Contacts of the helix formed by residues 141 - 146 (chain D) in PDB entry 1IR1
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 PRO 141 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33D ASP 3.3 25.8 - - - +
34D THR* 3.3 25.4 - - - +
35D ASP 3.5 12.3 - - - +
36D ILE* 3.5 16.4 - - + -
105D LEU* 4.6 1.8 - - + -
139D ARG* 3.4 17.0 - - - +
140D ILE* 1.3 88.6 - - + +
142D VAL* 1.3 65.3 + - - +
143D ALA* 3.1 3.6 - - + +
144D TYR* 2.9 28.1 + - + +
145D VAL* 3.0 10.2 + - - +
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Residues in contact with VAL 142 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33D ASP* 4.8 5.3 + - + +
140D ILE 3.7 0.8 + - - +
141D PRO* 1.3 72.2 - - - +
143D ALA* 1.3 66.5 + - + +
145D VAL* 3.6 8.8 - - - +
146D LYS* 3.1 30.0 + - + +
367D SER* 3.8 33.2 - - - +
369D VAL* 3.5 32.7 - - + +
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Residues in contact with ALA 143 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33D ASP 5.8 0.2 - - - +
34D THR* 4.5 15.7 - - + -
105D LEU* 4.0 26.3 - - + +
141D PRO* 3.1 4.3 - - + +
142D VAL* 1.3 84.8 - - + +
144D TYR* 1.3 59.4 + - - +
146D LYS* 3.9 9.4 + - - +
147D THR* 3.7 14.9 - - - +
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Residues in contact with TYR 144 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36D ILE* 3.9 18.8 - - + -
105D LEU* 3.9 18.8 - - + +
108D PHE* 3.6 24.1 - - + +
109D GLU 2.8 29.6 + - - -
110D GLU* 4.0 6.7 - - + -
112D SER 3.4 16.1 + - - -
116D MET* 4.0 24.9 + - + +
140D ILE* 3.9 14.1 - - + -
141D PRO* 2.9 24.3 + - + +
143D ALA* 1.3 75.8 - - - +
145D VAL* 1.3 65.0 + - - +
146D LYS 3.2 1.6 - - - -
147D THR* 2.7 40.3 + - + -
148D PHE* 3.2 31.0 - + - -
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Residues in contact with VAL 145 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
140D ILE* 3.8 26.0 - - + +
141D PRO 3.0 19.5 + - - +
142D VAL* 3.6 11.9 - - - +
144D TYR* 1.3 77.4 - - - +
146D LYS* 1.3 62.0 + - + +
147D THR 3.1 1.6 + - - -
148D PHE* 3.1 21.1 + - - +
320D LEU* 4.3 21.7 - - + +
366D GLN* 4.5 2.0 - - - +
367D SER 4.2 10.1 - - - +
368D TRP* 3.8 18.6 - - + +
369D VAL* 3.9 5.8 - - + -
371D THR* 3.2 27.2 + - + +
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Residues in contact with LYS 146 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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210A PRO* 4.0 24.9 - - - +
213A ARG* 5.1 4.9 - - - +
142D VAL* 3.1 20.2 + - + +
143D ALA* 4.1 9.4 - - - +
144D TYR 3.2 0.4 - - - -
145D VAL* 1.3 77.2 - - + +
147D THR* 1.3 58.2 + - + +
148D PHE 3.2 8.2 + - - +
369D VAL* 3.9 31.9 + - + +
371D THR* 6.0 0.4 - - - +
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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