Contacts of the helix formed by residues 199 - 205 (chain F) in PDB entry 4Q43
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 THR 199 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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174F GLN 3.5 14.6 + - - -
175F THR* 3.4 28.5 - - + +
176F LEU 3.2 9.9 - - - +
177F PRO* 4.2 0.2 - - + -
178F LEU* 3.4 12.8 - - - +
198F ARG* 1.3 110.9 - - - +
200F CYS* 1.3 64.1 + - - +
202F ASP* 2.7 39.3 + - - +
203F VAL* 3.5 10.6 + - - +
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Residues in contact with CYS 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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147F PHE* 5.7 0.7 - - - -
173F LEU* 3.5 20.9 - - + +
176F LEU* 2.8 34.5 + - - -
178F LEU* 3.8 9.4 - - - -
181F ILE* 3.7 29.6 - - - -
199F THR* 1.3 70.1 - - - +
201F GLY* 1.3 66.8 + - - +
203F VAL* 2.9 13.5 + - - +
204F GLN* 2.9 18.0 + - - +
225F ARG 4.7 1.1 - - - -
226F SER* 3.7 30.0 - - - +
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Residues in contact with GLY 201 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
173F LEU 3.7 1.8 + - - -
174F GLN* 3.3 47.0 + - - +
199F THR 3.2 1.0 - - - -
200F CYS* 1.3 79.0 - - - +
202F ASP* 1.3 61.4 + - - +
204F GLN* 3.5 20.7 + - - +
205F LYS* 3.7 8.3 + - - +
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Residues in contact with ASP 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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196F GLY 4.1 17.7 - - - +
197F LEU* 4.1 17.1 - - + +
198F ARG* 3.4 10.6 + - - +
199F THR* 2.7 37.5 + - - +
200F CYS 3.1 0.8 - - - -
201F GLY* 1.3 76.6 - - - +
203F VAL* 1.3 61.4 + - - +
204F GLN 3.3 0.2 - - - -
205F LYS* 3.6 14.2 + - - +
206F CYS* 3.8 9.5 + - - +
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Residues in contact with VAL 203 (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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178F LEU* 3.7 23.1 - - + -
192F LEU* 5.7 1.3 - - + -
197F LEU* 4.0 16.8 - - + -
199F THR 3.5 14.6 - - - +
200F CYS 2.9 2.7 + - - +
202F ASP* 1.3 74.4 - - - +
204F GLN* 1.3 65.0 + - - +
205F LYS 3.1 2.0 - - - -
206F CYS* 3.0 21.3 + - + +
211F LEU* 3.8 27.6 - - + -
222F LEU* 4.0 14.4 - - + +
223F TRP* 4.2 9.4 - - - -
226F SER* 3.2 29.6 - - - +
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Residues in contact with GLN 204 (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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170F PRO* 5.0 5.5 + - - +
173F LEU* 3.9 19.2 - - - +
174F GLN* 3.7 21.1 + - - +
200F CYS 2.9 19.6 + - - +
201F GLY* 3.6 13.4 - - - +
202F ASP 3.3 0.2 - - - -
203F VAL* 1.3 78.7 - - - +
205F LYS* 1.3 56.7 + - - +
206F CYS 3.3 8.0 + - - +
223F TRP* 5.1 1.0 + - - -
226F SER* 2.9 32.3 + - - +
227F GLN* 3.8 31.4 + - - +
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Residues in contact with LYS 205 (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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201F GLY 3.7 7.5 + - - +
202F ASP* 3.6 12.9 + - - +
203F VAL 3.1 1.0 - - - -
204F GLN* 1.3 76.8 - - - +
206F CYS* 1.3 58.8 + - - +
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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