Contacts of the helix formed by residues 219 - 229 (chain A) in PDB entry 5FHK
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 ALA 219 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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99A TYR* 3.8 24.5 - - + +
100A ASN* 3.9 5.8 - - - +
191A GLY* 4.7 0.4 - - - -
192A HIS 4.6 1.8 - - - -
217A ALA* 3.2 2.9 - - - +
218A ASN* 1.3 84.8 + - - +
220A LEU* 1.3 63.7 + - - +
221A ASN* 3.3 19.3 - - - +
222A VAL* 3.5 14.5 - - + +
223A VAL* 3.3 20.2 - - - +
126B THR* 4.7 8.7 - - + +
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Residues in contact with LEU 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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100A ASN* 3.0 33.7 + - + +
191A GLY* 3.5 31.0 - - - +
192A HIS 3.7 11.9 - - - +
193A PRO* 4.4 4.3 - - + -
194A LEU* 4.1 10.3 - - + -
219A ALA* 1.3 71.0 - - - +
221A ASN* 1.3 67.4 + - - +
222A VAL 3.3 0.4 - - - -
223A VAL* 3.2 7.5 + - + +
224A ARG* 2.9 23.4 + - - +
235A LEU 4.1 16.4 - - - +
236A MET* 3.9 14.1 - - + +
237A PRO* 3.5 34.3 - - + -
240A MET* 4.0 14.1 - - + -
262A ARG* 5.0 0.2 - - - +
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Residues in contact with ASN 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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100A ASN* 4.5 1.4 + - - -
219A ALA* 3.3 21.2 - - - +
220A LEU* 1.3 77.8 - - - +
222A VAL* 1.3 79.7 + - - +
224A ARG* 3.3 12.7 + - - +
225A SER* 3.2 19.2 + - - -
240A MET* 4.2 14.1 - - + +
103B LYS* 3.8 34.6 - - + +
221B ASN* 5.8 3.8 - - - +
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Residues in contact with VAL 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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215A PHE* 3.7 7.9 - - + -
217A ALA* 3.6 20.4 - - + -
219A ALA* 3.5 18.8 - - + +
221A ASN* 1.3 93.2 + - - +
223A VAL* 1.3 64.7 + - - +
225A SER* 3.3 9.6 + - - -
226A ALA 3.3 15.6 + - - -
102B THR* 3.9 20.9 - - + -
103B LYS* 4.1 15.5 - - + +
107B MET* 3.6 34.8 - - + +
124B LEU* 4.7 7.2 - - + -
126B THR* 5.2 3.4 - - + -
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Residues in contact with VAL 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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189A LEU* 3.8 23.1 - - + +
190A LYS 3.7 7.6 - - - +
191A GLY* 3.6 23.3 - - - +
215A PHE* 4.0 11.7 - - + -
217A ALA* 3.9 11.9 - - + -
219A ALA 3.3 18.6 - - - +
220A LEU* 3.2 11.8 + - + +
222A VAL* 1.3 74.5 - - - +
224A ARG* 1.3 65.8 + - - +
226A ALA* 3.2 4.7 + - - +
227A CYS* 3.1 19.9 + - - +
234A THR* 3.4 26.9 - - - +
236A MET* 4.1 4.5 - - + -
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Residues in contact with ARG 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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220A LEU 2.9 12.8 + - - +
221A ASN* 3.5 11.7 + - - +
223A VAL* 1.3 75.3 - - - +
225A SER* 1.3 77.1 + - - +
227A CYS* 3.1 6.3 + - + +
228A SER* 2.9 52.7 + - - -
234A THR* 5.4 0.2 - - - -
236A MET* 3.8 18.3 - - + +
240A MET* 4.6 9.2 - - + -
241A ILE* 4.0 20.6 - - + -
244A TYR* 2.9 45.2 + - - -
250A LEU* 4.4 9.0 - - + -
103B LYS* 3.4 35.0 - - - +
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Residues in contact with SER 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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221A ASN 3.2 9.6 + - - -
222A VAL* 3.5 12.9 + - - -
223A VAL 3.2 0.4 - - - -
224A ARG* 1.3 99.7 - - - +
226A ALA* 1.3 61.9 + - - +
228A SER* 3.4 4.7 + - - -
229A GLU* 3.2 18.7 + - - +
103B LYS* 4.6 7.9 - - - -
107B MET* 3.8 16.8 - - - +
111B ASN* 3.1 22.6 + - - -
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Residues in contact with ALA 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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189A LEU* 3.9 11.2 - - + -
215A PHE* 4.0 20.6 - - + -
222A VAL 3.3 9.0 + - - +
223A VAL 3.2 8.3 + - - +
225A SER* 1.3 76.5 + - - +
227A CYS* 1.3 64.1 + - - +
229A GLU* 3.2 10.2 + - - +
230A GLY 3.4 0.3 + - - -
231A LEU* 3.3 31.3 + - + +
107B MET* 4.4 0.4 - - + -
111B ASN* 3.3 24.7 - - - +
114B MET* 4.4 1.3 - - + -
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Residues in contact with CYS 227 (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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165A VAL* 3.7 4.0 - - - -
166A ALA* 3.6 22.9 - - - -
167A SER* 3.5 12.5 + - - -
189A LEU* 3.5 11.8 - - + +
223A VAL 3.1 10.9 + - - +
224A ARG* 3.3 11.2 - - - +
226A ALA* 1.3 74.0 - - - +
228A SER* 1.3 60.9 + - - +
230A GLY* 2.8 19.4 + - - -
231A LEU 4.7 0.2 - - - +
232A GLY 3.7 9.0 - - - +
234A THR* 3.5 31.2 - - + -
250A LEU* 3.5 22.4 - - + -
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Residues in contact with SER 228 (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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167A SER* 3.7 11.2 - - - -
169A GLU* 5.2 1.0 - - - +
224A ARG* 2.9 34.9 + - - -
225A SER* 3.6 9.6 - - - -
227A CYS* 1.3 75.1 - - - +
229A GLU* 1.3 59.4 + - - +
230A GLY 3.1 3.5 + - - -
244A TYR* 3.8 13.0 - - - -
249A SER* 5.2 3.1 + - - +
250A LEU* 4.1 16.7 - - - +
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Residues in contact with GLU 229 (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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169A GLU* 3.6 12.8 - - - +
225A SER 3.2 9.3 + - - +
226A ALA 3.6 8.1 - - - +
227A CYS 3.1 1.0 - - - -
228A SER* 1.3 76.9 - - - +
230A GLY* 1.3 61.5 + - - +
231A LEU* 3.4 10.0 + - + +
108B PRO* 5.1 2.1 - - - +
111B ASN* 3.7 33.2 + - + +
115B SER* 5.7 4.9 + - - -
131D ASP 5.4 2.1 - - - +
132D GLN* 3.1 36.1 + - - +
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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