Contacts of the strand formed by residues 220 - 227 (chain A) in PDB entry 2Q7V
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 220 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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134A PHE* 3.7 22.9 - - + -
137A LYS 3.1 2.0 + - - -
138A GLY* 3.6 28.7 - - - +
139A VAL* 3.9 1.8 - - + +
214A ILE* 3.7 13.2 - - + -
215A GLN 3.4 8.5 - - - +
216A GLY* 4.2 0.4 - - - -
219A SER* 1.3 81.8 + - - +
221A SER* 1.3 61.7 + - - +
222A GLY 3.8 11.4 - - - +
238A THR* 3.5 19.3 - - + +
239A ASP* 3.4 29.5 + - - +
241A VAL* 3.8 22.4 - - + -
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Residues in contact with SER 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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215A GLN* 2.8 10.3 + - - +
216A GLY* 3.4 21.3 + - - -
217A ALA 5.1 0.4 - - - -
219A SER 3.5 2.0 + - - -
220A VAL* 1.3 74.4 - - - +
222A GLY* 1.3 60.4 + - - +
237A ALA* 3.6 10.0 - - - +
238A THR 2.9 23.8 + - - +
239A ASP* 5.6 1.6 - - - -
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Residues in contact with GLY 222 (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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214A ILE* 3.6 2.9 - - - +
215A GLN* 2.9 40.9 + - - +
220A VAL* 3.8 2.1 - - - +
221A SER* 1.3 81.4 + - - +
223A VAL* 1.3 67.9 + - - +
235A GLU* 3.7 4.3 - - - -
236A LEU 3.3 12.6 - - - -
237A ALA* 4.2 0.4 - - - -
238A THR* 3.4 7.8 + - - -
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Residues in contact with VAL 223 (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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156A VAL* 4.3 14.8 - - + -
181A ILE* 4.7 1.1 - - + -
211A VAL* 3.8 21.5 - - + -
213A GLU 3.2 9.4 - - - +
214A ILE* 4.1 4.5 - - + -
215A GLN* 4.1 1.1 - - - -
222A GLY* 1.3 79.2 - - - +
224A LYS* 1.3 60.1 + - - +
225A LEU* 3.9 15.7 - - + -
234A SER 3.9 0.5 - - - +
235A GLU* 3.3 8.3 + - - +
236A LEU* 2.8 60.0 + - + +
238A THR* 4.1 2.7 - - + -
241A VAL* 3.6 29.8 - - + -
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Residues in contact with LYS 224 (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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211A VAL* 3.6 3.5 - - - +
212A GLU* 2.7 50.8 + - + +
213A GLU* 2.9 41.7 + - + +
215A GLN* 3.7 8.9 - - - +
223A VAL* 1.3 74.6 - - - +
225A LEU* 1.3 58.0 + - - +
226A ARG* 6.1 1.7 - - - +
233A VAL* 3.7 28.0 - - + -
234A SER 3.4 6.5 - - - +
235A GLU* 3.6 13.0 + - + +
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Residues in contact with LEU 225 (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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181A ILE* 3.9 12.8 - - + -
206A ILE* 4.2 17.3 - - + -
209A THR* 3.6 20.2 - - + -
210A ALA 3.4 2.2 - - - -
211A VAL* 3.8 30.3 - - + -
212A GLU* 5.0 2.1 - - - +
223A VAL* 3.9 11.4 - - + +
224A LYS* 1.3 79.0 - - - +
226A ARG* 1.3 62.3 + - - +
232A GLU 4.3 0.7 - - - -
233A VAL* 3.3 11.4 - - - +
234A SER* 2.7 48.7 + - - +
236A LEU* 4.1 29.8 - - + -
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Residues in contact with ARG 226 (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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209A THR* 3.3 5.0 - - - -
210A ALA 2.9 32.8 + - - +
212A GLU* 3.2 46.1 + - + +
224A LYS* 6.1 1.8 - - - +
225A LEU* 1.3 74.6 - - - +
227A ASN* 1.3 68.0 + - - +
228A LEU* 3.4 13.4 + - + +
231A GLY* 3.0 39.7 + - - -
232A GLU 3.3 4.3 - - - -
233A VAL* 3.2 21.6 - - - +
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Residues in contact with ASN 227 (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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207A TRP 4.7 4.9 + - - -
208A ASP* 3.4 14.7 + - - +
209A THR* 4.1 9.9 + - - +
225A LEU 4.3 0.4 - - - -
226A ARG* 1.3 73.6 - - - +
228A LEU* 1.3 57.8 + - - +
229A LYS* 2.8 35.6 + - - +
230A THR* 2.9 32.8 + - - +
231A GLY* 2.7 32.7 + - - -
232A GLU* 2.9 26.5 + - + +
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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