Contacts of the helix formed by residues 293 - 304 (chain C) 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 C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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289C CYS 3.3 17.0 - - - +
290C LEU* 3.2 22.2 + - + +
291C SER 3.0 1.8 - - - -
292C SER* 1.3 80.8 - - - +
294C LYS* 1.3 58.1 + - - +
295C ASP 3.4 1.8 - - - -
296C GLU* 3.3 36.6 - - + +
297C ARG* 2.9 36.6 + - + +
275D GLY 5.3 4.5 - - - +
277D PRO* 4.7 7.2 - - + -
340D MET* 3.8 26.7 - - + -
433D TYR* 4.6 2.7 - - + -
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Residues in contact with LYS 294 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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255C ARG* 3.4 34.8 - - + +
256C ASP* 2.9 29.6 + - - +
257C SER* 4.9 0.7 - - - -
291C SER 3.5 4.6 + - - +
292C SER 2.9 8.0 + - - +
293C LEU* 1.3 75.9 - - - +
295C ASP* 1.3 65.1 + - - +
297C ARG* 3.1 22.0 + - - +
298C ILE* 3.0 49.2 + - + +
436D GLU* 2.5 33.2 + - - +
437D MET* 3.1 18.2 - - - -
458D LEU* 4.6 9.6 - - - +
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Residues in contact with ASP 295 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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255C ARG* 4.9 11.1 + - - -
293C LEU 3.4 0.4 - - - -
294C LYS* 1.3 78.8 - - - +
296C GLU* 1.3 61.7 + - - +
298C ILE* 3.3 24.1 + - - +
299C GLN* 3.4 20.9 + - + +
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Residues in contact with GLU 296 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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293C LEU* 3.3 35.7 + - + +
294C LYS 3.2 0.6 - - - -
295C ASP* 1.3 79.1 - - - +
297C ARG* 1.3 61.7 + - - +
299C GLN* 3.7 7.8 + - + +
300C ALA* 3.2 20.8 + - - +
340D MET* 4.6 3.0 - - - +
387D GLN* 3.7 37.2 + - + +
388D ASN* 3.4 16.8 + - - +
391D LEU* 5.4 3.9 - - + +
433D TYR* 2.9 35.2 + - + +
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Residues in contact with ARG 297 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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256C ASP* 3.1 25.9 + - - -
290C LEU* 3.1 25.4 + - + +
291C SER* 2.8 24.0 + - - +
293C LEU* 2.9 15.5 + - + +
294C LYS* 3.1 17.9 + - - +
296C GLU* 1.3 75.9 - - - +
298C ILE* 1.3 59.3 + - - +
300C ALA* 3.3 1.0 + - - +
301C SER* 2.8 30.0 + - - -
432D GLY 3.3 21.3 - - - -
433D TYR* 3.3 34.1 - - + +
434D ARG 4.4 0.5 - - - +
435D HIS 2.9 25.3 + - - +
436D GLU* 3.2 17.4 + - - -
438D LEU* 3.6 18.4 - - - +
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Residues in contact with ILE 298 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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294C LYS* 3.0 49.7 + - + +
295C ASP* 3.3 18.8 + - - +
297C ARG* 1.3 77.9 - - - +
299C GLN* 1.3 71.0 + - - +
301C SER* 2.4 27.5 + - - +
302C LYS* 3.5 21.4 - - - +
436D GLU* 4.0 27.1 - - + +
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Residues in contact with GLN 299 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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295C ASP* 3.4 15.2 + - - +
296C GLU* 4.0 7.2 - - - +
297C ARG 3.3 0.4 - - - -
298C ILE* 1.3 89.4 - - - +
300C ALA* 1.3 61.9 + - - +
302C LYS* 3.4 36.2 + - - +
303C LYS* 3.6 19.4 + - - +
391D LEU* 5.0 11.7 - - + -
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Residues in contact with ALA 300 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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296C GLU 3.2 10.8 + - - +
297C ARG 3.8 0.7 - - - +
298C ILE 3.3 0.4 - - - -
299C GLN* 1.3 76.7 - - - +
301C SER* 1.3 60.9 + - - +
302C LYS 3.1 0.2 - - - -
303C LYS 4.5 0.4 - - - +
304C LEU* 2.8 42.8 + - + +
391D LEU* 4.2 13.4 - - + +
433D TYR* 3.5 51.1 - - + +
434D ARG 4.4 1.6 - - - -
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Residues in contact with SER 301 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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297C ARG 2.8 12.5 + - - -
298C ILE* 2.4 33.3 + - - +
300C ALA* 1.3 77.5 - - - +
302C LYS* 1.3 62.0 + - - +
304C LEU 3.6 10.9 - - - +
434D ARG 3.2 23.8 + - - -
436D GLU* 3.9 24.2 + - - +
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Residues in contact with LYS 302 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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298C ILE* 3.5 29.5 - - - +
299C GLN* 3.7 33.0 + - - +
300C ALA 3.1 1.0 - - - -
301C SER* 1.3 81.0 - - - +
303C LYS* 1.3 68.2 + - + +
304C LEU 4.8 0.2 - - - -
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Residues in contact with LYS 303 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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299C GLN 3.6 15.5 + - - +
300C ALA 3.2 2.9 + - - +
302C LYS* 1.3 87.4 - - + +
304C LEU* 1.3 63.3 + - + +
305C LYS* 4.0 1.6 + - - +
391D LEU* 4.7 19.7 - - + -
393D ASP* 5.3 5.2 + - - -
396D LYS* 3.3 42.9 + - + +
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Residues in contact with LEU 304 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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300C ALA* 2.8 28.8 + - + +
301C SER* 3.6 15.9 - - - +
302C LYS 4.8 0.2 - - - -
303C LYS* 1.3 75.3 - - + +
305C LYS* 1.3 60.3 + - - +
390D LEU* 3.8 30.3 - - + +
391D LEU* 5.0 3.1 - - + -
396D LYS* 3.8 23.3 - - + +
399D VAL* 6.0 0.9 - - + -
430D TYR* 3.9 33.7 - - + +
433D TYR* 3.8 31.4 - - + -
434D ARG* 3.8 23.8 + - + +
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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