Contacts of the helix formed by residues 270 - 275 (chain I) in PDB entry 5AYZ
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 270 (chain I).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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137I THR* 3.7 17.3 - - - +
139I LYS* 4.3 7.0 - - - -
269I MET* 1.3 71.9 - - - +
271I MET* 1.3 62.9 + - - +
272I LEU 3.0 1.4 + - - -
273I THR* 3.1 15.4 + - - -
274I GLN* 3.1 17.7 + - - +
401I NCN 3.1 36.5 + - - -
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Residues in contact with MET 271 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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117I ALA* 4.2 11.0 - - + -
251I ILE 3.8 11.2 - - - +
252I THR* 4.1 11.0 - - + -
253I LEU* 3.8 33.4 - - + -
269I MET* 3.6 31.9 - - + -
270I GLY* 1.3 75.6 - - - +
272I LEU* 1.3 79.2 + - + +
274I GLN* 4.6 1.8 - - - -
275I ALA* 2.9 52.8 + - + +
276I ALA 3.6 0.2 + - - -
401I NCN 4.4 4.2 + - - +
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Residues in contact with LEU 272 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114I ILE* 3.7 16.7 - - - +
117I ALA* 3.4 38.4 - - + +
118I ALA* 3.8 6.1 - - - +
121I ALA* 4.2 10.1 - - + -
134I VAL* 4.0 21.5 - - + -
135I ALA 3.8 23.8 - - - +
136I GLY* 5.3 0.7 - - - -
152I LEU* 3.9 25.6 - - + -
157I ALA* 4.6 1.8 - - + -
253I LEU* 4.6 0.2 - - + -
269I MET* 3.6 20.4 - - + +
270I GLY 3.0 1.4 + - - -
271I MET* 1.3 90.6 - - + +
273I THR* 1.3 58.5 + - + +
276I ALA* 3.4 17.0 - - - +
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Residues in contact with THR 273 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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114I ILE* 4.1 20.8 - - + +
136I GLY* 5.7 0.7 - - - -
137I THR* 4.3 9.1 + - - +
139I LYS 2.5 28.5 + - - -
140I THR* 4.4 6.2 - - + +
141I THR* 5.2 0.2 + - - -
148I GLU* 3.9 27.5 - - + +
152I LEU* 4.1 26.2 - - + -
269I MET 4.6 1.1 + - - -
270I GLY 3.1 6.0 + - - -
272I LEU* 1.3 82.4 - - + +
274I GLN* 1.3 61.3 + - - +
275I ALA 3.8 0.7 - - - -
276I ALA* 4.7 4.0 + - - -
110J ARG* 3.4 12.3 + - - -
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Residues in contact with GLN 274 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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139I LYS* 3.5 50.8 - - + +
270I GLY 3.1 11.7 + - - +
271I MET* 4.6 1.1 - - - -
273I THR* 1.3 78.6 - - - +
275I ALA* 1.3 59.5 + - + +
276I ALA 3.6 1.1 - - - -
401I NCN 4.6 6.7 + - - -
102J ARG* 4.9 1.6 + - - -
106J ASN* 4.1 3.8 - - - +
109J ALA* 4.1 8.3 - - - +
110J ARG* 3.0 27.9 + - - +
276J ALA 4.9 0.7 - - - +
277J PRO* 3.7 3.3 - - - +
278J ALA* 3.4 43.5 + - + +
279J LEU 5.0 5.1 + - - -
280J ASP* 6.1 1.0 - - - +
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Residues in contact with ALA 275 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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271I MET* 2.9 34.0 + - + +
274I GLN* 1.3 80.1 - - + +
276I ALA* 1.3 58.0 + - - +
277I PRO* 3.2 12.9 - - - +
277J PRO* 4.2 20.6 - - + -
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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