Contacts of the helix formed by residues 167 - 174 (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 HIS 167 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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84B LEU 3.9 7.9 - - - -
85B CYS* 4.4 2.9 - - + -
86B PRO* 3.3 23.3 - - + +
137B CYS* 3.4 13.7 - - + +
140B CYS* 3.7 1.1 - - - -
148B LYS 3.0 26.7 - - - -
149B ALA 4.1 3.4 + - - -
151B THR 2.9 23.0 + - - -
153B ALA 3.0 31.2 - - - -
154B CYS* 4.1 3.9 - - - -
166B PHE* 1.3 78.4 - - - +
168B VAL* 1.3 66.6 + - - +
169B THR* 3.9 7.9 - - + +
170B CYS* 3.1 13.1 + - - +
171B ALA 3.0 18.0 + - - -
304B ZN 2.2 32.9 - - - -
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Residues in contact with VAL 168 (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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84B LEU 5.7 0.6 + - - +
104B VAL* 3.3 45.8 - - + +
105B CYS* 3.7 19.4 - - - -
108B TYR* 3.9 14.1 - - + -
109B ILE* 3.6 34.5 - - + -
153B ALA 4.8 1.4 + - - +
155B MET* 3.9 24.5 - - + +
166B PHE 3.4 3.6 + - - -
167B HIS* 1.3 71.3 - - - +
169B THR* 1.3 62.5 + - - +
171B ALA* 3.2 5.9 + - - +
172B GLN* 3.0 20.4 + - - +
177B LEU* 3.9 3.6 - - + +
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Residues in contact with THR 169 (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* 3.5 28.9 - - + -
86B PRO* 4.7 1.1 - - + -
87B HIS* 3.3 47.0 - - + +
102B HIS* 4.0 5.5 + - - -
104B VAL* 4.6 4.1 - - - +
105B CYS* 4.2 6.0 - - - -
167B HIS* 3.0 5.9 - - + +
168B VAL* 1.3 81.5 - - - +
170B CYS* 1.3 71.9 + - - +
172B GLN* 3.5 18.1 + - - +
173B PHE* 3.4 19.8 + - - +
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Residues in contact with CYS 170 (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* 5.2 2.5 - - - -
137B CYS* 3.9 8.1 - - - -
139B ILE* 3.9 22.5 - - + +
140B CYS* 3.7 8.1 - - - -
143B GLN* 6.2 0.2 - - - -
148B LYS* 6.1 1.1 - - - -
167B HIS* 3.1 15.6 + - + +
169B THR* 1.3 87.5 - - - +
171B ALA* 1.3 64.7 + - - +
172B GLN 3.4 0.2 + - - -
173B PHE* 3.4 7.3 + - - +
174B ALA* 3.2 22.2 + - - +
304B ZN 2.3 36.6 - - - -
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Residues in contact with ALA 171 (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 ILE* 4.0 10.2 - - + +
166B PHE* 3.5 35.0 - - + -
167B HIS 3.0 6.0 + - - +
168B VAL* 3.2 9.2 + - - +
170B CYS* 1.3 75.8 - - - +
172B GLN* 1.3 60.9 + - - +
174B ALA* 3.1 2.7 + - - -
175B GLY 3.0 4.7 + - - -
176B LEU* 2.8 37.4 + - + -
177B LEU* 3.9 15.5 - - + -
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Residues in contact with GLN 172 (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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143A GLN* 5.4 2.1 - - - +
25B CYS 5.1 0.6 + - - -
26B CYS* 2.8 37.3 + - - +
27B VAL* 4.2 7.9 + - - +
28B CYS 5.5 1.6 + - - -
87B HIS* 5.8 1.6 - - - -
104B VAL* 4.0 24.0 - - + +
168B VAL 3.0 8.3 + - - +
169B THR* 3.5 17.0 + - - +
170B CYS 3.2 0.4 - - - -
171B ALA* 1.3 76.7 - - - +
173B PHE* 1.3 58.0 + - - +
175B GLY* 2.9 21.0 + - - -
176B LEU 4.8 0.7 - - - +
177B LEU* 3.6 26.2 - - + +
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Residues in contact with PHE 173 (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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139A ILE* 4.2 7.7 - - + +
143A GLN* 3.0 70.7 + - + +
145A ARG* 5.6 6.5 - - - -
148A LYS* 5.6 5.6 - - - -
173A PHE* 5.8 10.3 - - + -
174A ALA* 5.6 0.5 - - - +
87B HIS* 5.8 9.4 - + - -
169B THR 3.4 8.4 + - - +
170B CYS* 3.4 10.7 + - - +
171B ALA 3.4 0.4 - - - -
172B GLN* 1.3 78.9 - - - +
174B ALA* 1.3 57.8 + - - +
175B GLY 3.3 1.0 + - - -
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Residues in contact with ALA 174 (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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138A TYR* 5.6 1.6 + - - -
139A ILE* 5.7 6.7 - - - +
174A ALA* 4.3 32.3 - - + +
176A LEU* 5.6 2.3 - - - +
195A LYS* 4.3 8.8 - - - +
139B ILE* 4.4 8.7 - - + -
170B CYS 3.2 15.3 + - - +
171B ALA 3.1 5.6 + - - +
173B PHE* 1.3 76.2 - - - +
175B GLY* 1.3 61.7 + - - +
176B LEU* 3.3 29.2 + - + +
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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