Contacts of the strand formed by residues 198 - 204 (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 THR 198 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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51A GLN* 5.9 0.3 + - - -
171A TYR* 4.6 1.4 - - - -
188A LEU* 4.4 3.7 - - + +
193A LEU* 5.3 1.6 - - + -
194A SER 3.3 24.2 - - - +
195A ALA* 2.8 25.7 + - - +
196A TYR 3.4 1.4 + - - +
197A ASN* 1.3 89.7 - - - +
199A ARG* 1.3 69.2 + - - +
214A VAL* 3.9 20.1 - - + +
215A ARG 3.3 5.2 - - - -
216A LEU* 3.8 21.8 - - + -
250A ASP* 5.8 0.2 - - - -
325A ARG* 3.3 28.8 + - - +
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Residues in contact with ARG 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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50A LEU* 3.3 28.3 + - - +
51A GLN* 5.1 3.6 - - - +
170A THR* 2.9 30.5 + - - -
171A TYR* 3.4 23.3 - - + +
198A THR* 1.3 80.1 - - - +
200A LEU* 1.3 61.3 + - - +
201A PHE* 3.7 25.2 - - + -
213A GLU 3.5 1.7 - - - +
214A VAL* 3.5 6.7 - - - +
215A ARG* 3.1 30.6 + - - +
250A ASP* 3.0 36.7 + - - +
251A TYR* 3.2 27.2 + - - +
325A ARG* 4.2 5.2 - - - +
722A ASP* 3.5 21.2 + - - -
726A TRP* 4.1 8.9 - - - -
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Residues in contact with LEU 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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171A TYR 2.9 7.9 + - - -
172A PHE* 3.1 54.8 - - + +
173A SER* 3.1 4.0 + - - -
176A CYS* 4.3 8.4 - - - -
180A ASP 3.9 14.6 - - - +
184A ALA* 3.6 29.6 - - + -
199A ARG* 1.3 73.5 - - - +
201A PHE* 1.3 66.2 + - - +
212A TYR* 4.2 29.4 - - + -
213A GLU 3.5 15.0 - - - +
214A VAL* 3.8 20.9 - - + -
244A PHE* 4.4 0.4 - - + -
325A ARG* 4.0 7.6 - - - +
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Residues in contact with PHE 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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170A THR 4.5 4.0 - - - -
173A SER* 3.7 9.6 - - - -
199A ARG* 3.7 42.6 - - + -
200A LEU* 1.3 84.8 - - - +
202A LYS* 1.3 61.5 + - - +
203A GLU* 4.1 2.8 + - + +
211A TYR 3.5 2.9 - - - +
212A TYR* 3.5 2.1 - - - -
213A GLU* 2.9 54.0 + - - +
215A ARG* 3.4 48.0 - - + -
722A ASP* 5.0 0.4 - - - -
725A PHE* 3.4 48.2 - + + -
726A TRP* 4.3 16.2 - + - -
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Residues in contact with LYS 202 (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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173A SER* 2.9 13.0 + - - -
175A ASN* 2.8 68.7 + - - +
176A CYS* 3.9 9.6 - - - +
177A THR* 5.6 0.8 - - - +
180A ASP* 3.1 36.2 + - - -
201A PHE* 1.3 72.0 - - - +
203A GLU* 1.3 63.5 + - - +
204A VAL* 4.7 7.4 - - + -
210A PRO* 3.7 27.1 - - + +
211A TYR 3.3 5.8 - - - +
212A TYR* 3.7 19.7 - - + -
725A PHE* 5.6 0.2 - - - -
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Residues in contact with GLU 203 (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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175A ASN* 4.7 1.1 - - - +
201A PHE* 4.1 2.2 - - + +
202A LYS* 1.3 78.6 - - - +
204A VAL* 1.3 63.4 + - - +
211A TYR* 2.7 46.7 + - + +
213A GLU* 4.9 4.2 - - - +
724A ARG* 2.4 49.8 + - - +
725A PHE* 3.6 16.6 - - + -
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Residues in contact with VAL 204 (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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175A ASN* 5.1 9.1 - - - +
202A LYS* 4.7 9.6 - - + -
203A GLU* 1.3 78.9 - - - +
205A ASP* 1.3 66.4 + - - +
208A GLY* 3.7 25.4 - - - +
209A LYS 3.5 3.6 - - - -
210A PRO* 4.1 13.2 - - + -
211A TYR* 5.5 0.2 - - - -
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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