Contacts of the strand formed by residues 184 - 188 (chain A) in PDB entry 2C53
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 184 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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81A ARG 3.1 12.9 + - - +
82A VAL* 3.2 15.2 - - + +
83A VAL* 2.8 34.3 + - - +
183A LEU* 1.3 73.8 - - - +
185A PHE* 1.3 67.9 + - - +
186A MET* 4.3 1.8 - - + -
204A CYS* 3.4 10.5 - - + +
206A LEU* 4.1 12.3 - - + -
228A ALA* 3.8 37.7 - - + +
231A TYR* 3.6 29.4 - - + -
232A LEU* 4.1 12.8 - - + -
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Residues in contact with PHE 185 (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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83A VAL* 3.4 28.0 - - + -
173A ILE* 3.8 26.7 - - + -
177A ALA* 4.3 13.2 - - + -
183A LEU* 4.0 24.7 - - + -
184A VAL* 1.3 76.7 - - - +
186A MET* 1.3 61.5 + - - +
187A LEU* 3.9 14.6 - - + -
196A ILE* 4.0 10.5 - - + -
198A PRO* 3.6 40.4 - - + -
203A HIS* 3.8 26.9 - + + -
204A CYS 2.7 13.9 + - - +
205A VAL* 4.4 5.4 - - + -
206A LEU* 2.8 33.3 + - - +
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Residues in contact with MET 186 (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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82A VAL* 3.9 11.4 - - + -
83A VAL 2.9 7.9 + - - +
84A ILE* 3.7 27.3 - - + +
85A ILE 3.4 24.3 + - - +
184A VAL* 4.3 3.8 - - + -
185A PHE* 1.3 76.1 - - - +
187A LEU* 1.3 62.9 + - - +
188A TRP* 3.7 39.5 + - + +
206A LEU* 3.4 6.7 - - + -
224A HIS* 3.5 42.6 - - + +
225A PHE* 4.0 5.4 - - + +
228A ALA* 3.5 20.4 - - + -
242A TRP* 3.8 20.4 - - + -
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Residues in contact with LEU 187 (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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85A ILE* 3.8 25.8 - - + -
185A PHE* 4.3 16.2 - - + -
186A MET* 1.3 78.4 - - - +
188A TRP* 1.3 62.9 + - - +
192A ALA* 4.0 14.6 - - + +
193A GLN* 3.1 31.8 + - + +
196A ILE* 3.6 27.6 - - + +
198A PRO* 4.4 6.3 - - + -
205A VAL* 3.7 26.2 - - + -
206A LEU 2.8 12.7 + - - +
207A LYS* 3.2 9.7 - - + -
208A PHE 3.1 21.5 + - - -
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Residues in contact with TRP 188 (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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84A ILE* 3.7 32.5 - - + -
85A ILE 5.0 6.2 + - - +
101A PHE* 4.0 25.4 - + + -
116A VAL* 3.8 26.9 - - + -
138A TRP* 5.6 0.7 - + - -
186A MET* 3.7 22.9 + - + +
187A LEU* 1.3 81.4 - - - +
189A GLY* 1.3 61.4 + - - +
192A ALA* 3.7 14.4 + - - +
208A PHE* 3.4 13.2 - - + -
209A SER 3.7 9.9 - - - +
210A ASN* 4.2 10.4 + - - -
211A PRO* 3.8 13.8 - - + +
219A PHE* 3.6 19.4 - + - -
222A CYS* 4.3 0.4 - - - -
224A HIS* 3.0 33.6 + + + -
225A PHE* 3.6 31.6 - + - -
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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