Contacts of the helix formed by residues 178 - 186 (chain B) in PDB entry 5UQ3
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 SER 178 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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122A ARG* 4.2 36.7 - - - +
153A GLY* 6.2 1.1 - - - -
176B ILE 4.2 0.8 + - - -
177B VAL* 1.3 77.3 - - - +
179B ARG* 1.3 59.7 - - - +
180B ARG* 4.3 6.1 - - - +
181B CYS* 3.2 24.7 + - - +
182B CYS* 2.9 26.4 + - - -
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Residues in contact with ARG 179 (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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153A GLY* 3.6 34.2 + - - +
154A VAL* 4.1 11.6 - - - +
155A PRO* 3.7 29.1 - - + +
99B TYR* 3.8 7.7 + - + +
177B VAL 3.8 1.0 + - - -
178B SER* 1.3 73.2 - - - +
180B ARG* 1.3 58.5 + - - +
182B CYS* 3.1 8.5 + - - +
183B GLU* 2.8 58.8 + - - +
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Residues in contact with ARG 180 (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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178B SER* 3.3 6.3 - - - +
179B ARG* 1.3 79.4 - - - +
181B CYS* 1.3 58.7 + - - +
183B GLU* 3.3 12.0 + - - +
184B GLU* 2.9 49.7 + - - +
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Residues in contact with CYS 181 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67B GLN* 4.8 16.6 - - - -
106B VAL* 4.8 11.7 - - - -
110B ARG* 5.5 4.5 - - - -
177B VAL* 4.1 17.0 - - + -
178B SER* 3.2 25.6 + - - +
180B ARG* 1.3 79.9 - - - +
182B CYS* 1.3 60.1 + - - +
184B GLU* 3.4 12.2 + - - +
185B VAL* 3.2 33.2 + - - +
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Residues in contact with CYS 182 (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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154A VAL* 4.6 3.1 - - - -
99B TYR* 3.5 27.8 - - + -
102B ALA* 3.9 5.1 - - + +
103B MET* 3.7 27.6 - - - -
106B VAL* 5.4 1.1 - - - -
177B VAL* 3.6 24.9 - - - -
178B SER 2.9 21.1 + - - -
179B ARG* 3.3 10.1 - - - +
181B CYS* 1.3 78.5 - - - +
183B GLU* 1.3 60.2 + - - +
185B VAL* 3.2 23.0 - - - +
186B MET* 3.2 14.4 - - - +
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Residues in contact with GLU 183 (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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98B LYS* 5.1 1.1 - - - +
99B TYR* 3.0 23.7 + - + +
179B ARG* 2.8 57.4 + - - +
180B ARG* 3.8 8.8 - - - +
182B CYS* 1.3 75.4 - - - +
184B GLU* 1.3 61.6 + - - +
185B VAL 3.3 0.4 - - - -
186B MET* 3.2 25.2 - - + +
187B ALA* 3.2 13.2 + - - +
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Residues in contact with GLU 184 (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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180B ARG* 2.9 37.6 + - - +
181B CYS* 3.8 12.3 - - - +
182B CYS 3.2 0.4 - - - -
183B GLU* 1.3 78.7 - - - +
185B VAL* 1.3 62.4 + - + +
186B MET 3.3 0.2 - - - -
187B ALA* 3.4 21.3 + - + +
188B ILE* 4.3 10.2 + - - +
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Residues in contact with VAL 185 (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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67B GLN* 5.7 9.4 - - + +
71B MET* 3.2 28.5 - - - +
102B ALA* 3.6 24.9 - - + +
105B PHE* 3.9 35.9 - - + -
106B VAL* 4.3 10.8 - - + -
181B CYS* 3.2 20.4 - - - +
182B CYS* 3.2 17.5 - - - +
184B GLU* 1.3 78.5 - - + +
186B MET* 1.3 57.6 + - - +
187B ALA 3.3 3.1 - - - -
188B ILE* 3.6 7.0 - - - +
195B TRP* 3.6 3.9 - - + -
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Residues in contact with MET 186 (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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98B LYS* 2.9 61.5 - - - +
99B TYR* 4.6 2.9 - - + +
102B ALA* 3.8 8.7 - - + -
182B CYS 3.2 18.2 - - - +
183B GLU* 3.2 26.2 - - - +
185B VAL* 1.3 76.8 - - - +
187B ALA* 1.3 59.7 + - - +
188B ILE 3.1 5.4 - - - -
190B PRO* 3.6 11.8 - - - +
195B TRP* 3.2 58.6 - - + -
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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