Contacts of the helix formed by residues 141 - 145 (chain B) in PDB entry 2IHM
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 TYR 141 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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139B PRO 4.1 0.2 - - - +
140B ALA* 1.3 90.9 - - + +
142B ALA* 1.3 57.6 + - - +
143B CYS* 3.0 20.4 - - - -
144B GLN* 2.9 43.9 + - - +
145B ARG* 3.8 10.6 - - - -
445B GLU* 3.5 13.0 - - - +
448B ARG* 2.9 39.2 + - - -
449B PHE* 3.3 44.4 - + + -
452B GLN* 3.6 15.6 + - - +
453B GLU* 2.8 33.9 + - + +
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Residues in contact with ALA 142 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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141B TYR* 1.3 72.2 - - - +
143B CYS* 1.3 57.3 + - - +
144B GLN 3.1 0.9 - - - -
145B ARG* 2.9 52.3 - - - +
147B SER* 4.3 2.5 + - - +
184B SER* 4.0 0.2 - - - +
441B PHE* 3.9 15.0 - - + -
442B PHE* 3.9 13.3 - - + -
445B GLU* 3.5 15.7 + - + +
496B ALA* 3.6 29.2 - - + -
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Residues in contact with CYS 143 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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141B TYR* 3.0 23.4 - - - -
142B ALA* 1.3 79.0 - - - +
144B GLN* 1.3 55.7 + - - +
145B ARG 3.5 0.7 - - - -
442B PHE* 3.8 15.9 - - + -
445B GLU* 3.7 10.3 - - - +
446B LEU* 3.8 33.0 - - + +
449B PHE* 3.6 27.8 - - - -
481B PHE* 4.8 0.7 - - - -
486B LEU* 4.0 27.2 - - + +
487B LYS 4.9 0.7 + - - +
489B LEU* 3.5 15.8 - - - +
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Residues in contact with GLN 144 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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139B PRO* 3.5 20.3 - - + +
140B ALA* 3.8 7.1 + - - +
141B TYR* 2.9 42.8 + - + +
143B CYS* 1.3 79.1 - - - +
145B ARG* 1.3 59.1 + - - +
449B PHE* 3.6 25.9 - - + -
486B LEU* 4.0 20.6 - - + +
489B LEU* 4.9 2.0 - - - -
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Residues in contact with ARG 145 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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138B MET* 3.9 12.3 - - - +
139B PRO* 2.8 50.0 + - + -
140B ALA* 3.5 18.8 + - - +
141B TYR 3.8 8.0 - - - -
142B ALA* 2.9 35.8 - - - +
143B CYS 3.5 1.6 - - - -
144B GLN* 1.3 81.6 - - - +
146B PRO* 1.3 73.2 - - + +
147B SER* 3.8 3.9 + - - +
181B ARG 4.5 1.4 + - - -
184B SER* 3.0 42.0 + - - -
185B VAL* 3.7 14.0 - - - +
188B SER* 3.4 31.6 + - - +
203B PRO* 5.2 0.4 - - - +
204B TYR* 5.6 0.4 - - - -
441B PHE* 4.8 2.2 - - - -
489B LEU* 3.8 12.7 - - - +
493B GLN 4.3 0.7 - - - +
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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