Contacts of the helix formed by residues 130 - 134 (chain M) 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 M).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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103M LYS* 3.7 18.5 - - + +
104M PRO* 4.9 3.8 - - - +
128M VAL* 3.1 13.9 + - + +
129M VAL* 1.3 78.0 - - - +
131M GLN* 1.3 65.5 + - - +
132M ASN* 3.2 5.1 + - + -
133M ARG* 3.3 19.7 + - + +
134M ARG* 4.9 0.9 - - - +
190M SER* 3.3 42.6 + - - -
191M HIS* 4.0 14.3 - - - +
194M ASP* 4.2 31.9 - - + +
304M TYR* 3.8 10.2 - - - -
320M THR* 3.7 28.7 + - + +
325M GLY* 5.6 2.7 - - - -
328M SER* 3.9 20.3 + - - -
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Residues in contact with GLN 131 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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287D ARG* 4.9 3.4 - - - +
129M VAL* 3.4 8.4 - - + +
130M LYS* 1.3 74.3 - - - +
132M ASN* 1.3 62.4 + - - +
133M ARG 3.1 0.2 - - - -
134M ARG* 2.9 27.2 + - - +
135M ASN* 4.1 3.5 + - - +
191M HIS* 3.8 6.9 + - - -
298M GLY 6.2 0.2 - - - -
300M GLY* 3.5 44.2 - - - +
301M HIS* 3.5 18.0 + - - +
304M TYR* 4.0 19.5 - - + -
500M NAI 3.0 41.6 + - - -
550M HP7 3.6 17.7 - - + +
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Residues in contact with ASN 132 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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130M LYS* 3.2 2.1 + - + -
131M GLN* 1.3 76.6 - - - +
133M ARG* 1.3 61.8 + - - +
134M ARG 2.8 7.7 + - - -
135M ASN* 3.0 39.8 + - - +
138M LEU* 3.5 16.6 - - + +
191M HIS* 3.6 40.9 + - + +
192M TYR* 4.0 21.2 + - - -
195M LEU* 5.4 3.3 - - + +
267M ALA* 5.4 2.8 + - - +
268M VAL* 4.4 6.7 - - - +
550M HP7 3.9 20.0 - - - +
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Residues in contact with ARG 133 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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130M LYS* 3.3 15.3 + - + +
131M GLN 3.1 0.8 - - - -
132M ASN* 1.3 78.4 - - - +
134M ARG* 1.3 66.1 + - + +
135M ASN 3.4 0.6 - - - +
138M LEU* 5.5 0.2 - - - -
139M GLN* 2.8 28.8 + - - +
194M ASP* 2.6 43.9 + - - +
195M LEU* 5.5 0.8 - - + +
198M TRP* 3.4 59.9 - - + +
319M GLU* 3.3 12.7 + - + -
320M THR* 3.2 26.9 + - - +
324M GLU* 2.6 55.0 + - - +
327M GLN* 5.8 1.2 - - - +
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Residues in contact with ARG 134 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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130M LYS 4.9 0.7 - - - +
131M GLN* 2.9 17.0 + - - +
132M ASN 2.8 2.0 - - - -
133M ARG* 1.3 85.7 + - + +
135M ASN* 1.3 67.3 + - - +
136M ALA* 3.3 2.6 + - - -
139M GLN* 3.3 34.6 + - - +
292M GLU* 5.0 2.4 - - - +
300M GLY 5.5 0.9 - - - +
303M LEU* 4.1 49.2 - - + +
304M TYR* 4.3 18.4 - - + +
307M ASN* 5.2 1.1 - - - -
319M GLU* 2.5 42.5 + - - +
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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