Contacts of the helix formed by residues 137 - 143 (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 CYS 137 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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136B THR* 1.3 69.7 - - - +
138B TYR* 1.3 61.2 + - - +
139B ILE* 3.1 15.7 + - - -
140B CYS* 3.3 13.4 - - + +
141B ASP* 2.9 28.1 + - - +
149B ALA 3.0 10.7 + - - +
154B CYS* 3.6 5.5 - - - -
165B ALA 3.4 6.1 - - - -
166B PHE* 3.6 7.2 - - - +
167B HIS* 3.4 35.7 - - + +
170B CYS* 3.9 1.3 - - - -
304B ZN 2.3 36.8 - - - -
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Residues in contact with TYR 138 (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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174A ALA 5.2 2.9 + - - -
136B THR* 3.1 5.9 + - - +
137B CYS* 1.3 72.8 - - - +
139B ILE* 1.3 81.4 + - + +
141B ASP* 3.5 8.2 - - - +
142B GLU* 2.8 68.1 + - + +
164B GLN* 3.6 27.1 - - + +
165B ALA 2.8 26.8 + - - +
166B PHE* 3.6 21.8 - + - -
176B LEU* 3.6 13.9 - - + +
194B CYS* 3.9 14.8 - - + -
195B LYS* 3.0 40.5 + - + +
196B TYR* 5.4 2.5 - + - -
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Residues in contact with ILE 139 (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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173A PHE 4.1 7.9 - - - +
174A ALA* 5.5 6.5 - - - +
137B CYS* 3.1 8.4 - - - -
138B TYR* 1.3 113.3 - - + +
140B CYS* 1.3 64.9 + - - +
142B GLU* 3.4 4.2 + - - +
143B GLN* 3.2 42.0 + - - +
166B PHE* 4.1 8.7 - - + -
170B CYS* 3.9 40.8 - - + +
171B ALA* 4.0 9.2 - - - +
174B ALA* 4.4 6.7 - - + -
176B LEU* 4.3 9.4 - - + -
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Residues in contact with CYS 140 (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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86B PRO* 4.3 4.7 - - - -
137B CYS* 3.3 5.5 + - - +
139B ILE* 1.3 77.8 - - - +
141B ASP* 1.3 54.7 + - - +
143B GLN* 3.4 10.5 + - - -
144B GLY 3.3 3.3 + - - -
145B ARG* 2.7 40.6 + - + +
148B LYS* 3.8 26.0 - - - -
149B ALA* 3.5 22.9 - - + +
167B HIS* 3.5 12.6 - - - -
170B CYS* 3.7 7.2 - - - -
304B ZN 2.4 33.2 - - - -
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Residues in contact with ASP 141 (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* 3.7 10.9 - - - +
136B THR* 3.8 22.2 - - + +
137B CYS 2.9 18.7 + - - +
138B TYR* 3.5 8.9 - - - +
140B CYS* 1.3 76.2 - - - +
142B GLU* 1.3 60.3 + - + +
144B GLY* 2.9 19.1 + - - -
145B ARG 4.4 2.0 - - - +
146B GLU* 4.9 11.4 - - - +
149B ALA* 4.1 4.2 - - + +
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Residues in contact with GLU 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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29A SER* 4.1 21.1 + - - +
31A GLU* 5.2 1.3 - - - +
175A GLY* 4.0 15.2 - - - -
138B TYR* 2.8 45.5 + - + +
139B ILE* 3.4 5.5 + - - +
140B CYS 3.4 0.2 - - - -
141B ASP* 1.3 69.6 - - + +
143B GLN* 1.3 60.5 + - + +
144B GLY* 3.0 6.0 + - - -
195B LYS* 2.7 36.4 + - - -
196B TYR* 4.8 4.5 + - - -
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Residues in contact with GLN 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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21A MET 4.5 7.0 - - - +
22A ILE* 3.4 19.6 - - + +
23A GLY 2.7 30.0 + - - -
29A SER* 5.3 1.6 - - - -
172A GLN 5.1 1.6 - - - +
173A PHE* 2.8 59.5 + - + +
139B ILE* 3.2 28.2 + - - +
140B CYS* 3.8 12.2 - - - +
141B ASP 3.2 0.8 - - - -
142B GLU* 1.3 77.4 - - + +
144B GLY* 1.3 52.1 + - - +
145B ARG* 3.9 15.4 - - + +
148B LYS* 5.3 5.4 + - - -
170B CYS* 6.6 0.2 - - - -
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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