Contacts of the helix formed by residues 249 - 255 (chain A) in PDB entry 1I60
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 ARG 249 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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205A GLU* 2.9 35.9 + - - +
214A ASP 4.5 0.2 + - - -
215A GLU 3.4 16.2 + - - +
216A ASP 3.6 2.4 + - - -
217A ARG 3.1 32.8 + - - +
218A VAL* 3.5 14.3 - - - +
247A LEU* 3.7 3.2 - - + +
248A PHE* 1.3 77.2 - - - +
250A PRO* 1.3 71.9 - - + +
251A GLU* 2.9 34.4 + - - +
252A TYR* 3.1 50.2 + - + +
253A TYR* 3.6 15.9 + - - -
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Residues in contact with PRO 250 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12A GLU* 5.8 1.8 - - - +
215A GLU* 4.0 24.0 - - + +
248A PHE 3.4 9.2 - - - +
249A ARG* 1.3 88.7 - - + +
251A GLU* 1.3 63.5 + - - +
253A TYR* 3.0 32.8 + - + +
254A LYS* 3.8 7.7 + - - +
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Residues in contact with GLU 251 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
249A ARG* 2.9 37.3 + - + +
250A PRO* 1.3 79.7 - - - +
252A TYR* 1.3 81.3 + - + +
254A LYS* 2.8 53.1 + - - +
255A LEU* 4.3 3.8 + - - +
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Residues in contact with TYR 252 (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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9A THR 4.9 8.5 - - - +
13A ASN* 3.5 6.4 + - - -
218A VAL* 3.3 16.1 - - - +
219A TRP* 3.0 87.3 + + + -
222A GLN* 4.3 4.6 + - - -
247A LEU* 4.0 14.6 - - + -
249A ARG* 3.1 42.8 + - + +
251A GLU* 1.3 93.3 + - + +
253A TYR* 1.3 62.8 + - - +
254A LYS 3.0 5.8 - - - -
255A LEU* 3.2 30.9 + - + +
260A ALA* 4.5 3.8 - - + +
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Residues in contact with TYR 253 (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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8A ALA 2.9 21.3 + - - -
9A THR* 3.3 27.1 - - - -
11A LEU* 3.4 24.9 - - + +
12A GLU* 3.5 50.9 - - + +
13A ASN* 3.3 34.1 - - - +
247A LEU* 4.9 1.3 - - + -
248A PHE* 3.4 23.7 - - - -
249A ARG 3.9 14.8 - - - -
250A PRO* 3.0 28.6 + - + +
252A TYR* 1.3 77.1 - - + +
254A LYS* 1.3 59.4 + - - +
255A LEU 3.2 1.2 - - - +
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Residues in contact with LYS 254 (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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250A PRO 4.2 5.4 - - - +
251A GLU* 2.8 51.9 - - - +
252A TYR 3.0 0.4 - - - -
253A TYR* 1.3 77.4 - - - +
255A LEU* 1.3 64.2 + - + +
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Residues in contact with LEU 255 (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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13A ASN* 2.8 21.1 + - - +
219A TRP* 4.2 23.6 - - + +
251A GLU 4.6 2.7 - - - +
252A TYR* 3.2 33.4 + - + +
253A TYR 3.5 3.1 - - - +
254A LYS* 1.3 84.7 - - + +
256A THR* 1.3 68.0 + - - +
259A GLU* 3.6 23.6 - - + +
260A ALA* 4.2 11.2 - - + +
263A THR* 5.0 4.3 - - + +
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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