Contacts of the helix formed by residues 294 - 301 (chain A) in PDB entry 3KMR
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 ARG 294 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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217A ARG* 4.3 8.7 - - - +
282A ASP* 2.8 49.3 + - - +
293A ASN* 1.3 74.8 - - - +
295A THR* 1.3 59.4 + - - +
297A MET* 3.3 2.3 + - - +
298A HIS* 3.0 28.2 + - - +
306A THR* 3.6 18.7 - - + +
307A ASP* 2.9 34.4 + - - +
310A PHE* 3.3 45.5 - - + +
311A ALA 5.2 0.2 - - - +
314A ASN* 4.4 10.7 - - - +
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Residues in contact with THR 295 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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213A SER 3.8 7.6 - - - +
214A SER 3.8 6.7 + - - +
215A GLU 3.8 13.6 + - - +
216A GLN 3.6 33.2 - - - +
217A ARG* 3.8 19.4 + - + +
293A ASN* 3.2 9.6 + - - -
294A ARG* 1.3 78.4 - - - +
296A GLN* 1.3 57.5 + - - +
298A HIS* 3.4 5.9 - - - +
299A ASN* 2.9 38.8 + - - +
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Residues in contact with GLN 296 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
209A THR* 5.9 1.8 - - - +
210A THR* 2.9 31.8 + - - +
212A ASN 3.1 27.5 - - - +
213A SER 4.1 0.9 - - - +
214A SER* 3.7 17.2 - - - -
224A LEU* 3.9 9.8 - - + +
291A THR 4.2 4.2 + - - -
292A LEU* 3.5 27.5 - - + +
293A ASN* 2.8 45.7 + - - +
295A THR* 1.3 70.8 - - - +
297A MET* 1.3 55.2 + - - +
299A ASN* 3.2 7.0 + - - +
300A ALA* 2.8 37.1 + - - +
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Residues in contact with MET 297 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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273A ILE* 3.9 12.8 - - + -
284A MET* 3.7 32.8 - - + -
286A PHE* 3.7 28.0 - - + -
292A LEU* 3.9 16.6 - - + +
293A ASN 2.9 20.2 + - - +
294A ARG 3.6 5.2 - - - +
296A GLN* 1.3 72.6 - - - +
298A HIS* 1.3 65.5 + - - +
300A ALA* 3.3 10.8 + - - +
301A GLY 3.5 0.9 + - - -
302A PHE* 3.3 61.8 + - + -
306A THR* 4.5 1.6 - - + -
309A VAL* 5.4 0.9 - - + -
310A PHE* 3.8 25.1 - - + -
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Residues in contact with HIS 298 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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217A ARG* 3.7 43.8 + - + +
218A VAL 3.1 23.1 - - - -
219A SER* 4.8 8.8 - - - +
294A ARG 3.0 13.1 + - - +
295A THR 3.4 9.0 - - - +
297A MET* 1.3 76.0 - - - +
299A ASN* 1.3 78.8 + - - +
301A GLY* 3.4 5.9 + - - -
303A GLY* 3.2 53.5 + - - +
306A THR* 3.2 18.9 + - + +
394A ARG* 5.1 0.2 + - - -
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Residues in contact with ASN 299 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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213A SER* 2.8 34.3 + - - +
216A GLN 3.0 17.3 - - - +
217A ARG* 3.6 3.6 - - - +
218A VAL* 2.9 37.5 + - + +
220A LEU* 3.5 8.2 - - - +
221A ASP* 2.8 35.4 + - + +
224A LEU* 4.2 1.3 - - + -
295A THR* 2.9 21.2 + - - +
296A GLN* 3.2 5.6 + - - +
298A HIS* 1.3 88.5 + - - +
300A ALA* 1.3 62.3 + - - +
301A GLY 3.5 0.3 + - - -
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Residues in contact with ALA 300 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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220A LEU* 3.8 2.2 - - - +
224A LEU* 3.9 20.2 - - + +
225A TRP* 3.3 22.0 - - - +
228A PHE* 3.3 40.6 - - + -
292A LEU* 4.3 11.2 - - + -
296A GLN 2.8 20.5 + - - +
297A MET* 3.3 8.5 + - - +
299A ASN* 1.3 74.3 - - - +
301A GLY* 1.3 55.5 + - - +
302A PHE* 5.2 1.1 - - + -
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Residues in contact with GLY 301 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1A EQN 3.9 4.4 - - - +
220A LEU* 4.2 2.9 - - - -
228A PHE* 4.3 4.3 - - - -
298A HIS 3.4 2.2 + - - -
299A ASN 3.3 3.6 - - - -
300A ALA* 1.3 80.1 - - - +
302A PHE* 1.3 61.9 + - - +
303A GLY 3.3 3.1 - - - -
394A ARG* 2.8 34.1 + - - +
398A LEU* 3.7 27.9 - - - +
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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