Contacts of the helix formed by residues 217 - 226 (chain A) in PDB entry 5V5Z
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 PHE 217 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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209A MET* 5.1 4.0 - - - -
212A ILE* 3.5 24.0 - - + +
213A PHE* 3.5 39.3 - + - -
215A ARG* 2.7 37.3 + - - +
216A SER* 1.3 70.8 - - - +
218A ALA* 1.3 54.8 + - - +
219A GLN 3.1 0.4 - - - -
220A LEU* 2.7 45.3 + - + +
221A TYR* 3.1 9.7 + + - +
253A ILE* 3.7 39.3 - - + -
256A THR* 3.8 35.4 - - + -
257A TYR* 4.4 15.7 - + - -
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Residues in contact with ALA 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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198A PHE* 5.9 2.9 - - + -
213A PHE* 3.9 28.1 - - + +
215A ARG 3.6 2.3 + - - +
216A SER* 2.9 11.3 - - - +
217A PHE* 1.3 79.0 - - - +
219A GLN* 1.3 56.9 + - - +
221A TYR* 3.0 8.1 + - - +
222A SER* 2.7 32.2 + - - +
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Residues in contact with GLN 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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216A SER* 3.3 26.5 + - - +
217A PHE 3.1 1.0 - - - -
218A ALA* 1.3 78.2 - - - +
220A LEU* 1.3 57.2 + - + +
222A SER* 3.3 20.7 + - - -
223A ASP* 2.8 49.7 + - - +
226A LYS* 4.1 8.2 + - - +
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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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215A ARG* 4.3 12.6 - - - +
216A SER 4.8 5.4 - - - +
217A PHE* 2.7 39.0 + - + +
219A GLN* 1.3 73.9 - - + +
221A TYR* 1.3 54.2 + - - +
223A ASP* 3.3 11.4 + - - +
224A LEU* 2.9 22.0 + - - +
248A ALA 5.5 0.2 - - - -
249A ALA* 3.4 25.0 - - - +
252A LYS* 3.8 53.2 - - + +
253A ILE* 3.9 16.7 - - + +
256A THR* 5.4 0.4 - - - +
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Residues in contact with TYR 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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197A ILE* 4.1 13.0 - - + -
213A PHE* 3.3 31.0 - + + -
217A PHE* 3.1 12.9 + + - +
218A ALA* 3.0 11.0 + - - +
220A LEU* 1.3 74.6 - - - +
222A SER* 1.3 55.1 + - - +
223A ASP 3.2 0.2 - - - -
224A LEU* 3.5 27.7 - - + +
225A ASP* 2.7 36.8 + - - +
253A ILE* 3.7 19.7 - - + +
257A TYR* 2.8 33.1 + - - -
302A ILE* 4.3 6.0 - - + +
305A LEU* 3.1 31.8 - - + +
306A MET* 3.9 22.9 - - + +
309A GLN* 6.1 1.1 - - - +
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Residues in contact with SER 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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218A ALA* 2.7 20.8 + - - +
219A GLN* 3.4 22.1 + - - -
221A TYR* 1.3 72.1 - - - +
223A ASP* 1.3 61.3 + - - +
225A ASP* 3.4 5.8 + - - +
226A LYS* 3.2 49.2 + - - +
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Residues in contact with ASP 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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219A GLN* 2.8 39.1 + - - +
220A LEU* 3.4 18.3 - - - +
221A TYR 3.2 0.2 - - - -
222A SER* 1.3 78.1 - - - +
224A LEU* 1.3 62.0 + - - +
226A LYS* 3.9 18.7 + - - +
227A GLY 4.2 1.6 + - - -
242A HIS* 4.4 2.4 - - - +
245A ARG* 3.2 48.2 + - + +
246A ARG* 3.6 18.2 + - - +
249A ALA* 3.8 4.9 - - + -
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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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125A VAL* 3.3 35.9 - - + +
220A LEU 2.9 13.5 + - - +
221A TYR* 3.1 37.6 + - + +
223A ASP* 1.3 76.0 - - - +
225A ASP* 1.3 66.5 + - - +
227A GLY* 3.3 10.0 + - - -
228A PHE* 3.5 9.7 + - - +
246A ARG* 3.7 30.4 - - + +
249A ALA* 3.9 2.9 - - + -
250A GLN* 3.7 14.4 - - + +
253A ILE* 4.0 10.3 - - + -
302A ILE* 4.0 14.1 - - + -
306A MET* 4.0 7.4 - - - -
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Residues in contact with ASP 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 TYR 2.7 20.7 + - - +
222A SER* 3.7 8.5 - - - +
224A LEU* 1.3 67.8 - - - +
226A LYS* 1.3 53.5 + - + +
227A GLY 2.5 6.4 + - - -
228A PHE* 2.5 45.1 + - - +
229A THR* 4.4 0.7 - - - +
306A MET* 3.7 17.3 - - + +
309A GLN* 4.4 8.1 + - - -
310A HIS* 3.2 33.3 + - - -
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Residues in contact with LYS 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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219A GLN* 4.1 10.9 + - - +
222A SER* 3.2 41.5 + - - +
223A ASP* 3.9 18.4 + - - +
224A LEU 3.4 1.0 - - - -
225A ASP* 1.3 73.8 - - + +
227A GLY* 1.3 50.6 + - - +
228A PHE 3.5 0.2 - - - -
229A THR* 4.0 15.2 + - - +
242A HIS* 2.6 47.9 + - + +
245A ARG* 5.4 6.5 - - - +
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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