Contacts of the strand formed by residues 203 - 207 (chain C) in PDB entry 3V9G
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 203 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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106C ILE* 3.6 38.6 - - + -
109C ALA* 4.9 6.5 - - + -
110C LEU* 4.3 5.4 - - + -
202C GLY* 1.3 74.6 - - - -
204C VAL* 1.3 69.5 + - - +
205C ALA* 4.2 5.6 - - + -
229C VAL* 3.5 22.2 - - + +
231C LEU* 4.4 15.0 - - + -
273C VAL* 3.9 23.6 - - + -
276C SER* 3.4 28.3 - - - -
278C HIS* 3.1 17.9 + - + -
279C LEU* 3.6 36.5 - - + +
280C CYS* 3.1 25.9 + - - -
281C GLY 3.7 1.0 + - - -
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Residues in contact with VAL 204 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
200C LEU* 4.5 6.7 - - + -
203C PHE* 1.3 79.4 - - - +
205C ALA* 1.3 71.9 + - - +
206C ALA* 4.7 0.7 - - + +
223C PRO* 4.3 22.7 - - + -
228C ASN* 4.0 31.4 - - + +
229C VAL 2.9 11.2 + - - +
230C VAL* 3.2 14.1 - - + +
231C LEU 2.9 24.3 + - - -
280C CYS* 4.0 10.1 - - - -
281C GLY* 3.5 19.7 - - - +
283C ASN* 4.4 9.0 - - + +
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Residues in contact with ALA 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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203C PHE* 4.1 6.0 - - + -
204C VAL* 1.3 73.2 - - - +
206C ALA* 1.3 60.1 + - - +
207C ILE* 4.0 1.6 - - + -
231C LEU 3.5 5.4 - - - +
269C PHE* 4.0 16.2 - - + -
273C VAL* 4.0 32.3 - - + -
279C LEU* 4.3 2.2 - - + -
281C GLY 3.0 12.5 + - - +
282C ILE* 3.4 11.2 - - + +
283C ASN 2.8 26.3 + - - +
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Residues in contact with ALA 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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204C VAL* 3.9 1.9 + - + -
205C ALA* 1.3 72.5 - - - +
207C ILE* 1.3 62.7 + - - +
208C SER 4.0 0.9 - - - -
219C LEU* 3.6 35.2 - - + +
220C ALA* 3.9 7.2 - - + +
230C VAL* 3.8 19.1 - - + -
231C LEU 2.9 7.9 + - - +
232C TRP* 3.5 8.4 - - + -
233C LYS 2.9 27.2 + - - -
269C PHE* 4.6 0.2 - - - -
283C ASN* 3.5 5.8 - - + -
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Residues in contact with ILE 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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205C ALA* 4.7 2.7 - - + +
206C ALA* 1.3 78.4 - - - +
208C SER* 1.3 64.3 + - - +
209C PRO* 4.5 1.0 - - - +
219C LEU* 3.3 12.7 - - - +
233C LYS* 3.7 23.1 - - + -
269C PHE* 3.6 32.8 - - + -
270C GLY* 5.6 6.1 - - - -
273C VAL* 5.6 1.8 - - + -
282C ILE* 4.2 24.5 - - + -
283C ASN 3.0 9.9 + - - +
284C PHE* 3.7 16.5 - - - -
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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