Contacts of the helix formed by residues 5163 - 5167 (chain E) in PDB entry 1Y1S
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 TYR5163 (chain E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2007C PHE* 4.1 9.4 + - - +
2075C SER 4.9 3.6 - - - -
2076C ILE* 4.6 7.9 - - + -
2079C GLU* 3.6 31.6 - - + +
2080C GLU* 2.7 33.5 + - + +
2083C GLN* 4.3 10.5 + - - -
5161E THR 3.4 0.2 - - - -
5162E PHE* 1.3 110.8 - + + +
5164E PRO* 1.3 78.6 - - + +
5165E GLY 3.4 0.2 - - - -
5166E GLN 3.2 7.6 + - - -
5167E GLU 3.3 0.2 + - - -
5168E ARG* 3.0 42.1 + - - +
5170E ASP 4.8 3.6 - - - -
5171E THR* 3.4 32.8 - - + -
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Residues in contact with PRO5164 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2079C GLU* 5.7 1.1 - - - +
2122C HIS 3.1 22.2 - - - +
2123C PHE* 3.5 34.8 - - + -
2209C GLN* 5.8 0.4 - - - +
5161E THR* 3.7 12.3 - - - +
5163E TYR* 1.3 94.9 - - + +
5165E GLY* 1.3 55.4 + - - +
5167E GLU* 2.7 25.7 + - - +
5168E ARG 4.6 1.3 - - - +
5175E ARG 5.3 5.2 - - - +
5176E VAL* 3.8 25.2 - - + +
5177E VAL* 5.0 0.7 - - + -
5180E PHE* 3.8 13.7 - - - +
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Residues in contact with GLY5165 (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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2122C HIS* 3.4 17.8 + - - -
5116E LEU* 4.5 2.6 - - - +
5159E SER* 3.5 14.7 + - - -
5161E THR* 2.7 25.1 + - - -
5163E TYR 3.4 0.2 + - - -
5164E PRO* 1.3 71.6 - - - +
5166E GLN* 1.3 56.6 + - - +
5167E GLU 3.3 1.3 - - - -
5180E PHE* 4.1 22.1 - - - -
5183E SER* 5.1 0.2 + - - -
5187E TRP* 5.2 0.3 + - - -
5195E TYR* 3.6 15.6 + - - -
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Residues in contact with GLN5166 (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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5159E SER* 4.2 4.9 - - - -
5161E THR 3.1 21.3 + - - +
5162E PHE* 3.4 26.6 - - - +
5163E TYR 3.2 1.6 + - - -
5164E PRO 3.0 0.8 - - - -
5165E GLY* 1.3 79.4 - - - +
5167E GLU* 1.3 61.6 + - - +
5168E ARG* 3.1 13.8 + - - +
5184E MET* 4.3 0.5 - - - +
5195E TYR* 3.2 46.5 - - + +
5196E GLU 4.6 0.6 + - - -
5197E MET* 3.6 9.9 - - - +
5223E ARG* 2.8 35.1 + - - +
8005E URA 2.8 42.5 + - - +
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Residues in contact with GLU5167 (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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5164E PRO 2.7 14.7 + - - +
5165E GLY 3.3 1.4 + - - -
5166E GLN* 1.3 80.2 - - - +
5168E ARG* 1.3 60.3 + - - +
5169E TYR* 3.0 38.6 + - + +
5176E VAL* 4.6 5.6 - - + -
5180E PHE 3.2 20.2 - - - +
5182E GLY* 2.5 26.6 + - - -
5183E SER* 3.2 5.1 + - - +
5184E MET* 2.7 45.8 + - + +
5185E GLU 4.3 0.9 + - - -
5223E ARG* 3.2 9.9 + - - -
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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