Contacts of the strand formed by residues 198 - 203 (chain A) in PDB entry 4N2F
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 TYR 198 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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5A ARG* 5.2 0.7 + - - -
16A GLU 3.9 6.7 + - - -
17A ALA* 3.6 11.5 - - - +
18A VAL* 3.4 43.0 + - + -
194A LEU* 3.9 20.3 - - + +
195A PRO* 3.4 27.7 + - + +
196A ALA 3.5 13.0 - - - -
197A GLY* 1.3 80.5 - - - +
199A GLU* 1.3 65.1 + - - +
272A LEU* 4.0 14.6 - - + -
273A LEU 3.2 15.3 - - - +
274A GLU* 3.9 28.9 + - + -
282A LEU* 6.2 0.2 - - - -
285A ILE* 3.5 30.4 - - + +
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Residues in contact with GLU 199 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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194A LEU* 4.1 6.3 - - - -
198A TYR* 1.3 77.5 - - - +
200A ILE* 1.3 63.4 + - - +
201A VAL* 4.0 17.6 - - + +
238A VAL* 3.6 32.5 - - + +
239A VAL 5.8 0.4 - - - +
272A LEU* 3.6 2.5 - - - +
273A LEU* 2.8 38.7 + - + +
282A LEU* 3.8 27.9 - - + +
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Residues in contact with ILE 200 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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116A ILE* 5.4 0.2 - - + -
118A ILE* 4.5 20.2 - - + -
186A LEU* 4.2 4.5 - - + -
188A THR* 4.7 12.6 - - + -
194A LEU* 4.0 11.6 - - + +
199A GLU* 1.3 76.6 - - - +
201A VAL* 1.3 69.1 + - - +
238A VAL* 3.6 2.4 - - - +
239A VAL* 2.9 56.1 + - + +
241A TYR* 4.0 31.9 - - + -
270A VAL* 3.5 27.1 - - + -
271A SER 3.4 6.3 - - - +
272A LEU* 4.0 16.2 - - + -
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Residues in contact with VAL 201 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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199A GLU* 4.0 9.6 - - + +
200A ILE* 1.3 82.7 - - - +
202A LEU* 1.3 73.0 + - - +
203A TYR* 4.0 9.9 - - + -
236A TYR* 3.8 23.8 - - + -
237A HIS 3.4 10.5 - - - +
238A VAL* 3.9 19.3 - - + -
239A VAL* 4.5 0.2 - - - -
269A HIS 4.0 0.2 - - - +
270A VAL* 3.4 6.2 - - - -
271A SER* 2.9 34.0 + - - +
273A LEU* 3.6 32.3 - - + -
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Residues in contact with LEU 202 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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120A LEU* 4.0 23.1 - - + -
184A MET* 4.0 16.8 - - + -
186A LEU* 5.3 2.0 - - + -
201A VAL* 1.3 73.1 - - - +
203A TYR* 1.3 65.7 + - - +
214A VAL* 4.6 0.2 - - + -
229A ILE* 3.9 18.4 - - + -
230A LEU* 3.6 25.1 - - + +
236A TYR* 3.2 0.9 - - - -
237A HIS* 2.8 40.8 + - + +
239A VAL* 4.1 9.5 - - + +
250A PHE* 3.9 20.2 - - + -
268A ILE* 4.2 4.0 - - + -
269A HIS 3.3 14.4 - - - +
270A VAL* 3.8 20.0 - - + -
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Residues in contact with TYR 203 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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201A VAL* 4.0 14.1 - - + -
202A LEU* 1.3 80.3 - - - +
204A ILE* 1.3 75.6 + - - +
230A LEU* 4.1 3.6 - - - -
235A LEU 3.1 15.3 - - - +
236A TYR* 3.8 10.3 - - + -
268A ILE* 3.8 0.9 - - - +
269A HIS* 2.9 68.6 + + + +
271A SER* 3.3 33.4 + - - -
273A LEU* 6.2 0.2 - - + -
284A PRO* 5.8 1.6 - - - +
287A THR* 3.8 14.2 + - - +
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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