Contacts of the helix formed by residues 145 - 151 (chain B) in PDB entry 5DAH
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 145 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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21A MET* 3.7 35.2 + - - +
22A ILE 4.6 0.7 - - - -
23A GLY* 4.3 4.5 - - - +
140B CYS* 2.7 23.7 + - + +
141B ASP* 4.2 1.0 + - - +
143B GLN* 3.9 23.1 - - + +
144B GLY* 1.3 75.6 - - - +
146B GLU* 1.3 57.4 + - - +
148B LYS* 3.7 39.4 - - + +
149B ALA* 2.9 29.0 + - - +
306B SO4 2.6 56.9 + - - +
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Residues in contact with GLU 146 (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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31A GLU* 6.1 0.7 - - - +
141B ASP* 4.9 10.1 - - - +
144B GLY 3.7 4.1 + - - +
145B ARG* 1.3 75.0 - - - +
147B SER* 1.3 62.5 + - - +
149B ALA* 3.5 16.6 + - - +
150B ALA* 3.5 11.4 + - - +
306B SO4 3.0 3.4 + - - -
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Residues in contact with SER 147 (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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146B GLU* 1.3 71.3 - - - +
148B LYS* 1.3 63.4 + - - +
150B ALA* 3.2 14.1 + - - +
151B THR* 3.4 11.1 + - - -
306B SO4 2.6 32.7 + - - -
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Residues in contact with LYS 148 (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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21A MET* 6.4 0.4 - - - +
86B PRO* 3.5 33.3 + - + +
87B HIS* 6.0 1.0 - - - +
140B CYS* 3.9 17.8 - - - -
143B GLN* 5.3 5.1 + - - -
145B ARG* 3.7 42.7 - - + +
147B SER* 1.3 79.2 - - - +
149B ALA* 1.3 58.9 + - - +
151B THR* 3.0 18.3 - - - +
167B HIS* 3.0 23.2 - - - -
306B SO4 3.2 16.4 + - - +
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Residues in contact with ALA 149 (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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135B LYS 3.6 2.3 - - - +
136B THR* 3.5 29.0 - - + -
137B CYS* 3.0 29.1 + - - +
140B CYS* 3.5 18.8 - - + -
141B ASP* 4.1 4.7 - - + +
145B ARG 2.9 19.1 + - - +
146B GLU* 3.5 11.9 - - - +
147B SER 3.1 0.6 - - - -
148B LYS* 1.3 77.4 - - - +
150B ALA* 1.3 59.6 + - + +
151B THR 3.4 0.6 + - - +
154B CYS* 4.7 0.7 - - - -
167B HIS* 4.1 5.3 + - - -
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Residues in contact with ALA 150 (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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133B TYR 4.6 8.7 - - - +
135B LYS 4.0 12.4 - - - +
136B THR* 4.9 6.7 - - - +
146B GLU 3.5 11.2 + - - +
147B SER* 3.2 5.6 + - - +
148B LYS 3.2 0.6 - - - -
149B ALA* 1.3 77.0 - - - +
151B THR* 1.3 65.4 + - - +
152B GLY 4.2 4.5 - - - +
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Residues in contact with THR 151 (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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85B CYS 4.1 1.9 + - - -
86B PRO* 3.5 39.3 - - + +
135B LYS 5.6 0.2 - - - +
147B SER 3.4 10.8 + - - -
148B LYS* 3.0 23.5 + - - +
149B ALA 4.4 0.3 - - - +
150B ALA* 1.3 81.4 - - - +
152B GLY* 1.3 68.2 + - - +
153B ALA 4.8 0.2 - - - -
154B CYS* 5.4 1.0 - - - -
167B HIS* 2.9 22.2 + - - -
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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