Contacts of the helix formed by residues 130 - 134 (chain F) in PDB entry 3Q2K
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 LYS 130 (chain F).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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103F LYS* 4.5 16.5 - - + +
104F PRO* 5.6 3.2 - - - +
128F VAL* 2.9 17.7 + - - +
129F VAL* 1.3 78.9 - - - +
131F GLN* 1.3 62.8 + - - +
132F ASN* 3.3 4.4 + - + -
133F ARG* 3.3 41.0 + - + +
134F ARG* 5.7 1.0 - - - +
190F SER* 4.7 6.9 + - - -
191F HIS* 4.7 10.3 - - - +
194F ASP* 3.6 27.6 + - + +
304F TYR* 3.8 11.6 - - - -
319F GLU* 4.9 2.8 - - - +
320F THR* 3.5 28.9 - - + +
324F GLU 5.2 0.7 - - - -
325F GLY* 4.7 8.2 + - - -
328F SER* 2.9 27.9 + - - -
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Residues in contact with GLN 131 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
129F VAL* 3.4 8.8 - - + +
130F LYS* 1.3 74.6 - - - +
132F ASN* 1.3 67.5 + - - +
133F ARG 3.2 1.0 + - - -
134F ARG* 3.5 16.8 + - - +
135F ASN* 4.1 4.2 - - - +
191F HIS* 3.5 12.5 + - - -
300F GLY* 3.5 43.0 - - - +
301F HIS* 3.4 25.4 - - - +
304F TYR* 4.1 17.4 - - + +
500F NAI 2.8 39.3 + - - -
550F HP7 4.4 12.1 - - - +
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Residues in contact with ASN 132 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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130F LYS 3.3 1.4 - - - -
131F GLN* 1.3 80.6 - - - +
133F ARG* 1.3 67.0 + - + +
134F ARG 2.9 5.4 + - - -
135F ASN* 3.2 38.4 + - - +
138F LEU* 3.4 28.7 - - + +
191F HIS* 4.1 29.2 + - + +
192F TYR* 5.1 6.7 + - - -
195F LEU* 6.1 2.2 - - + +
267F ALA 5.4 0.6 + - - -
268F VAL* 4.3 12.7 - - - +
550F HP7 3.8 24.4 - - - +
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Residues in contact with ARG 133 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
130F LYS* 3.4 32.8 - - + +
131F GLN 3.2 1.2 - - - -
132F ASN* 1.3 78.8 - - + +
134F ARG* 1.3 59.2 + - + +
135F ASN 3.5 2.1 + - - +
138F LEU* 4.5 3.2 - - - +
139F GLN* 3.8 11.7 - - - +
194F ASP* 2.8 40.1 + - - +
195F LEU* 5.9 1.3 - - + -
198F TRP* 3.1 75.3 - - + +
319F GLU* 3.6 28.4 + - - +
320F THR* 3.7 13.5 + - - -
324F GLU* 3.3 38.8 + - - +
327F GLN* 5.9 1.6 - - - +
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Residues in contact with ARG 134 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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130F LYS 5.7 0.4 - - - +
131F GLN 3.5 10.0 + - - +
132F ASN 3.0 1.4 - - - -
133F ARG* 1.3 78.8 - - + +
135F ASN* 1.3 66.5 + - - +
136F ALA* 3.5 2.1 + - - -
139F GLN* 3.9 24.8 + - - +
300F GLY* 6.1 0.7 - - - +
303F LEU* 3.7 48.8 + - + +
304F TYR* 5.7 5.2 - - + +
307F ASN* 4.2 19.4 - - - +
319F GLU* 3.8 45.7 + - - +
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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