Contacts of the helix formed by residues 130 - 134 (chain J) 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 J).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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103J LYS* 4.0 23.2 - - + +
104J PRO* 5.2 2.0 - - - +
128J VAL* 3.0 13.7 + - + +
129J VAL* 1.3 80.8 - - - +
131J GLN* 1.3 62.3 + - - +
132J ASN* 3.5 2.2 - - - -
133J ARG* 3.3 28.9 + - - +
134J ARG* 5.2 0.9 - - - +
190J SER* 3.3 32.3 + - - -
191J HIS* 4.3 8.9 - - - +
194J ASP* 3.7 28.3 - - - +
304J TYR* 3.9 10.3 - - - -
320J THR* 3.5 33.4 + - + +
324J GLU 5.8 0.2 - - - -
325J GLY* 5.5 4.7 - - - -
328J SER* 3.4 22.0 + - - -
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Residues in contact with GLN 131 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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129J VAL* 3.6 8.7 - - + +
130J LYS* 1.3 69.0 - - - +
132J ASN* 1.3 69.2 + - - +
133J ARG 3.0 2.5 - - - -
134J ARG* 2.9 27.2 + - + +
135J ASN* 4.0 2.1 + - - +
191J HIS* 3.5 8.9 + - - -
298J GLY 6.2 1.0 - - - -
300J GLY* 3.7 43.3 - - - +
301J HIS* 3.7 15.3 + - - +
304J TYR* 4.3 15.3 - - + -
500J NAI 3.1 40.3 + - - -
550J HP7 3.2 19.1 - - - +
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Residues in contact with ASN 132 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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130J LYS 3.4 1.0 + - - -
131J GLN* 1.3 79.9 + - - +
133J ARG* 1.3 62.4 + - - +
135J ASN* 2.8 39.6 + - - +
138J LEU* 3.5 17.6 - - + +
191J HIS* 3.5 40.5 + - + +
192J TYR* 4.3 20.0 + - - -
194J ASP* 6.0 1.3 - - - +
195J LEU* 5.4 2.0 - - + -
267J ALA* 5.4 2.0 + - - +
268J VAL* 4.5 6.1 - - - +
550J HP7 3.8 20.7 + - - +
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Residues in contact with ARG 133 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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130J LYS* 3.3 16.1 + - - +
131J GLN 3.0 2.0 + - - -
132J ASN* 1.3 78.9 - - - +
134J ARG* 1.3 61.7 + - + +
135J ASN 3.4 1.7 + - - +
138J LEU* 4.9 0.2 - - - -
139J GLN* 2.9 26.8 + - - +
194J ASP* 2.7 42.3 + - - +
195J LEU* 5.7 1.1 - - + +
198J TRP* 3.3 60.5 - - + +
319J GLU* 3.7 24.2 + - - +
320J THR* 3.0 32.6 + - - +
324J GLU* 2.8 47.2 + - - +
327J GLN* 5.9 1.0 - - - +
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Residues in contact with ARG 134 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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130J LYS 5.2 1.1 - - - +
131J GLN* 2.9 22.5 + - - +
133J ARG* 1.3 77.6 - - + +
135J ASN* 1.3 64.7 + - - +
136J ALA* 3.3 2.6 + - - -
139J GLN* 3.5 30.5 - - - +
300J GLY* 4.8 3.4 - - - +
303J LEU* 3.7 64.0 - - + +
304J TYR* 4.2 15.0 - - + +
307J ASN* 5.5 6.1 - - - +
319J GLU* 2.3 37.9 + - - +
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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