Contacts of the strand formed by residues 210 - 217 (chain A) in PDB entry 5E2Q
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 PRO 210 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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202A LYS* 3.7 28.7 - - + +
203A GLU 3.7 5.2 - - - +
204A VAL* 4.1 7.4 - - + -
208A GLY 3.5 6.5 - - - +
209A LYS* 1.3 92.7 - - + +
211A TYR* 1.3 61.2 + - - +
212A TYR* 4.2 21.1 + - + +
242A SER* 5.1 5.6 - - - +
243A PRO* 3.5 20.8 - - - +
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Residues in contact with TYR 211 (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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201A PHE 3.5 1.6 - - - +
202A LYS* 3.3 4.9 - - - -
203A GLU* 2.7 43.5 + - + +
205A ASP* 3.2 32.2 + - + -
209A LYS* 3.6 25.1 + - + +
210A PRO* 1.3 75.4 - - - +
212A TYR* 1.3 63.4 + - - +
213A GLU* 5.5 0.2 - - - +
243A PRO* 3.6 35.7 - - + +
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Residues in contact with TYR 212 (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 ASP* 2.7 41.4 + - + -
183A LEU* 4.0 17.2 - - + +
200A LEU* 4.2 20.6 - - + -
201A PHE 3.5 1.3 - - - -
202A LYS* 3.7 31.5 - - + -
210A PRO* 4.2 22.8 - - + +
211A TYR* 1.3 75.7 - - - +
213A GLU* 1.3 61.0 + - - +
242A SER* 4.0 24.5 - - - -
243A PRO 3.1 10.6 + - - +
244A PHE* 3.4 41.3 - + + -
245A GLN* 2.9 27.1 + - - +
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Residues in contact with GLU 213 (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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199A ARG 3.5 1.2 - - - +
200A LEU* 3.5 6.2 - - - +
201A PHE* 2.9 59.3 + - + +
203A GLU* 4.9 5.4 - - - +
212A TYR* 1.3 74.0 - - - +
214A VAL* 1.3 66.1 + - - +
215A ARG* 3.2 25.4 + - - +
245A GLN* 3.3 15.9 - - + +
247A THR* 2.8 37.4 + - + +
724A ARG* 4.9 2.1 + - - -
725A PHE* 4.6 4.2 - - - -
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Residues in contact with VAL 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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184A ALA* 5.4 1.1 - - + -
187A PHE* 4.2 12.1 - - + -
188A LEU* 3.9 25.4 - - + -
193A LEU* 4.8 2.2 - - + -
198A THR* 3.9 25.1 - - + +
199A ARG 3.5 4.3 - - - +
200A LEU* 3.8 18.2 - - + -
213A GLU* 1.3 72.1 - - - +
215A ARG* 1.3 59.0 + - - +
216A LEU* 3.7 12.0 + - + +
244A PHE* 4.1 20.4 - - + -
245A GLN 2.8 12.1 + - - +
246A VAL* 3.4 9.2 - - + -
247A THR* 3.0 26.3 + - - +
325A ARG* 6.2 0.7 - - - +
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Residues in contact with ARG 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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197A ASN 3.8 0.2 - - - +
198A THR* 3.3 3.3 - - - -
199A ARG* 3.1 29.4 + - - +
201A PHE* 3.4 31.9 - - + -
213A GLU* 3.2 21.9 + - - +
214A VAL* 1.3 72.0 - - - +
216A LEU* 1.3 70.6 + - - +
247A THR* 3.3 17.7 - - - +
248A ARG 4.3 9.9 - - - +
249A GLY 5.0 0.7 - - - -
250A ASP* 3.2 38.0 + - + +
722A ASP* 3.2 37.6 + - - -
724A ARG* 5.1 2.4 - - - +
725A PHE* 3.6 14.6 - - - -
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Residues in contact with LEU 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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193A LEU* 4.2 22.4 - - + -
197A ASN* 3.4 10.5 - - - +
198A THR* 3.8 24.5 - - + -
214A VAL* 3.7 16.2 - - + +
215A ARG* 1.3 73.4 - - - +
217A ALA* 1.3 60.8 - - - +
230A VAL* 4.0 20.6 - - + -
233A LYS* 5.7 1.3 - - + -
246A VAL* 3.8 16.2 - - + -
247A THR 2.8 22.3 + - - +
248A ARG* 3.2 17.0 - - + -
249A GLY 3.2 0.5 + - - -
250A ASP* 3.2 22.8 + - - +
288A GLY* 3.3 24.9 - - - +
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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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197A ASN* 2.9 23.4 + - + +
216A LEU* 1.3 70.1 - - - +
218A SER* 1.3 65.2 + - - +
250A ASP* 3.7 8.1 - - + +
251A TYR* 3.8 19.7 - - + -
255A LEU* 3.8 6.5 - - + +
284A SER 4.1 4.3 - - - +
285A PHE* 4.8 1.2 - - - -
288A GLY* 3.5 14.0 - - - -
314A PHE* 3.5 37.3 - - + -
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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