Contacts of the helix formed by residues 125 - 129 (chain E) in PDB entry 1QRP
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 TYR 125 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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36E SER* 2.8 20.3 + - - -
124E ALA* 1.3 74.3 - - - +
126E PRO* 1.3 70.8 - - + +
127E SER* 3.1 7.5 + - - +
128E ILE* 3.4 9.2 + - - +
184E VAL* 4.1 7.1 - - + +
187E GLU* 4.0 26.8 - - + +
188E GLY* 2.9 46.1 + - - +
189E TYR 3.8 11.7 - - - -
190E TRP* 3.8 34.1 - + - -
315E ARG* 3.2 38.8 - - - +
318E ASN* 2.8 40.6 + - - +
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Residues in contact with PRO 126 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
124E ALA 4.0 0.2 - - - -
125E TYR* 1.3 88.1 - - + +
127E SER* 1.3 61.7 + - - +
129E SER* 3.0 22.0 + - - +
132E GLY* 5.0 4.5 - - - -
133E ALA 5.6 0.4 - - - +
134E THR* 5.9 0.7 - - - -
135E PRO* 3.9 20.8 - - + -
138E ASP* 3.2 37.0 - - + +
315E ARG* 3.8 10.3 - - - +
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Residues in contact with SER 127 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
125E TYR* 4.0 2.4 - - - +
126E PRO* 1.3 80.6 - - - +
128E ILE* 1.3 62.9 + - - +
129E SER 3.4 2.4 + - - +
187E GLU 2.9 26.5 + - - -
188E GLY* 3.5 10.4 - - - -
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Residues in contact with ILE 128 (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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35E SER* 4.2 11.9 - - - -
36E SER* 3.3 23.8 + - - +
37E ASN* 4.6 1.0 - - - +
124E ALA* 3.9 7.2 - - + -
125E TYR 3.5 4.0 - - - +
127E SER* 1.3 80.5 + - - +
129E SER* 1.3 63.2 + - - +
130E SER* 3.4 4.7 + - - -
188E GLY* 3.8 30.3 - - - +
189E TYR* 3.5 47.1 - - + +
327E HH0 4.5 34.6 - - + +
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Residues in contact with SER 129 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36E SER* 3.9 19.5 + - - -
37E ASN* 3.4 20.8 + - - -
126E PRO* 3.0 20.4 + - - +
127E SER 3.4 1.9 - - - +
128E ILE* 1.3 78.9 - - - +
130E SER* 1.3 64.7 + - - +
131E SER 3.6 0.3 + - - -
132E GLY* 3.2 13.2 + - - -
133E ALA 2.6 34.0 + - - -
135E PRO* 4.5 0.2 - - - -
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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