Contacts of the strand formed by residues 199 - 206 (chain C) in PDB entry 6CU0
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 199 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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142C TYR* 3.8 2.0 - - - -
144C PHE* 3.6 31.9 - + + -
145C PHE 3.5 10.1 - - - -
146C GLN* 4.1 13.7 - - + -
181C LEU* 3.8 6.8 - - - +
198C GLY* 1.3 74.8 - - - +
200C GLN* 1.3 73.1 + - - +
142E TYR* 3.2 21.5 - - - -
199E PHE* 3.4 44.2 - + - +
200E GLN* 4.6 3.6 - - - +
201E GLY 3.1 34.3 - - - -
199F PHE* 3.5 35.3 - + + +
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Residues in contact with GLN 200 (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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144C PHE* 3.1 3.3 - - - +
145C PHE* 2.8 40.5 + - + +
179C LEU* 3.7 16.3 - - + +
180C ALA 2.9 34.9 + - - +
181C LEU* 4.0 16.3 - - + +
199C PHE* 1.3 84.4 + - - +
201C GLY* 1.3 62.0 + - - +
202C ARG* 4.1 4.9 + - - -
146F GLN* 3.1 44.8 + - + +
148F GLU* 6.3 1.4 - - - +
197F PHE* 5.3 10.9 - - - +
199F PHE* 4.6 5.1 - - - +
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Residues in contact with GLY 201 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
142C TYR* 3.9 14.1 - - - -
143C VAL 3.1 13.5 - - - -
144C PHE* 3.7 8.1 - - - -
179C LEU* 4.1 1.8 - - - -
199C PHE* 3.8 4.9 - - - -
200C GLN* 1.3 78.7 - - - +
202C ARG* 1.3 62.0 + - - +
144F PHE* 3.9 3.8 - - - -
146F GLN* 3.0 17.2 - - - +
199F PHE* 3.4 15.8 - - - -
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Residues in contact with ARG 202 (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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142C TYR* 3.9 8.4 - - - -
143C VAL* 2.9 30.7 + - - +
178C ALA 3.9 16.7 + - - -
179C LEU* 3.4 25.7 - - + +
180C ALA 5.7 0.2 - - - +
200C GLN* 4.1 6.5 + - - -
201C GLY* 1.3 73.4 - - - +
203C LEU* 1.3 69.7 + - - +
204C LEU* 3.6 10.7 + - + +
94F GLN* 3.4 23.2 - - - +
96F VAL* 5.0 3.0 - - - +
117F GLY* 5.0 10.5 - - - -
144F PHE* 3.9 12.6 - - + -
146F GLN* 3.0 31.3 - - - +
231F GLY 3.3 25.5 + - - -
232F ALA* 4.5 4.0 + - - +
234F VAL* 3.5 15.4 - - + +
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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
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140C VAL* 4.0 13.7 - - + -
141C TYR 3.2 11.0 - - - +
142C TYR* 4.0 14.1 - - + +
202C ARG* 1.3 71.8 - - - +
204C LEU* 1.3 67.2 + - - +
240C VAL* 4.0 12.1 - - + -
92F PHE* 4.0 17.0 - - + -
93F ALA 3.4 27.6 - - - +
94F GLN* 2.9 38.8 + - + +
117F GLY* 4.9 1.7 - - - +
119F SER* 5.1 3.6 - - - +
144F PHE* 4.2 9.9 - - + -
237F LEU 3.8 11.9 - - - +
238F PHE* 3.8 24.9 - - + -
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Residues in contact with LEU 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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140C VAL* 4.3 2.9 - - - -
141C TYR 2.8 31.5 + - - +
143C VAL* 3.7 28.3 - - + -
165C LEU* 3.7 26.7 - - + -
167C LEU* 4.9 3.6 - - + -
178C ALA* 3.9 32.1 - - + +
179C LEU* 5.1 1.8 - - + -
202C ARG* 4.1 17.3 - - + +
203C LEU* 1.3 83.1 - - - +
205C HIS* 1.3 62.1 + - - +
206C LEU* 3.3 25.4 + - + +
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Residues in contact with HIS 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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139C GLY 3.5 7.0 - - - +
140C VAL* 4.0 18.1 - - + +
167C LEU* 5.1 4.9 - - - +
203C LEU 4.3 0.2 - - - -
204C LEU* 1.3 69.5 - - - +
206C LEU* 1.3 66.4 + - - +
207C SER* 4.2 1.2 + - - -
210C GLN* 4.9 3.5 + - - -
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Residues in contact with LEU 206 (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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135C VAL* 3.9 26.2 - - + -
138C ALA* 3.5 2.3 - - - +
139C GLY 2.8 36.6 + - - +
141C TYR* 3.6 33.7 - - + -
143C VAL* 4.6 3.1 - - + -
167C LEU* 4.2 28.7 - - + -
204C LEU* 3.8 27.6 - - + +
205C HIS* 1.3 79.5 - - - +
207C SER* 1.3 66.6 + - - +
210C GLN* 4.3 9.6 - - + +
237C LEU* 4.3 12.3 - - + -
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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