Contacts of the strand formed by residues 189 - 201 (chain A) in PDB entry 5X22
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 ARG 189 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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4A SER* 3.2 42.3 + - - +
5A LYS 3.6 17.3 + - - +
6A LEU* 3.3 33.1 - - - +
7A LYS 5.2 0.4 - - - +
29A GLU* 4.7 6.7 - - - -
185A ARG* 3.6 8.7 - - - +
186A LEU* 3.1 43.0 + - - +
187A GLY 4.3 0.9 - - - +
188A GLN* 1.3 78.8 - - - +
190A THR* 1.3 60.6 + - - +
192A LEU* 4.1 19.2 - - + +
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Residues in contact with THR 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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185A ARG* 3.3 33.9 - - - +
188A GLN 3.5 11.1 + - - +
189A ARG* 1.3 76.5 - - - +
191A ASP* 1.3 76.6 + - - +
192A LEU* 3.6 6.6 - - - +
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Residues in contact with ASP 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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30A ARG* 3.4 43.9 - - - +
183A ASP* 3.5 15.3 + - - -
184A THR 4.1 3.4 + - - -
185A ARG* 5.4 0.4 - - - +
190A THR* 1.3 82.7 - - - +
192A LEU* 1.3 61.1 + - - +
938C LYS* 2.8 34.5 + - - +
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Residues in contact with LEU 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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6A LEU* 4.0 20.4 - - + -
27A PRO* 3.8 18.8 - - + -
28A LEU 3.7 12.8 - - - +
29A GLU* 4.5 13.5 - - - +
30A ARG* 4.5 2.5 - - + +
183A ASP* 3.7 0.9 - - - -
184A THR* 2.9 48.5 + - + +
186A LEU* 3.7 31.6 - - + +
189A ARG* 4.1 21.1 - - + +
190A THR 4.2 7.9 - - - +
191A ASP* 1.3 82.7 - - - +
193A ASP* 1.3 61.6 + - - +
938C LYS* 3.1 11.4 + - - -
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Residues in contact with ASP 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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27A PRO* 3.6 5.9 - - - +
28A LEU* 2.7 49.9 + - + +
29A GLU 3.8 3.3 + - - +
30A ARG* 3.7 3.1 - - - +
31A GLY* 2.9 34.6 + - - -
33A GLY* 2.9 29.1 + - - +
34A VAL* 4.6 1.2 + - - +
181A VAL* 3.6 18.1 - - + +
182A GLU 4.0 1.3 - - - -
184A THR* 3.7 0.9 - - - -
192A LEU* 1.3 72.0 - - - +
194A LYS* 1.3 60.8 + - - +
195A LEU 4.0 0.4 - - - -
938C LYS* 2.5 33.0 + - - +
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Residues in contact with LYS 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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14A ARG* 6.2 0.2 - - - +
24A VAL* 3.7 26.9 - - + -
25A LEU 3.8 3.6 - - - -
26A GLU* 3.7 30.3 + - + +
180A GLN 3.4 2.8 - - - +
181A VAL* 3.4 6.2 - - - +
182A GLU* 2.9 66.9 + - + +
183A ASP 5.3 1.6 - - - +
184A THR* 3.9 15.7 - - + -
193A ASP* 1.3 73.6 - - - +
195A LEU* 1.3 60.4 + - - +
196A THR* 3.7 6.3 + - - +
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Residues in contact with LEU 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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23A PHE 3.3 2.6 - - - +
24A VAL* 3.3 4.5 - - - -
25A LEU* 2.9 42.5 + - + +
28A LEU* 3.7 21.8 - - + -
33A GLY* 3.3 33.0 - - - +
36A LEU* 3.7 27.1 - - + -
37A GLY* 3.9 7.4 - - - +
179A PHE* 3.6 24.2 - - + -
180A GLN 3.9 5.2 - - - +
181A VAL* 4.2 2.7 - - + +
193A ASP 4.0 0.8 - - - -
194A LYS* 1.3 72.3 - - - +
196A THR* 1.3 69.1 + - - +
197A LEU* 4.9 10.3 - - + +
225B PHE* 5.0 11.0 - - + -
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Residues in contact with THR 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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14A ARG* 4.5 2.7 - - - +
22A GLU* 4.7 5.4 - - + -
23A PHE 3.5 3.6 - - - +
24A VAL* 3.8 29.6 - - + +
179A PHE* 3.2 6.1 - - - +
180A GLN* 2.9 43.9 + - - -
182A GLU* 4.3 12.1 + - - -
194A LYS* 4.3 6.4 + - - -
195A LEU* 1.3 77.2 - - - +
197A LEU* 1.3 61.7 + - - +
198A ARG* 4.0 9.0 + - + +
934C PHE* 3.4 39.1 - - + -
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Residues in contact with LEU 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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22A GLU* 3.4 0.7 - - - -
23A PHE* 2.9 54.5 + - + +
37A GLY* 5.2 4.9 - - - +
40A LEU* 3.7 38.6 - - + -
44A LEU* 4.3 2.9 - - + -
177A VAL* 3.8 15.9 - - + -
178A ALA 3.6 13.5 - - - +
179A PHE* 4.3 11.2 - - + -
195A LEU* 4.1 10.5 + - + -
196A THR* 1.3 73.4 - - - +
198A ARG* 1.3 62.9 + - - +
199A ILE* 3.8 20.6 - - + -
211A LEU* 3.9 17.7 - - + -
225B PHE* 4.9 7.4 - - + -
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Residues in contact with ARG 198 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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20A TYR* 3.2 24.9 + - - +
21A GLY 3.4 4.3 - - - -
22A GLU* 4.5 4.9 + - + -
177A VAL* 3.5 4.7 - - - +
178A ALA* 2.9 46.1 + - - +
179A PHE* 5.6 0.7 - - - -
180A GLN* 6.0 3.1 - - + +
196A THR* 4.6 7.4 - - + +
197A LEU* 1.3 74.4 - - - +
199A ILE* 1.3 61.0 + - - +
200A TRP* 3.4 37.9 - - + -
863C ASP* 4.3 24.0 + - - +
929C ARG* 6.0 0.6 - - - +
932C GLU* 3.1 33.7 + - - +
934C PHE* 3.4 42.7 - - + -
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Residues in contact with ILE 199 (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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20A TYR* 3.3 9.1 - - - -
21A GLY 2.9 36.9 + - - +
23A PHE* 4.0 16.4 - - + -
44A LEU* 3.6 27.6 - - + -
174A VAL* 4.5 4.3 - - + -
176A ARG 3.7 6.5 - - - +
177A VAL* 4.4 8.7 - - + -
197A LEU* 3.8 17.0 - - + +
198A ARG* 1.3 78.5 - - - +
200A TRP* 1.3 61.4 - - - +
201A THR* 3.8 22.9 - - + -
207A PRO* 3.6 31.6 - - + +
210A ALA* 4.9 3.8 - - + -
211A LEU* 4.1 12.1 - - + -
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Residues in contact with TRP 200 (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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19A GLU* 3.5 6.3 - - + +
20A TYR* 3.3 40.7 - + + -
174A VAL* 3.7 2.4 - - - +
175A ARG* 2.8 34.3 + - + -
176A ARG* 2.9 82.5 + - + +
178A ALA* 4.2 5.2 - - + -
198A ARG* 3.4 55.4 - - + -
199A ILE* 1.3 72.1 - - - +
201A THR* 1.3 57.3 + - - +
863C ASP 4.1 10.5 - - - -
932C GLU* 5.8 2.0 - - - -
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Residues in contact with THR 201 (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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18A ARG 3.0 18.4 + - - -
19A GLU* 2.6 28.7 + - - +
173A PRO 3.4 13.5 - - - +
174A VAL* 4.2 16.2 - - + -
175A ARG* 3.9 9.1 - - - +
199A ILE* 3.8 20.6 + - + -
200A TRP* 1.3 79.7 - - - +
202A ASP* 1.3 59.8 + - - +
203A GLY 3.5 0.7 + - - -
205A VAL* 2.9 27.7 + - + +
206A THR 4.3 0.7 - - - -
207A PRO* 3.7 12.6 - - + +
210A ALA* 4.5 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