Contacts of the strand formed by residues 213 - 221 (chain A) in PDB entry 2MKJ
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 TYR 213 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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64A SER* 4.5 4.9 - - - +
66A LYS* 3.2 42.2 - - + -
68A PHE* 6.1 0.7 - - - +
112A PHE* 6.0 2.4 - - - -
152A ARG 6.0 1.3 - - - -
153A PRO 5.1 2.5 - - - -
154A TRP* 3.6 31.6 - + + -
182A ARG* 4.6 23.2 + - + +
183A PRO* 4.9 5.9 - - - +
207A THR* 3.6 3.8 - - - -
208A ASP* 2.8 30.5 + - - +
211A LEU* 3.6 26.8 - - + +
212A LYS* 1.3 77.7 - - - +
214A PRO* 1.3 104.6 - - + +
215A LYS* 3.7 5.8 - - + +
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Residues in contact with PRO 214 (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 TRP* 3.3 51.1 - - + -
181A PRO 5.2 0.9 - - - +
182A ARG* 3.6 32.4 - - + +
184A LEU 4.6 0.9 - - - +
205A ILE* 3.9 9.0 - - + -
206A ASP 3.3 13.0 - - - +
207A THR* 3.6 1.1 - - + -
213A TYR* 1.3 122.6 - - + +
215A LYS* 1.3 64.5 + - - +
216A GLY 5.0 2.9 - - - +
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Residues in contact with LYS 215 (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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66A LYS* 5.4 6.3 - - - +
182A ARG* 2.9 49.2 + - - +
206A ASP* 3.1 21.2 + - - +
207A THR 4.6 0.4 - - - -
208A ASP* 3.0 50.6 + - + +
211A LEU* 5.0 6.3 - - - +
213A TYR* 3.7 4.4 - - + +
214A PRO* 1.3 80.2 - - - +
216A GLY* 1.3 58.4 + - - +
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Residues in contact with GLY 216 (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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180A VAL* 3.1 26.3 - - - +
181A PRO 4.3 4.0 - - - +
182A ARG* 4.1 8.1 - - - +
205A ILE* 5.1 1.2 - - - +
206A ASP* 4.1 8.8 + - - +
214A PRO* 5.4 1.6 - - - +
215A LYS* 1.3 81.1 + - - +
217A ALA* 1.3 68.1 + - - +
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Residues in contact with ALA 217 (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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176A PHE* 3.5 35.4 - - + -
177A VAL 3.7 4.5 - - - +
178A GLY* 3.9 8.1 - - - -
179A GLY 4.6 3.8 - - - +
180A VAL* 3.7 15.4 + - - +
205A ILE* 3.8 0.5 - - - +
206A ASP* 2.8 34.4 + - + +
216A GLY* 1.3 79.6 - - - +
218A GLY* 1.3 53.0 + - - +
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Residues in contact with GLY 218 (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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176A PHE* 3.6 11.1 - - - -
177A VAL* 2.8 34.6 + - - +
180A VAL* 4.2 0.8 - - - +
189A LEU* 4.2 3.1 - - - -
204A GLY 3.6 1.6 - - - -
205A ILE* 3.6 13.2 - - - -
206A ASP* 3.6 14.1 - - - -
217A ALA* 1.3 74.9 - - - +
219A ARG* 1.3 63.6 + - - +
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Residues in contact with ARG 219 (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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169A LEU* 3.8 32.3 - - - +
170A ASP 5.3 0.2 - - - +
174A THR* 3.3 37.9 + - + +
175A ILE 3.4 14.4 - - - +
176A PHE* 4.6 2.2 - - + -
177A VAL* 4.2 4.0 - - - +
189A LEU* 4.2 2.0 - - - +
202A TYR* 4.4 18.6 - - + +
203A ALA* 3.6 0.2 - - - -
204A GLY 2.9 37.0 + - - +
205A ILE 5.2 5.6 - - - +
206A ASP* 5.5 2.7 - - - +
218A GLY* 1.3 75.9 - - - +
220A VAL* 1.3 68.3 + - - +
221A ALA* 5.6 0.2 - - - +
253A TYR* 4.3 26.7 + - + -
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Residues in contact with VAL 220 (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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174A THR* 3.5 5.5 - - - +
175A ILE* 2.8 53.0 + - + +
177A VAL* 4.3 12.1 - - + -
189A LEU* 3.5 26.2 - - + -
190A ALA* 5.7 0.7 - - - -
193A MET* 5.6 7.4 - - + -
200A VAL* 4.3 7.9 - - + -
202A TYR* 3.3 15.0 - - - +
203A ALA* 3.7 12.8 - - + +
219A ARG* 1.3 79.8 - - - +
221A ALA* 1.3 64.1 + - - +
222A PHE* 3.8 21.8 - - + -
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Residues in contact with ALA 221 (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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167A GLN* 4.6 4.7 - - - +
168A PRO 4.6 6.1 - - - +
169A LEU* 4.4 16.8 - - + -
170A ASP 5.0 0.2 - - - +
173A LYS* 3.3 15.3 - - + +
174A THR* 4.3 12.1 - - + +
201A CYS* 3.5 8.0 - - - +
202A TYR* 2.8 46.1 + - + +
219A ARG* 5.6 0.2 - - - +
220A VAL* 1.3 75.0 - - - +
222A PHE* 1.3 63.5 + - - +
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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