Contacts of the strand formed by residues 201 - 205 (chain C) in PDB entry 3QI6
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 201 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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97C MET* 4.2 11.9 - - + -
179C LYS* 5.9 0.2 - - + -
180C VAL 3.3 2.8 + - - +
181C LEU* 3.3 19.5 - - + -
182C VAL 2.9 24.6 + - - -
195C LEU* 4.2 0.4 - - - -
199C ALA* 3.6 2.5 - - - +
200C ASP* 1.3 79.9 - - + +
202C VAL* 1.3 80.3 + - - +
221C LEU* 4.1 13.2 - - + -
222C VAL 3.5 9.4 - - - +
223C THR* 4.5 0.4 - - - +
228C LEU* 3.4 33.2 - - + -
232C PHE* 3.7 29.4 - - + -
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Residues in contact with VAL 202 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75C GLU* 3.7 8.7 - - - +
182C VAL 3.3 10.1 - - - +
184C ASN* 3.6 23.6 - - + -
194C PRO* 3.5 34.1 - - + -
195C LEU* 3.7 26.2 - - + -
201C VAL* 1.3 78.2 - - - +
203C LEU* 1.3 62.0 + - - +
204C HIS* 3.7 19.5 - - + +
220C ALA 3.9 0.3 - - - +
221C LEU* 3.4 4.9 - - - -
222C VAL* 2.9 44.3 + - + +
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Residues in contact with LEU 203 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86C GLY 4.4 7.6 - - - +
89C ALA* 3.8 7.4 - - + +
90C ALA* 3.3 44.6 - - + +
152C TRP* 3.7 16.8 - - + -
181C LEU* 4.0 17.7 - - + +
182C VAL 2.9 6.2 + - - +
183C ASP* 3.4 25.5 - - - +
184C ASN 2.9 27.9 + - - -
185C THR* 4.4 0.4 - - - +
202C VAL* 1.3 73.2 - - - +
204C HIS* 1.3 80.0 + - - +
205C SER 4.0 2.0 - - - +
208C LLP 4.7 6.7 - - + -
220C ALA 3.4 7.4 - - - +
221C LEU* 3.8 13.9 - - + -
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Residues in contact with HIS 204 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71C LEU* 5.9 1.8 - - + -
75C GLU* 2.6 36.5 + - + -
86C GLY* 4.0 2.6 - - - -
184C ASN* 3.3 38.1 + - + -
185C THR* 3.9 6.6 + - - -
188C SER* 4.0 0.8 - - - -
189C PRO* 3.6 20.2 - - + +
202C VAL* 3.7 10.3 - - + +
203C LEU* 1.3 82.8 - - - +
205C SER* 1.4 60.1 + - - +
206C THR* 3.6 8.7 + - + -
210C ILE* 3.6 25.4 - - + +
219C GLY* 3.2 5.4 - - - -
220C ALA* 2.9 44.7 + - + +
222C VAL* 5.3 4.9 - - + -
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Residues in contact with SER 205 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86C GLY* 3.9 3.4 - - - -
185C THR* 3.1 23.9 + - - +
203C LEU* 4.0 2.6 - - - +
204C HIS* 1.4 69.9 + - - +
206C THR* 1.4 62.2 + - - +
207C THR* 3.1 13.5 + - - -
208C LLP 2.9 75.6 + - - +
209C TYR 4.6 0.9 + - - -
210C ILE* 5.1 1.9 + - - +
218C GLY 3.7 4.9 - - - -
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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