Contacts of the strand formed by residues 202 - 207 (chain C) in PDB entry 3H3B
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 ALA 202 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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89B ASN* 4.6 3.1 + - - +
157B LEU* 6.0 0.6 - - - +
182C ILE* 3.6 31.2 - - + -
194C TYR* 3.2 21.3 - - + -
198C PHE* 3.0 12.0 + - + +
199C LYS 4.0 7.4 - - - +
201C LYS* 1.3 77.9 - - + +
203C ALA* 1.3 62.6 + - - +
204C PHE* 4.3 4.0 - - + -
215C MET* 4.0 9.4 - - + -
216C GLN 3.4 4.0 - - - -
217C LEU* 3.8 16.2 - - + -
218C ASN* 5.6 0.4 - - - -
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Residues in contact with ALA 203 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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89B ASN* 4.4 10.3 - - - +
157B LEU* 4.7 8.1 - - + -
159B LEU* 3.6 37.8 - - + +
194C TYR* 3.3 7.0 - - - +
202C ALA* 1.3 77.0 - - - +
204C PHE* 1.3 64.7 + - - +
205C THR* 4.0 1.0 + - - +
214C PHE 3.9 0.3 - - - +
215C MET* 3.4 2.4 - - - -
216C GLN* 2.9 39.1 + - + +
218C ASN* 5.9 0.9 - - - +
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Residues in contact with PHE 204 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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90B TYR* 4.1 9.0 + - - -
159B LEU* 5.0 1.7 - - - +
161B LEU* 4.4 2.6 - - - +
170C TRP* 3.3 37.2 - + + -
182C ILE* 4.0 9.2 - - + -
183C GLY* 3.6 33.4 - - - -
184C HIS* 3.6 17.3 - - - -
185C ILE* 3.8 19.9 - - + +
192C SER* 3.6 23.4 + - - +
193C THR 3.8 2.7 - - - -
194C TYR* 2.7 45.2 + + - -
202C ALA* 4.3 3.4 - - + -
203C ALA* 1.3 77.6 - - - +
205C THR* 1.3 67.9 + - - +
214C PHE 3.4 4.7 - - - +
215C MET* 3.8 21.8 - - + -
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Residues in contact with THR 205 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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90B TYR* 4.1 7.9 - - - +
159B LEU* 4.5 18.6 - - + -
160B THR 3.9 18.2 - - - +
161B LEU* 3.9 21.8 - - + -
153C LYS* 4.4 7.3 + - - -
185C ILE* 4.2 4.7 - - - +
203C ALA 4.0 1.5 + - - +
204C PHE* 1.3 79.3 - - - +
206C VAL* 1.3 68.3 + - - +
213C ALA* 3.6 0.9 - - - +
214C PHE* 2.8 56.4 + - - +
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Residues in contact with VAL 206 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
161B LEU* 3.8 24.3 - - + +
163C PHE* 4.2 16.2 - - + -
185C ILE* 3.9 34.8 - - + -
186C SER 4.6 0.2 - - - +
187C SER* 3.7 29.2 - - - +
190C ALA* 4.5 7.0 - - + -
205C THR* 1.3 81.5 - - - +
207C ASP* 1.3 61.4 + - - +
208C THR* 4.1 4.7 + - - +
212C THR 3.6 5.8 - - - +
213C ALA* 3.9 15.3 - - + -
214C PHE* 4.7 3.8 - - - +
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Residues in contact with ASP 207 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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163C PHE* 4.1 2.6 - - - -
206C VAL* 1.3 73.9 - - - +
208C THR* 1.3 68.2 + - - +
209C SER* 3.3 16.6 + - - -
210C SER* 2.7 31.0 + - - +
211C SER* 3.1 18.0 + - - -
212C THR 2.8 20.0 + - - +
214C PHE* 4.4 11.6 - - + -
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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