Contacts of the helix formed by residues 141 - 145 (chain A) in PDB entry 4M0A
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 A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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139A PRO 4.2 0.9 - - - +
140A ALA* 1.3 87.5 - - + +
142A ALA* 1.3 65.3 + - - +
143A CYS* 3.9 15.3 - - - -
144A GLN* 3.1 36.5 + - - +
145A ARG* 3.4 10.3 + - - -
443A GLU* 3.4 14.4 - - - -
446A ARG* 3.5 37.3 + - + -
447A PHE* 3.6 36.3 - + + -
450A LYS* 3.7 13.9 - - - +
451A GLU* 2.6 44.5 + - + +
4D G 6.0 2.9 - - - -
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Residues in contact with ALA 142 (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 TYR* 1.3 70.8 - - - +
143A CYS* 1.3 57.8 + - - +
144A GLN 3.1 1.3 + - - -
145A ARG* 3.1 53.7 + - - +
147A THR* 4.5 2.5 + - - +
181A ARG* 6.4 0.4 - - + -
184A SER* 4.2 1.3 - - - +
439A LEU* 4.8 4.0 - - + -
440A PHE* 3.9 9.4 - - - -
443A GLU* 2.9 30.1 + - + +
494A ALA* 3.7 26.9 - - + -
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Residues in contact with CYS 143 (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 TYR* 3.9 9.2 - - - -
142A ALA* 1.3 77.8 - - - +
144A GLN* 1.3 60.7 + - - +
145A ARG 3.4 0.9 - - - -
440A PHE* 3.6 22.0 - - + +
443A GLU* 3.8 6.1 - - - +
444A LEU* 3.7 41.1 - - + +
447A PHE* 3.7 36.3 - - - -
479A PHE* 4.8 1.6 - - - -
484A LEU* 3.9 17.7 - - - +
485A GLU 5.0 1.2 - - - +
487A LEU* 3.6 15.4 - - - +
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Residues in contact with GLN 144 (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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139A PRO* 3.4 29.1 - - + +
140A ALA* 3.7 2.4 + - - +
141A TYR* 3.3 43.1 + - + +
142A ALA 3.1 1.0 - - - -
143A CYS* 1.3 79.5 - - - +
145A ARG* 1.3 59.3 + - - +
146A PRO* 4.7 0.7 - - - +
447A PHE* 3.5 25.9 - - + -
484A LEU* 3.8 21.7 - - + +
487A LEU* 5.0 1.8 - - - -
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Residues in contact with ARG 145 (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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138A MET* 3.5 21.2 - - - -
139A PRO* 2.9 35.5 + - + -
140A ALA 3.6 7.9 + - - -
141A TYR 3.4 16.5 + - - +
142A ALA* 3.1 40.1 - - - +
143A CYS 3.4 1.4 + - - -
144A GLN* 1.3 82.9 - - - +
146A PRO* 1.3 74.3 - - + +
147A THR* 3.5 7.3 + - - +
181A ARG* 4.1 3.6 + - - +
184A SER* 3.5 24.4 + - - -
185A VAL* 3.6 33.5 - - - +
188A ALA* 3.9 20.2 - - + +
204A HIS* 5.5 1.2 - - - -
440A PHE* 4.8 0.3 - - - -
443A GLU* 5.4 0.8 + - - -
487A LEU* 3.6 12.7 - - - +
491A GLN 4.1 0.9 - - - +
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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