Contacts of the strand formed by residues 198 - 203 (chain S) in PDB entry 5JBA
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 PRO 198 (chain S).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29S TRP* 4.0 17.0 - - + +
30S GLN* 3.2 21.8 - - - +
44S GLY 3.9 2.9 - - - +
45S SER* 3.1 26.2 - - - +
137S TYR 3.5 1.1 - - - +
138S VAL* 3.3 24.1 - - - +
139S SER* 3.6 18.3 + - - +
197S GLY* 1.3 86.0 - - - +
199S HIS* 1.3 59.4 + - - +
200S VAL* 3.6 22.9 - - + -
209S LEU* 3.9 4.9 - - + -
211S GLY 3.9 4.5 - - - +
212S VAL* 5.9 0.2 - - + -
213S ILE* 4.0 3.3 - - - +
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Residues in contact with HIS 199 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
131S LEU* 3.8 21.3 - - + -
135S SER 5.1 0.9 - - - -
136S GLY* 3.8 28.7 + - - -
137S TYR 3.3 4.3 - - - -
138S VAL* 3.7 22.4 - - + -
160S VAL* 4.1 15.7 + - + +
162S LEU* 6.0 2.0 + - + +
181S PHE* 3.7 23.3 - + - -
183S ALA* 4.6 3.0 - - + +
198S PRO* 1.3 72.0 - - - +
200S VAL* 1.3 62.4 + - - +
201S THR* 4.3 2.2 - - - -
209S LEU* 3.7 1.0 - - - +
210S THR* 2.8 53.0 + - - -
211S GLY* 2.9 28.8 + - - +
228S TYR* 4.1 11.7 - + + -
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Residues in contact with VAL 200 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27S PHE* 5.3 4.9 - - + -
29S TRP* 4.0 13.0 - - + +
121S ILE* 3.6 29.6 - - + -
136S GLY* 3.1 4.6 - - - -
137S TYR* 2.7 58.1 + - + +
198S PRO* 3.6 23.6 - - + -
199S HIS* 1.3 78.9 + - - +
201S THR* 1.3 63.5 + - - +
202S GLU* 4.2 1.1 + - + +
207S SER* 4.3 16.6 - - - +
208S PHE 3.3 9.6 - - - +
209S LEU* 4.2 2.0 - - + -
210S THR* 3.6 0.4 - - - -
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Residues in contact with THR 201 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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130S PHE* 3.4 33.9 + - + +
131S LEU* 4.4 1.2 - - - -
133S PHE* 4.2 16.2 - - + -
135S SER 4.0 18.3 + - - +
199S HIS* 4.3 5.5 - - - -
200S VAL* 1.3 72.9 + - - +
202S GLU* 1.3 69.0 + - - +
203S VAL* 3.6 4.7 + - + +
206S THR 3.7 0.3 - - - +
207S SER* 3.4 2.3 - - - -
208S PHE* 2.9 33.3 + - - +
210S THR* 2.9 30.9 + - - +
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Residues in contact with GLU 202 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
135E VAL* 5.8 4.2 - - - +
133S PHE* 5.3 2.8 - - - -
135S SER 5.1 1.2 + - - -
137S TYR* 4.7 22.4 - - + -
200S VAL* 4.2 2.7 + - + +
201S THR* 1.3 76.4 - - - +
203S VAL* 1.3 64.7 + - - +
204S GLU 3.8 2.4 + - - +
205S GLY* 3.9 32.8 - - - +
206S THR 3.8 2.2 - - - -
207S SER* 4.1 18.1 + - - +
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Residues in contact with VAL 203 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96E GLU* 4.1 20.1 - - - +
97E GLN* 5.5 2.8 - - + +
130S PHE* 3.7 52.5 - - + -
133S PHE* 4.3 12.6 - - + -
201S THR* 4.0 10.8 - - + +
202S GLU* 1.3 77.0 - - - +
204S GLU* 1.3 74.1 + - + +
206S THR* 2.8 28.2 + - - +
208S PHE* 4.0 13.0 - - + -
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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