Contacts of the helix formed by residues 197 - 202 (chain A) in PDB entry 4F2N
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 197 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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54A GLN* 3.2 8.3 - - - -
192A VAL* 3.8 6.5 - - - -
193A TRP 3.6 19.3 - - - -
194A GLU* 3.1 28.9 + - - +
196A ALA* 1.3 81.1 - - - +
198A TYR* 1.3 65.7 + + - +
200A ASP 3.2 2.8 + - - -
201A PHE* 2.8 37.4 + - + +
202A GLU 3.3 23.6 - - - -
203A ASN* 4.5 3.7 + - - -
205A ARG* 3.0 58.1 + - + +
208A TYR* 3.4 48.7 - + + -
62B HIS* 6.0 1.1 - + - -
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Residues in contact with TYR 198 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54A GLN* 3.6 0.6 + - - -
194A GLU* 2.9 27.9 + - + +
195A HIS 4.2 1.4 + - - -
197A TYR* 1.3 84.4 - + - +
199A LYS* 1.3 60.7 + - - +
202A GLU* 2.9 63.1 + - + +
203A ASN* 3.6 5.0 + - - -
54B GLN* 4.9 0.4 + - - -
57B LEU* 3.7 28.7 - - + +
62B HIS* 2.8 35.8 + + - -
195B HIS* 3.7 22.0 + - + +
198B TYR* 3.9 35.7 - + + -
199B LYS* 4.3 18.6 - - + +
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Residues in contact with LYS 199 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51A SER* 4.2 2.0 - - - +
53A ARG* 4.1 16.4 - - + +
54A GLN* 3.2 39.1 + - - +
57A LEU* 3.7 17.5 - - + -
198A TYR* 1.3 81.0 - - - +
200A ASP* 1.3 69.9 + - - +
202A GLU* 4.9 3.5 + - - +
198B TYR* 4.7 12.2 + - + -
199B LYS* 5.0 7.3 + - - +
202B GLU* 2.6 39.8 + - - +
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Residues in contact with ASP 200 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49A VAL 3.5 4.3 - - - +
50A MET* 3.3 10.4 - - - +
51A SER* 2.5 51.3 + - - -
54A GLN* 3.2 19.7 + - - +
197A TYR 3.2 2.0 + - - +
199A LYS* 1.3 83.7 - - - +
201A PHE* 1.3 82.6 + - + +
202A GLU* 3.8 1.3 - - - -
204A ARG* 3.8 10.7 + - - -
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Residues in contact with PHE 201 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49A VAL* 3.8 31.9 - - + -
50A MET* 6.0 1.3 - - + -
197A TYR* 2.8 24.3 + - + +
200A ASP* 1.3 87.4 - - + +
202A GLU* 1.3 72.8 + - - +
204A ARG* 2.9 65.6 + - - +
207A ASP* 3.9 0.7 - - + -
208A TYR* 3.6 45.3 - + + -
211A GLU* 3.5 39.0 - - + -
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Residues in contact with GLU 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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197A TYR* 3.3 12.1 - - - -
198A TYR* 2.9 52.1 + - + +
199A LYS 5.1 3.8 - - - +
200A ASP 5.6 0.4 - - - -
201A PHE* 1.3 79.6 - - - +
203A ASN* 1.3 67.1 + - - +
204A ARG* 3.2 6.5 + - - +
53B ARG* 2.8 42.4 + - - -
57B LEU* 3.6 23.5 - - + +
199B LYS* 2.9 31.9 + - + +
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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