Contacts of the helix formed by residues 217 - 227 (chain A) in PDB entry 5IYB
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 SER 217 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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215A LEU* 3.7 11.3 + - - +
216A LEU* 1.3 69.7 - - - +
218A PRO* 1.3 66.4 - - - +
219A GLU* 3.7 19.6 + - - +
220A ARG* 3.3 18.1 + - - +
221A VAL* 2.9 28.0 + - - +
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Residues in contact with PRO 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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93A PRO* 3.4 23.3 - - - +
94A VAL* 4.1 10.1 - - - -
95A PHE* 3.3 42.4 - - + +
215A LEU* 5.1 4.0 - - + -
216A LEU 3.5 6.7 - - - +
217A SER* 1.3 84.3 - - - +
219A GLU* 1.3 53.7 + - - +
221A VAL* 3.2 1.5 + - + +
222A HIS* 2.9 28.1 + - - +
249A ILE* 3.3 14.7 - - + +
307A VAL* 5.1 15.7 - - + -
311A GLN* 4.9 1.8 - - - +
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Residues in contact with GLU 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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92A LYS* 5.1 14.8 + - + +
93A PRO* 3.5 34.4 + - + +
217A SER* 3.3 11.7 + - - +
218A PRO* 1.3 75.7 - - - +
220A ARG* 1.3 72.7 + - - +
222A HIS* 2.8 23.2 - - + +
223A GLU* 3.0 8.1 + - - +
226A LYS* 4.4 1.9 + - - -
67Q LYS* 5.5 6.9 + - - -
228R MET* 5.4 15.8 - - + +
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Residues in contact with ARG 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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112A PHE* 6.4 2.2 - - + -
217A SER* 3.3 22.3 + - - +
219A GLU* 1.3 86.9 + - - +
221A VAL* 1.3 60.3 + - - +
222A HIS 2.9 1.1 - - - -
223A GLU* 2.5 53.2 + - + +
224A ILE* 2.9 18.1 + - + +
74Q CYS* 5.9 3.6 + - - +
76Q MET* 6.3 1.4 - - - +
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Residues in contact with VAL 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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95A PHE* 3.9 25.8 - - + -
103A THR* 6.2 1.1 - - - -
107A LEU* 4.4 22.0 - - + -
198A LEU* 5.0 0.7 - - + -
216A LEU* 4.6 13.7 - - + -
217A SER 2.9 23.3 + - - +
218A PRO 3.2 7.4 + - - +
220A ARG* 1.3 77.0 - - - +
222A HIS* 1.3 60.2 - - - +
224A ILE* 3.0 15.4 + - + +
225A PHE* 3.0 49.4 + - + -
249A ILE* 3.8 10.1 - - + -
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Residues in contact with HIS 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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28A PRO* 6.2 2.8 - - + +
93A PRO* 4.8 5.9 - - + +
218A PRO 2.9 12.1 + - - +
219A GLU* 2.8 18.1 + - - +
221A VAL* 1.3 77.5 - - - +
223A GLU* 1.3 59.0 + - - -
225A PHE* 3.2 6.1 + - - +
226A LYS* 2.8 51.8 + - + +
246A GLU* 3.3 44.1 + - + +
247A TRP* 5.7 1.2 - - - -
249A ILE* 3.8 18.1 + - + +
251A THR* 3.9 27.2 - - + +
228R MET* 4.6 12.4 - - + +
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Residues in contact with GLU 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 GLU 3.0 7.0 + - - +
220A ARG* 2.5 58.9 + - + +
222A HIS* 1.3 72.5 - - - +
224A ILE* 1.3 62.2 + - + +
226A LYS* 3.4 21.6 + - - +
227A ARG* 3.4 44.6 + - - +
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Residues in contact with ILE 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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107A LEU* 4.6 15.9 - - + -
110A VAL* 4.0 25.1 - - + -
111A CYS 4.6 4.0 - - - +
112A PHE* 3.6 39.3 - - + -
113A PHE* 4.7 10.1 - - - +
115A SER* 3.6 23.8 + - - +
220A ARG* 2.9 14.6 + - + +
221A VAL* 3.3 20.9 - - + +
223A GLU* 1.3 80.2 - - + +
225A PHE* 1.3 68.2 + - + +
227A ARG* 3.5 7.7 + - - +
228A ILE* 3.6 9.7 - - - +
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Residues in contact with PHE 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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103A THR* 4.3 27.4 - - + -
106A VAL* 4.1 26.7 - - + -
107A LEU* 4.2 21.1 - - + -
110A VAL* 5.3 1.8 - - + -
221A VAL* 3.0 35.0 + - + -
222A HIS* 3.2 8.2 + - - +
224A ILE* 1.3 77.5 - - + +
226A LYS* 1.3 64.7 + - - +
227A ARG 3.1 2.2 - - - -
228A ILE* 3.0 39.5 + - + +
244A ARG* 5.6 0.5 + - - -
245A PRO* 3.7 24.7 - - + -
246A GLU* 3.6 29.3 - - + +
249A ILE* 4.4 14.8 - - + -
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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 GLU 4.4 1.8 + - - -
222A HIS* 2.8 69.6 + - + +
223A GLU* 3.4 18.9 - - - +
224A ILE 3.5 0.8 - - - -
225A PHE* 1.3 73.0 - - - +
227A ARG* 1.3 61.9 + - + +
228A ILE 3.3 6.8 + - - +
244A ARG* 4.9 4.7 + - - -
246A GLU* 4.4 20.3 - - + +
228R MET* 4.3 35.1 - - + +
229R ASP* 5.0 16.8 - - - +
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Residues in contact with ARG 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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113A PHE* 3.7 28.3 + - - +
114A CYS 5.6 0.4 - - - -
115A SER* 3.2 33.2 + - - +
223A GLU* 3.4 41.7 + - - +
224A ILE* 3.5 2.8 + - - +
225A PHE 3.1 0.8 - - - -
226A LYS* 1.3 77.9 - - + +
228A ILE* 1.3 64.9 + - - +
229A SER* 3.3 4.2 + - - -
232A GLU* 4.7 0.5 - - - +
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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