Contacts of the helix formed by residues 188 - 194 (chain E) in PDB entry 5HMG
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 ASN 188 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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201A ARG* 4.5 19.0 - - - +
187E THR* 1.3 72.4 - - - +
189E GLN* 1.3 63.1 + - - +
191E GLN* 3.1 6.5 + - - +
192E THR* 3.0 30.4 + - + +
198E ALA* 4.4 11.4 - - - +
217E ILE* 3.6 28.4 - - - +
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Residues in contact with GLN 189 (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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187E THR* 3.2 33.0 + - - +
188E ASN* 1.3 77.8 - - - +
190E GLU* 1.3 55.1 + - + +
192E THR* 3.0 8.2 + - - -
193E SER* 2.9 32.7 + - - -
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Residues in contact with GLU 190 (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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183E HIS* 3.3 4.2 - - - -
185E PRO* 3.2 15.8 - - + +
186E SER* 2.9 33.1 + - - -
187E THR* 2.9 22.6 + - - +
189E GLN* 1.3 74.0 - - + +
191E GLN* 1.3 66.3 + - - +
193E SER* 3.4 5.5 + - - -
194E LEU* 3.0 34.9 + - + +
228E SER* 3.1 9.7 + - - -
329E SIA 2.8 41.1 + - - +
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Residues in contact with GLN 191 (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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185E PRO* 3.5 18.4 - - + +
187E THR 3.1 10.6 + - - +
188E ASN* 3.3 9.9 - - - +
190E GLU* 1.3 77.0 - - - +
192E THR* 1.3 59.0 + - + +
195E TYR* 2.8 39.5 + - - +
197E GLN* 3.0 20.9 + - - +
198E ALA* 3.3 26.5 - - - +
200E GLY* 3.8 10.9 + - - +
215E PRO* 4.2 2.4 - - - +
217E ILE* 4.0 18.7 - - + +
250E ASN* 2.9 41.0 + - - +
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Residues in contact with THR 192 (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 LYS* 4.3 1.6 + - - -
188E ASN* 3.0 19.0 + - + +
189E GLN* 3.0 14.0 + - - -
191E GLN* 1.3 76.2 - - + +
193E SER* 1.3 64.6 + - - +
196E VAL* 2.9 45.7 + - - +
197E GLN 4.0 7.4 - - - +
198E ALA* 4.2 14.8 - - + +
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Residues in contact with SER 193 (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 LYS* 2.7 37.6 + - - +
189E GLN 2.9 20.7 + - - -
190E GLU* 3.5 7.2 - - - -
192E THR* 1.3 76.7 + - - +
194E LEU* 1.3 65.1 + - - +
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Residues in contact with LEU 194 (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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153E TRP* 4.1 10.8 - - + -
155E THR* 3.8 10.1 - - + -
156E LYS* 2.9 34.4 + - - +
183E HIS* 3.8 15.7 - - + -
190E GLU* 3.0 21.0 + - + +
193E SER* 1.3 85.9 - - - +
195E TYR* 1.3 100.7 + - + +
196E VAL 3.5 0.2 - - - -
329E SIA 3.2 43.7 - - - +
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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