Contacts of the helix formed by residues 221 - 225 (chain A) in PDB entry 5C4B
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 GLY 221 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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106A ASN* 6.0 0.2 - - - -
142A MET* 3.3 27.0 - - - +
219A HIS* 3.3 13.6 + - - -
220A VAL* 1.3 74.7 - - - +
222A VAL* 1.3 60.0 + - - -
223A GLU* 2.9 29.0 + - - +
224A ILE* 3.1 15.1 + - - +
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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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102A ILE* 4.3 3.0 - - + +
105A LEU* 3.7 17.9 - - + +
106A ASN* 3.7 22.0 - - - +
109A PHE* 3.6 38.8 - - + -
116A ILE* 4.7 1.3 - - + -
142A MET* 3.9 7.0 - - - -
145A HIS* 3.5 37.7 - - + +
221A GLY* 1.3 66.9 - - - -
223A GLU* 1.3 63.7 + - - +
224A ILE 3.0 6.1 - - - +
225A LEU* 3.0 40.2 + - + +
317A LYS* 4.1 1.2 + - - -
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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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95A VAL* 3.8 15.7 - - + +
100A PHE* 3.7 24.7 - - + -
102A ILE* 3.3 5.7 - - - +
105A LEU* 3.7 26.8 - - + +
219A HIS* 2.6 33.3 + - - -
221A GLY 2.9 26.9 + - - +
222A VAL* 1.3 79.5 - - - +
224A ILE* 1.3 58.1 + - + +
225A LEU 3.3 0.2 - - - -
317A LYS* 2.8 26.0 + - - +
323A TYR* 2.7 35.9 + - - +
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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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141A PHE* 4.7 0.2 - - + -
142A MET* 3.7 22.9 - - + -
208A VAL* 4.1 11.4 - - + -
220A VAL* 4.2 9.4 - - + -
221A GLY 3.1 14.3 + - - +
222A VAL 3.0 2.0 - - - -
223A GLU* 1.3 79.6 - - - +
225A LEU* 1.3 67.6 + - + +
226A THR* 3.6 6.2 - - - +
229A PHE* 3.3 42.3 - - + +
269A PHE* 4.2 12.1 - - + -
317A LYS* 3.9 3.3 - - - +
319A LEU* 3.7 27.9 - - + +
323A TYR* 3.5 35.0 - - + -
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Residues in contact with LEU 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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109A PHE* 3.7 33.4 - - + -
114A THR* 4.0 2.0 - - + -
116A ILE* 3.7 28.0 - - + -
142A MET* 4.1 10.5 - - + -
206A TYR* 3.7 37.5 - - + -
208A VAL* 4.5 6.1 - - + -
222A VAL* 3.0 37.8 + - + +
224A ILE* 1.3 86.2 - - + +
226A THR* 1.3 61.9 + - - +
229A PHE* 5.0 4.9 - - + -
317A LYS* 2.8 26.0 + - - -
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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