Contacts of the strand formed by residues 155 - 159 (chain E) in PDB entry 1QGN
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 155 (chain E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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150E VAL* 4.8 1.0 - - - +
153E GLY 5.2 0.4 - - - +
154E GLY* 1.3 74.4 - - - -
156E ILE* 1.3 81.8 + - - +
157E VAL* 4.1 9.2 - - + -
179E ILE* 5.0 0.4 - - - -
180E THR* 2.8 28.8 + - - +
181E ALA 3.5 18.2 - - - -
182E THR* 2.8 27.8 + - - -
199E LYS* 3.3 40.4 - - + +
200E LYS 3.6 19.6 + - - +
201E VAL* 4.1 7.0 - - + -
202E ASN* 3.0 38.3 + - - +
203E LEU 3.9 0.2 + - - -
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Residues in contact with ILE 156 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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146E LEU* 3.3 33.7 - - + -
150E VAL* 4.2 12.1 - - + -
155E HIS* 1.3 76.2 - - - +
157E VAL* 1.3 60.9 + - - +
158E THR* 4.4 17.7 - - + +
170E ILE* 4.1 17.5 - - + -
174E LEU* 4.8 5.2 - - + -
179E ILE* 4.7 8.1 - - + -
180E THR 2.8 8.5 + - - +
181E ALA* 2.9 28.4 - - + -
182E THR 2.7 30.3 + - - -
201E VAL* 5.2 0.2 - - - -
202E ASN 5.2 0.2 - - - +
203E LEU* 3.5 29.8 - - + +
205E PHE* 4.6 0.9 - - + -
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Residues in contact with VAL 157 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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155E HIS* 4.1 0.7 - - + -
156E ILE* 1.3 78.9 - - - +
158E THR* 1.3 65.5 + - - +
182E THR* 3.3 33.4 - - + +
184E ILE* 4.2 10.5 - - + -
192E LEU* 4.1 14.8 - - + -
195E ALA* 4.6 4.9 - - + -
201E VAL* 3.3 34.5 - - + -
203E LEU 3.2 9.2 + - - +
204E PHE* 3.1 29.0 - - + -
205E PHE 2.9 25.5 + - - -
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Residues in contact with THR 158 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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156E ILE* 4.4 11.1 - - + +
157E VAL* 1.3 78.4 - - - +
159E THR* 1.3 68.1 + - - +
162E CYS* 4.4 13.9 - - - +
167E ARG* 5.5 1.7 - - - -
170E ILE* 4.3 18.7 - - + +
182E THR 3.0 4.9 + - - -
183E VAL* 3.1 18.0 - - - +
184E ILE* 2.9 27.7 + - - +
204E PHE* 4.4 2.5 - - - -
205E PHE* 2.8 46.4 - - + +
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Residues in contact with THR 159 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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158E THR* 1.3 82.6 + - - +
160E THR* 1.3 61.6 + - - +
161E ASP* 3.0 20.2 + - - +
162E CYS* 3.4 24.0 + - - +
167E ARG* 4.6 1.7 + - - -
183E VAL* 3.7 7.3 - - - +
184E ILE* 3.0 13.9 - - + -
185E ASP 4.6 1.3 - - - +
186E PRO* 3.8 32.4 - - + +
204E PHE* 4.7 9.0 - - + -
205E PHE 4.3 0.6 + - - -
206E THR* 3.2 31.3 + - - +
207E GLU* 5.5 0.9 - - - +
210E THR* 4.4 2.8 + - - +
217E VAL* 4.8 2.0 - - + -
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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