Contacts of the helix formed by residues 217 - 226 (chain A) in PDB entry 4FPD
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 VAL 217 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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19A LEU 4.3 10.8 - - - +
20A MET* 4.4 12.8 - - - -
23A GLY* 4.1 28.5 - - - -
27A PHE* 3.9 7.1 - - + -
50A PRO* 4.3 15.0 - - + -
213A VAL* 3.0 23.6 + - + +
216A LYS* 1.3 81.0 - - - +
218A GLY* 1.3 71.4 + - - +
220A GLY* 3.1 1.7 + - - -
221A LEU* 3.0 36.7 + - + +
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Residues in contact with GLY 218 (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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213A VAL* 2.9 16.7 + - - +
214A SER* 3.5 8.5 - - - -
217A VAL* 1.3 78.3 - - - +
219A LEU* 1.3 61.7 + - - +
221A LEU* 3.3 12.7 + - - +
222A ILE* 3.2 23.6 + - - +
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Residues in contact with LEU 219 (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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93A LEU* 5.7 2.9 - - + -
97A LEU* 5.6 0.4 - - + -
174A LEU* 4.9 2.5 - - + -
177A VAL* 4.0 28.5 - - + -
178A THR* 4.1 28.7 - - + +
181A LEU* 4.6 13.2 - - + -
182A TRP* 5.9 1.8 - - + +
214A SER 2.7 20.4 + - - +
215A ALA* 3.8 18.6 - - + +
217A VAL 3.4 0.4 - - - -
218A GLY* 1.3 69.3 - - - +
220A GLY* 1.3 55.8 + - - +
222A ILE* 2.9 22.5 + - + +
223A LEU* 2.5 62.8 + - + +
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Residues in contact with GLY 220 (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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27A PHE* 4.0 7.0 - - - -
46A THR* 3.9 16.2 - - - +
93A LEU* 6.0 3.1 - - - -
215A ALA 4.5 1.5 + - - -
216A LYS 3.6 16.6 + - - -
217A VAL 3.1 8.2 + - - -
219A LEU* 1.3 78.7 - - - +
221A LEU* 1.3 52.2 + - - +
223A LEU* 3.7 8.9 - - - +
224A LEU* 2.8 35.7 + - - +
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Residues in contact with LEU 221 (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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26A TYR* 3.4 36.6 - - + +
27A PHE* 3.7 16.1 - - + -
30A LYS* 5.4 3.4 - - - +
217A VAL* 3.0 28.7 + - + +
218A GLY* 3.4 13.2 - - - +
220A GLY* 1.3 75.6 - - - +
222A ILE* 1.3 60.2 + - + +
224A LEU* 3.9 2.6 - - - +
225A ARG* 3.0 36.4 + - - +
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Residues in contact with ILE 222 (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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173A VAL 5.8 3.4 - - - +
174A LEU* 5.4 8.5 - - + -
177A VAL* 6.2 2.2 - - + -
218A GLY 3.4 14.8 - - - +
219A LEU* 2.9 24.8 + - + +
221A LEU* 1.3 73.9 - - + +
223A LEU* 1.3 60.9 + - + +
225A ARG* 3.5 3.9 - - - +
226A SER* 2.7 38.8 + - - +
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Residues in contact with LEU 223 (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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42A PHE* 3.8 18.8 - - + -
46A THR* 5.7 0.9 - - - +
93A LEU* 4.8 15.9 - - + +
96A GLY* 6.1 1.3 - - - -
97A LEU* 3.7 24.5 - - + +
100A LEU* 4.3 8.8 - - + +
174A LEU* 3.3 46.9 - - + -
219A LEU* 2.5 44.2 + - + +
220A GLY* 3.7 7.0 - - - +
222A ILE* 1.3 75.0 - - - +
224A LEU* 1.3 71.9 + - - +
225A ARG 3.1 0.5 + - - -
226A SER* 3.6 9.4 + - - +
227A ARG* 3.6 8.7 - - - -
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Residues in contact with LEU 224 (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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27A PHE* 5.1 6.7 - - + -
30A LYS* 4.8 12.3 - - + +
42A PHE* 2.9 40.9 - - + +
43A TYR* 2.9 54.3 - - + +
46A THR* 3.9 19.5 - - + +
220A GLY 2.8 21.6 + - - +
221A LEU* 3.9 4.5 - - - +
223A LEU* 1.3 71.3 - - - +
225A ARG* 1.3 58.3 + - - +
227A ARG* 2.4 40.0 - - + +
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Residues in contact with ARG 225 (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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26A TYR* 5.4 1.6 + - - -
30A LYS* 3.9 26.5 - - - +
221A LEU* 3.0 19.7 + - - +
222A ILE* 3.5 9.2 - - - +
223A LEU 3.1 0.2 + - - -
224A LEU* 1.3 79.4 - - - +
226A SER* 1.3 55.4 - - - +
227A ARG* 1.9 31.1 + - - +
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Residues in contact with SER 226 (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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100A LEU* 5.2 6.2 - - - +
170A THR* 6.0 2.0 - - - -
174A LEU* 5.1 9.9 - - - +
222A ILE* 2.7 25.7 + - - +
223A LEU* 3.6 7.2 + - - +
225A ARG* 1.3 75.6 - - - +
227A ARG* 1.3 70.2 + - - +
228A ALA 4.2 1.6 - - - -
229A ILE* 3.9 32.7 - - - +
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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