Contacts of the helix formed by residues 293 - 304 (chain B) in PDB entry 5UQ9
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 LEU 293 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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277A PRO* 4.6 8.5 - - + -
340A MET* 3.7 30.3 - - + -
344A GLN* 6.2 2.5 - - - +
433A TYR* 4.7 7.4 - - + -
260B GLN* 5.8 5.4 - - - +
289B CYS 3.9 15.0 - - - +
290B LEU* 3.3 10.7 + - + +
291B SER 3.1 2.0 - - - -
292B SER* 1.3 79.0 - - - +
294B LYS* 1.3 63.3 + - - +
295B ASP 3.4 2.5 - - - +
296B GLU* 3.9 36.8 - - + +
297B ARG* 3.0 32.0 + - + +
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Residues in contact with LYS 294 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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436A GLU* 2.9 24.6 + - - +
437A MET* 3.3 24.1 - - - +
458A LEU* 5.1 8.7 - - - +
255B ARG* 3.5 38.6 - - + +
256B ASP* 3.5 24.5 - - + +
257B SER* 5.0 0.4 - - - -
291B SER 3.6 3.6 + - - +
292B SER 3.0 6.7 + - - +
293B LEU* 1.3 75.0 - - - +
295B ASP* 1.3 62.1 + - - +
297B ARG* 3.2 25.8 + - - +
298B ILE* 2.9 56.6 + - + +
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Residues in contact with ASP 295 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
255B ARG* 4.8 7.5 + - - -
293B LEU* 3.4 0.4 - - - +
294B LYS* 1.3 84.7 - - - +
296B GLU* 1.3 63.8 + - + +
298B ILE* 3.5 13.4 + - - +
299B GLN* 3.3 22.5 + - - +
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Residues in contact with GLU 296 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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340A MET* 5.1 2.5 - - - +
343A ARG* 5.2 2.8 - - - -
387A GLN* 3.3 45.2 + - + +
388A ASN* 3.9 6.4 + - - -
391A LEU* 5.3 4.6 - - + +
433A TYR* 2.8 37.9 + - + +
293B LEU* 3.4 35.4 + - + +
294B LYS 3.3 0.4 - - - -
295B ASP* 1.3 79.4 - - + +
297B ARG* 1.3 59.1 + - - +
299B GLN* 3.5 5.7 + - - +
300B ALA* 2.9 29.2 + - - +
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Residues in contact with ARG 297 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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432A GLY 3.6 11.7 - - - -
433A TYR* 3.5 30.5 - - + +
434A ARG 4.2 0.7 - - - +
435A HIS 3.1 17.5 + - - +
436A GLU* 3.1 28.8 + - - -
438A LEU* 3.5 35.4 - - - +
256B ASP* 2.8 30.5 + - - +
290B LEU* 3.4 22.7 + - + +
291B SER* 3.0 11.9 + - - +
293B LEU* 3.0 16.4 + - + +
294B LYS* 3.4 21.4 - - - +
296B GLU* 1.3 74.9 - - - +
298B ILE* 1.3 62.3 + - - +
300B ALA* 3.9 0.7 - - - +
301B SER* 3.0 29.1 + - - -
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Residues in contact with ILE 298 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
436A GLU* 3.9 31.4 - - + +
294B LYS* 2.9 48.2 + - + +
295B ASP* 3.8 13.7 - - - +
296B GLU 3.3 0.2 - - - -
297B ARG* 1.3 78.3 - - - +
299B GLN* 1.3 60.0 + - - +
301B SER* 2.7 21.2 + - - -
302B LYS* 3.3 23.5 - - - +
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Residues in contact with GLN 299 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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387A GLN* 5.8 1.6 - - - +
391A LEU* 3.6 28.0 - - + +
295B ASP 3.3 14.5 + - - +
296B GLU* 4.0 4.9 - - - +
298B ILE* 1.3 80.1 - - - +
300B ALA* 1.3 62.2 + - - +
302B LYS* 3.4 13.8 + - + +
303B LYS* 3.5 30.4 + - + +
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Residues in contact with ALA 300 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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391A LEU* 4.3 12.1 - - + +
433A TYR* 3.4 32.5 - - + +
434A ARG* 4.2 1.8 - - - -
296B GLU 2.9 19.2 + - - +
297B ARG 3.9 1.1 - - - +
298B ILE 3.3 0.2 - - - -
299B GLN* 1.3 75.7 - - - +
301B SER* 1.3 59.1 + - - +
303B LYS 3.0 0.6 + - - +
304B LEU* 2.5 56.2 + - + +
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Residues in contact with SER 301 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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434A ARG 3.2 22.2 + - - -
436A GLU* 3.6 24.2 - - - +
297B ARG 3.0 12.2 + - - -
298B ILE* 2.7 22.5 + - - -
300B ALA* 1.3 76.7 - - - +
302B LYS* 1.3 70.5 + - - +
304B LEU 3.6 11.8 - - - +
305B LYS* 4.0 12.6 + - - -
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Residues in contact with LYS 302 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
436A GLU* 4.7 11.5 + - - -
298B ILE* 3.3 27.7 + - - +
299B GLN* 3.8 9.2 - - + +
300B ALA 3.1 1.0 - - - -
301B SER* 1.3 92.9 - - - +
303B LYS* 1.3 62.6 + - + +
305B LYS* 5.1 6.4 + - - +
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Residues in contact with LYS 303 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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390A LEU 5.0 0.4 + - - -
391A LEU* 3.3 47.9 + - + +
393A ASP* 5.1 3.3 + - - -
396A LYS* 3.8 39.9 + - + +
299B GLN* 3.5 30.3 - - + +
300B ALA 3.0 2.2 + - - +
302B LYS* 1.3 84.0 - - + +
304B LEU* 1.3 63.2 + - + +
305B LYS* 3.9 10.6 + - - +
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Residues in contact with LEU 304 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
390A LEU* 3.5 37.5 - - + +
391A LEU* 5.1 2.5 - - + -
396A LYS* 3.9 20.9 - - + +
430A TYR* 3.8 30.7 - - + +
433A TYR* 3.8 30.1 - - + -
434A ARG* 3.9 19.1 + - + +
300B ALA* 2.5 34.3 + - + +
301B SER* 3.6 12.0 - - - +
303B LYS* 1.3 76.4 - - + +
305B LYS* 1.3 66.7 + - - +
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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