Contacts of the strand formed by residues 200 - 207 (chain C) in PDB entry 2JJD
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 GLU 200 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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196C ASP* 3.6 1.9 - - - -
197C GLY 2.9 29.0 + - - +
198C TYR 3.1 8.3 + - - +
199C LYS* 1.3 79.8 - - - +
201C LYS* 1.3 75.5 + - - +
202C ASN 3.3 0.5 + - - +
203C LYS* 3.5 29.2 + - + +
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Residues in contact with LYS 201 (chain C).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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196C ASP* 3.4 14.8 - - - +
200C GLU* 1.3 78.8 - - - +
202C ASN* 1.3 74.6 + - - +
203C LYS 3.4 0.2 + - - -
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Residues in contact with ASN 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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194C TYR* 3.3 50.2 - - + +
195C ILE 3.8 7.2 - - - -
196C ASP* 2.7 24.8 + - - +
200C GLU* 3.3 1.0 + - - +
201C LYS* 1.3 80.1 - - - +
203C LYS* 1.3 64.5 + - - +
204C PHE 3.2 5.3 + - - -
330C PRO* 3.6 15.8 - - + +
373C GLN* 4.9 1.6 + - - -
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Residues in contact with LYS 203 (chain C).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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195C ILE 3.3 3.2 + - - -
197C GLY* 3.8 15.7 - - - +
200C GLU* 3.5 34.5 + - + +
201C LYS 3.4 2.8 + - - -
202C ASN* 1.3 76.0 - - - +
204C PHE* 1.3 84.4 + - + +
330C PRO* 3.4 4.9 - - - +
331C ILE* 3.0 25.8 + - - +
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Residues in contact with PHE 204 (chain C).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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194C TYR* 3.6 5.7 - - - -
195C ILE* 3.0 31.9 + - + +
196C ASP 4.4 1.8 - - - -
197C GLY* 4.3 10.1 - - - -
202C ASN 4.2 2.9 - - - -
203C LYS* 1.3 96.4 - - + +
205C ILE* 1.3 66.5 + - - +
330C PRO* 4.0 4.8 - - - +
331C ILE* 3.4 30.3 - - + +
333C VAL* 3.7 20.2 - - + -
345C PHE* 4.1 18.6 - + - -
346C ILE* 3.9 46.2 - - + -
349C ASP* 4.2 22.2 - - + -
350C ALA 5.7 0.7 - - - -
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Residues in contact with ILE 205 (chain C).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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176C VAL* 3.6 26.5 - - + -
192C ALA* 3.8 27.4 - - + -
193C SER 3.5 4.3 - - - +
194C TYR* 3.9 7.0 - - + -
204C PHE* 1.3 78.9 - - - +
206C ALA* 1.3 59.7 + - - +
207C ALA* 3.5 6.4 + - + -
221C MET* 3.9 18.2 - - + -
225C GLN* 3.8 20.9 - - + -
330C PRO* 3.7 27.4 - - + -
331C ILE 2.8 13.5 + - - +
332C VAL* 3.6 12.5 - - + -
333C VAL* 2.8 31.1 + - - +
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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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192C ALA* 3.4 1.6 - - - -
193C SER 2.9 28.9 + - - +
195C ILE* 3.6 31.7 - - + +
204C PHE* 4.1 1.4 - - - +
205C ILE* 1.3 69.2 - - - +
207C ALA* 1.3 59.3 + - - +
333C VAL 3.4 5.8 - - - -
338C GLY 3.8 18.6 - - - +
342C THR* 4.1 9.4 - - - +
346C ILE* 4.3 6.3 - - + -
374C ARG* 3.5 13.9 + - - -
377C MET* 4.3 1.3 - - + -
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Residues in contact with ALA 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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190C ILE* 5.9 1.1 - - + -
191C ASN 3.7 5.8 - - - +
192C ALA* 3.6 17.5 - - + -
205C ILE* 3.5 9.6 + - + -
206C ALA* 1.3 74.8 - - - +
208C GLN* 1.3 65.3 + - - +
218C PHE* 4.6 3.6 - - + -
221C MET* 4.3 13.5 - - + -
332C VAL* 4.4 5.4 - - + -
333C VAL 3.0 10.3 + - - +
334C HIS* 3.0 29.5 - - + +
338C GLY* 3.5 11.6 - - - -
374C ARG* 4.6 0.2 - - - -
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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