Contacts of the helix formed by residues 197 - 202 (chain F) 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 F).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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62E HIS* 6.5 0.2 - + - -
54F GLN* 3.2 7.6 - - - -
191F ASP 4.8 0.2 - - - -
192F VAL* 3.9 5.2 - - - -
193F TRP 3.5 20.9 - - - -
194F GLU* 3.4 23.1 + - - +
196F ALA* 1.3 80.3 - - - +
198F TYR* 1.3 62.6 + + - +
199F LYS 3.1 0.7 + - - -
200F ASP 3.2 2.1 + - - -
201F PHE* 2.7 42.4 + - + +
202F GLU 3.3 27.6 - - - -
203F ASN* 4.4 4.3 + - - -
205F ARG* 2.9 65.4 + - + +
208F TYR* 3.4 48.2 - + + -
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Residues in contact with TYR 198 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54E GLN* 5.0 0.2 - - - -
57E LEU* 3.8 27.8 - - + +
62E HIS* 2.7 33.1 + + - -
195E HIS* 3.5 35.3 + - + +
198E TYR* 3.8 35.0 - + + -
199E LYS* 4.4 14.3 + - + -
54F GLN* 3.6 0.4 + - - -
194F GLU* 2.8 30.9 + - + +
195F HIS 4.2 1.6 + - - -
197F TYR* 1.3 79.8 - + - +
199F LYS* 1.3 60.4 + - - +
202F GLU* 2.8 63.6 + - + +
203F ASN* 3.5 3.8 + - - -
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Residues in contact with LYS 199 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
198E TYR* 4.4 9.6 + - + +
199E LYS* 5.5 5.9 + - - +
202E GLU* 2.9 33.0 + - + +
51F SER* 4.5 1.3 - - - +
53F ARG* 3.7 18.2 - - - +
54F GLN* 3.1 37.6 + - + +
57F LEU* 4.0 11.9 - - + -
198F TYR* 1.3 82.1 - - - +
200F ASP* 1.3 69.6 + - - +
202F GLU* 4.8 3.8 + - - +
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Residues in contact with ASP 200 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49F VAL 3.5 4.2 - - - +
50F MET* 3.3 9.9 - - - +
51F SER* 2.6 51.9 + - - -
54F GLN* 3.2 19.0 + - - +
197F TYR 3.2 1.6 + - - -
199F LYS* 1.3 81.9 - - - +
201F PHE* 1.3 80.7 + - + +
202F GLU* 3.8 1.5 - - - +
204F ARG* 4.0 8.5 + - - -
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Residues in contact with PHE 201 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49F VAL* 3.9 25.6 - - + -
50F MET* 6.2 0.9 - - + -
197F TYR* 2.7 30.9 + - + +
200F ASP* 1.3 85.3 - - + +
202F GLU* 1.3 72.8 + - - +
204F ARG* 3.0 59.0 + - - +
207F ASP* 4.0 3.1 - - + -
208F TYR* 3.7 48.2 - + + -
211F GLU* 3.6 41.7 - - + -
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Residues in contact with GLU 202 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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53E ARG* 2.7 42.7 + - - +
57E LEU* 3.5 14.7 - - + +
199E LYS* 2.7 32.9 + - - +
197F TYR* 3.3 12.6 - - - -
198F TYR* 2.8 49.6 + - + +
199F LYS 5.1 3.8 - - - +
200F ASP 5.5 0.7 - - - -
201F PHE* 1.3 80.9 - - - +
203F ASN* 1.3 68.9 + - - +
204F ARG* 3.2 7.7 + - - +
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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