Contacts of the helix formed by residues 292 - 302 (chain A) in PDB entry 2W4K
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 ASN 292 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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211A LEU 2.9 14.7 + - - +
212A SER 3.9 6.8 - - - +
239A GLU 3.6 6.5 + - - -
240A TYR* 3.2 37.2 + - - +
242A SER* 5.6 2.2 + - - -
243A ASN* 6.2 1.3 - - + -
290A ALA 3.7 1.4 + - - -
291A VAL* 1.3 71.9 - - - +
293A MET* 1.3 49.6 + - - +
294A GLU* 3.8 8.0 + - - +
295A LYS* 3.4 36.0 + - - +
296A PHE* 2.7 35.0 + - - +
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Residues in contact with MET 293 (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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105A LEU 4.0 19.1 - - - +
108A LYS 3.9 9.6 - - - +
109A GLU 3.5 21.8 - - - +
110A SER* 3.7 17.3 - - - +
111A LEU* 3.6 33.2 - - + +
291A VAL* 3.1 19.1 + - + +
292A ASN* 1.3 68.9 + - - +
294A GLU* 1.3 62.2 + - - +
296A PHE* 4.1 18.4 - - + -
297A LYS* 2.8 56.7 + - - +
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Residues in contact with GLU 294 (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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292A ASN* 3.4 6.3 + - - +
293A MET* 1.3 79.8 - - - +
295A LYS* 1.3 90.9 + - - +
297A LYS* 3.8 8.3 - - - +
298A LYS* 2.8 56.4 + - - +
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Residues in contact with LYS 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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212A SER 3.2 18.6 - - - +
213A GLY* 3.9 8.5 - - - +
239A GLU* 3.6 37.0 + - - +
240A TYR* 3.6 28.3 - - + +
292A ASN* 3.3 26.3 + - - +
294A GLU* 1.3 100.6 + - - +
296A PHE* 1.3 66.7 + - - +
298A LYS* 3.0 24.8 + - + +
299A PHE 3.1 10.4 + - - -
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Residues in contact with PHE 296 (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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102A PHE* 3.5 57.7 - + + -
105A LEU* 3.8 13.9 - - + -
106A ALA* 3.5 35.9 - - + -
111A LEU* 6.2 0.7 - - + -
209A ILE* 3.7 11.7 - - + -
210A LEU* 3.6 25.8 - - + -
213A GLY* 3.7 12.2 - - - +
291A VAL* 4.0 12.8 - - + -
292A ASN 2.7 21.5 + - - +
293A MET* 3.3 14.8 + - + +
295A LYS* 1.3 72.7 - - - +
297A LYS* 1.3 64.8 + - - +
299A PHE* 2.9 16.8 + + + +
300A ALA* 3.1 11.8 + - + -
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Residues in contact with LYS 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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106A ALA* 2.8 39.2 + - + +
107A GLU* 4.1 2.2 + - - +
108A LYS 2.5 29.6 + - - +
109A GLU* 4.5 4.1 - - - +
293A MET* 2.8 42.6 + - - +
294A GLU* 3.8 7.2 - - - +
296A PHE* 1.3 72.3 - - - +
298A LYS* 1.3 61.6 + - + +
300A ALA* 3.5 2.6 + - - +
301A ALA* 3.3 21.0 + - - +
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Residues in contact with LYS 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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294A GLU* 2.8 36.6 + - - +
295A LYS* 3.0 23.0 + - + +
297A LYS* 1.3 75.6 - - + +
299A PHE* 1.3 63.5 + - - +
301A ALA* 3.2 15.8 + - - +
302A ARG* 3.3 10.6 + - - +
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Residues in contact with PHE 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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102A PHE* 4.0 19.5 - + + -
142A PRO* 4.8 8.3 - - + -
183A PHE* 5.0 0.2 - + - -
209A ILE* 3.6 44.2 - - + -
213A GLY* 3.5 31.1 + - - +
214A ALA 4.8 1.8 - - - -
215A SER* 4.5 7.4 - - - -
295A LYS 3.1 4.9 + - - -
296A PHE* 2.9 11.5 + + + +
298A LYS* 1.3 76.0 - - - +
300A ALA* 1.3 69.9 + - + +
302A ARG* 3.0 77.0 + - + +
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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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102A PHE* 4.2 12.8 - - + +
103A ASP* 3.7 23.4 - - - +
106A ALA* 3.6 31.0 - - + -
296A PHE* 3.1 13.5 + - + +
297A LYS 4.0 2.5 - - - +
298A LYS 3.3 0.2 - - - -
299A PHE* 1.3 82.8 - - - +
301A ALA* 1.3 60.8 + - - +
302A ARG 4.4 3.2 - - - -
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Residues in contact with ALA 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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297A LYS 3.3 12.3 + - - +
298A LYS* 3.2 13.2 + - - +
299A PHE 3.1 0.4 - - - -
300A ALA* 1.3 76.7 - - - +
302A ARG* 1.3 66.4 + - - +
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Residues in contact with ARG 302 (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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182A GLU* 2.9 42.4 + - - -
183A PHE* 3.9 16.2 - - - -
215A SER* 4.3 1.0 - - - -
218A LEU* 3.8 16.1 - - - +
298A LYS 3.3 5.9 + - - +
299A PHE* 3.0 57.6 + - + +
300A ALA 4.4 2.9 - - - -
301A ALA* 1.3 86.8 - - - +
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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