + - - +
156A VAL* 3.3 38.4 - - + -
158A TRP* 5.0 4.5 - - + -
165A VAL* 4.8 9.9 - - + -
186A LYS* 3.9 22.0 - - + +
187A GLU* 1.3 74.8 - - - +
189A PRO* 1.4 82.9 - - + +
190A GLN* 3.5 11.0 + - + +
425A GLN* 4.1 20.0 - - + +
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Residues in contact with PRO 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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151A LYS* 4.2 27.5 - - + +
152A LYS 3.5 10.8 - - - +
153A THR* 4.1 10.3 - - + +
187A GLU 4.8 0.4 - - - +
188A ILE* 1.4 94.8 - - + +
190A GLN* 1.3 65.0 + - - +
488A ASP* 4.8 5.2 - - - +
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Residues in contact with GLN 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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151A LYS* 3.4 9.9 - - - +
152A LYS 2.9 31.5 + - - +
154A SER* 3.7 21.4 + - - -
155A ALA 4.8 0.2 + - - -
156A VAL* 3.4 22.8 - - - +
188A ILE* 3.9 8.9 + - + +
189A PRO* 1.3 80.3 - - - +
191A TRP* 1.3 64.3 + - - +
192A PHE* 3.4 15.4 - - + -
421A GLY* 6.1 1.3 - - - -
423A SER* 3.2 26.4 - - - +
425A GLN* 3.2 13.8 - - - +
488A ASP* 4.9 0.7 - - - +
74B C 2.7 31.9 + - - +
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Residues in contact with TRP 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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140A PHE* 4.4 11.4 - + + -
144A TYR* 4.1 23.3 - + - -
149A VAL* 4.0 17.7 - - + -
150A TYR 4.0 0.2 - - - -
151A LYS* 3.8 48.6 - - + +
190A GLN* 1.3 73.0 - - - +
192A PHE* 1.3 65.1 + - - +
421A GLY* 3.6 1.2 - - - -
422A VAL* 3.0 36.6 + - + -
423A SER* 2.7 28.4 + - - +
432A ILE* 4.1 18.2 - - + -
434A MET* 3.6 38.5 - - + +
442A VAL* 4.0 20.2 - - + -
486A GLU* 3.4 28.1 + - - +
488A ASP* 5.2 0.7 - - - -
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Residues in contact with PHE 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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149A VAL* 3.4 8.9 - - - +
150A TYR* 2.9 51.6 + - + +
152A LYS* 3.7 40.6 - - + -
154A SER* 3.6 35.4 - - - -
190A GLN* 3.4 26.5 - - + -
191A TRP* 1.3 76.1 - - - +
193A ILE* 1.3 63.5 + - - +
329A GLU* 4.9 4.0 - - - -
419A ASP* 3.4 20.2 - - + -
420A TRP 3.4 4.3 - - - -
421A GLY* 3.3 31.0 - - - -
422A VAL* 4.7 0.4 - - - +
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Residues in contact with ILE 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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140A PHE* 4.2 24.7 - - + -
143A LEU* 4.6 20.0 - - + -
148A LEU* 3.4 13.5 - - + +
149A VAL* 4.4 5.6 - - + -
192A PHE* 1.3 77.9 - - - +
194A LYS* 1.3 62.3 + - - +
195A ILE 2.9 8.8 + - - -
419A ASP* 3.6 4.7 - - - +
420A TRP* 3.0 42.8 + - + +
422A VAL* 3.7 26.2 - - + -
494A MET* 3.8 17.7 - - + -
543A PHE* 3.8 28.3 - - + -
544A PHE* 6.1 0.9 - - + -
547A LEU* 6.2 0.4 - - + -
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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