Contacts of the strand formed by residues 183 - 187 (chain H) in PDB entry 2Q5E
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 PHE 183 (chain H).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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193G VAL* 4.8 1.6 - - - +
205G ARG* 3.4 16.9 + - - -
106H ILE* 4.0 23.8 - - + -
112H LEU* 4.1 16.4 - - + -
150H LEU* 3.8 36.1 - - + -
159H CYS* 3.6 14.1 - - + -
160H VAL 3.8 4.7 - - - -
161H LEU* 3.4 38.8 - - + +
174H THR* 3.8 22.0 - - + -
177H LEU* 5.1 3.8 - - + -
178H ASP* 3.1 25.4 + - + +
182H VAL* 1.3 72.7 - - + +
184H ARG* 1.3 65.1 + - - +
185H ALA 3.3 11.0 - - - +
186H ARG* 4.5 16.5 + - + +
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Residues in contact with ARG 184 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
189G ARG* 3.1 21.6 + - - +
190G GLU* 3.8 14.3 + - - +
192G CYS 2.6 39.7 + - - +
193G VAL* 3.4 11.2 - - + +
194G PHE* 2.9 23.8 + - - +
199G TYR* 3.8 24.5 + - - -
205G ARG* 4.0 10.3 - - - +
92H PRO* 3.9 22.0 - - - +
93H GLU 5.0 0.8 + - - -
95H THR* 3.6 32.0 - - - +
97H GLU* 5.0 7.9 - - - +
98H ASP* 5.3 7.9 - - - +
159H CYS 3.7 3.8 + - - +
182H VAL 3.2 8.1 + - - +
183H PHE* 1.3 74.5 - - - +
185H ALA* 1.3 60.0 + - - +
186H ARG* 5.4 0.4 - - - +
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Residues in contact with ALA 185 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
194G PHE* 3.3 17.9 - - + +
91H LEU* 3.6 31.9 - - + -
92H PRO* 5.4 1.1 - - + -
158H GLU* 5.7 2.5 - - - +
159H CYS 4.4 2.8 + - - -
160H VAL* 3.6 16.6 - - + -
161H LEU 3.2 21.1 + - - -
183H PHE* 3.8 4.9 - - - +
184H ARG* 1.3 80.5 - - + +
186H ARG* 1.3 65.1 + - - +
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Residues in contact with ARG 186 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
193G VAL* 5.6 4.7 - - + +
194G PHE 2.9 9.5 + - - +
195G HIS* 3.8 5.2 - - + -
196G GLN* 3.0 27.5 + - - +
202G ASP* 4.9 5.3 + - - -
205G ARG* 5.1 4.9 - - - +
225G PHE* 3.4 28.3 - - - -
161H LEU* 3.7 19.5 - - + -
171H ASP* 2.8 47.7 + - - +
174H THR* 3.5 28.8 + - - +
175H ASP* 2.6 34.7 + - - +
178H ASP* 5.0 5.5 + - - +
183H PHE* 4.5 13.1 + - + +
184H ARG 5.4 0.7 - - - +
185H ALA* 1.3 77.9 - - - +
187H LEU* 1.3 63.8 + - - +
188H PHE* 3.7 21.0 - - + -
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Residues in contact with LEU 187 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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194G PHE* 4.1 14.4 - - + -
196G GLN* 4.1 8.3 - - + -
90H LEU* 3.9 30.5 - - + +
91H LEU* 4.1 12.1 - - + -
160H VAL* 4.1 18.2 - - + -
161H LEU 2.9 13.1 + - - +
162H PHE* 3.8 39.3 - - + -
163H THR* 3.0 24.4 + - - +
186H ARG* 1.3 79.7 - - - +
188H PHE* 1.3 70.3 + - - +
191H SER* 3.9 13.7 - - - +
206H LEU* 4.2 10.5 - - + -
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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