Contacts of the helix formed by residues 295 - 311 (chain A) in PDB entry 5LLU
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 GLY 295 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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294A LEU* 1.3 79.5 - - - +
296A MET* 1.3 60.5 + - - +
298A MET* 4.1 3.4 - - - +
299A VAL* 3.3 26.7 + - - +
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Residues in contact with MET 296 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
145A ILE* 4.0 38.0 - - + +
294A LEU 5.5 0.7 - - - +
295A GLY* 1.3 73.8 - - - +
297A TYR* 1.4 55.4 + - - +
299A VAL* 3.4 7.6 + - - +
300A THR* 2.7 41.3 + - - -
392A PHE* 4.2 15.0 - - + -
395A GLN* 3.3 26.9 - - - +
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Residues in contact with TYR 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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294A LEU* 3.7 22.4 - - + +
295A GLY 3.3 0.2 - - - -
296A MET* 1.4 77.9 - - - +
298A MET* 1.4 61.2 + - - +
300A THR* 3.2 7.1 + - - -
301A VAL* 3.0 47.4 + - + +
385A TYR* 3.1 28.5 - + - -
388A VAL* 4.1 7.6 - - + -
389A ALA* 3.4 31.0 - - + +
392A PHE* 3.6 46.9 - + + -
448A ILE* 3.4 28.4 - - + +
451A VAL* 3.9 11.9 - - + -
455A LEU* 3.7 20.9 - - + -
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Residues in contact with MET 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 LEU 3.1 15.8 + - - +
295A GLY* 4.1 3.1 - - - +
297A TYR* 1.4 81.0 - - - +
299A VAL* 1.3 71.6 + - + +
302A ILE* 3.1 51.5 + - + +
451A VAL* 3.7 33.0 - - + -
454A LEU* 4.5 14.6 - - + -
455A LEU* 3.6 23.6 - - + +
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Residues in contact with VAL 299 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
145A ILE* 5.9 4.0 - - + -
295A GLY 3.3 15.2 + - - +
296A MET* 3.4 10.7 + - - +
297A TYR 3.2 0.6 - - - -
298A MET* 1.3 88.6 - - + +
300A THR* 1.4 57.8 + - - +
302A ILE* 3.3 4.1 + - - -
303A VAL* 2.8 53.6 + - + +
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Residues in contact with THR 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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141A LEU* 4.0 17.5 - - + +
142A VAL* 4.0 27.8 - - + +
145A ILE* 3.4 28.0 - - + +
296A MET* 2.7 29.8 + - - -
297A TYR* 3.2 6.2 + - - -
299A VAL* 1.4 70.2 - - - +
301A VAL* 1.3 56.4 + - - +
303A VAL* 4.4 3.3 - - - +
304A GLY* 2.8 27.5 + - - -
384A LEU* 5.0 0.7 - - - +
388A VAL* 3.8 24.2 - - + +
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Residues in contact with VAL 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 TYR* 3.0 32.9 + - + +
299A VAL 3.3 0.2 - - - -
300A THR* 1.3 73.1 - - - +
302A ILE* 1.4 54.3 + - - +
304A GLY* 3.1 2.6 + - - -
305A LEU* 2.8 54.5 + - + +
384A LEU* 3.9 7.2 - - + +
385A TYR* 4.2 30.3 - - + -
388A VAL* 3.7 26.0 - - + -
455A LEU* 3.8 26.0 - - + +
459A ARG* 5.7 0.2 - - + -
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Residues in contact with ILE 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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298A MET* 3.1 47.9 + - + +
299A VAL* 3.9 3.1 - - - +
301A VAL* 1.4 71.6 - - - +
303A VAL* 1.3 67.6 + - + +
305A LEU* 3.3 9.8 + - + +
306A VAL* 3.2 28.6 + - + +
454A LEU* 4.7 4.5 - - + -
455A LEU* 3.8 16.8 - - + -
458A PHE* 3.7 40.6 - - + -
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Residues in contact with VAL 303 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
141A LEU* 5.1 5.8 - - + -
299A VAL* 2.8 40.6 + - + +
300A THR* 4.4 3.1 - - - +
302A ILE* 1.3 75.6 - - + +
304A GLY* 1.3 57.4 + - - +
306A VAL* 3.0 24.9 + - + +
307A ILE* 3.1 31.8 + - + +
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Residues in contact with GLY 304 (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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137A LEU* 3.9 4.0 - - - +
141A LEU* 3.7 24.1 - - - +
300A THR 2.8 20.6 + - - -
301A VAL 3.4 2.2 - - - -
303A VAL* 1.3 76.9 - - - +
305A LEU* 1.3 54.9 + - - +
307A ILE* 3.7 0.9 + - - +
308A HIS* 3.3 19.9 + - - +
384A LEU* 3.4 24.9 - - - +
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Residues in contact with LEU 305 (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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301A VAL* 2.8 37.9 + - + +
302A ILE* 3.7 9.2 - - + +
303A VAL 3.3 0.2 - - - -
304A GLY* 1.3 71.8 - - - +
306A VAL* 1.4 57.6 + - + +
308A HIS* 4.6 3.1 - - + +
309A GLY* 2.8 32.0 + - - -
381A GLY* 3.7 37.2 - - - +
384A LEU* 4.0 14.6 - - + -
455A LEU* 4.5 2.0 - - - +
458A PHE* 3.8 18.6 - - + -
459A ARG* 3.7 26.0 - - + +
462A VAL* 3.8 22.8 - - + +
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Residues in contact with VAL 306 (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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302A ILE* 3.3 22.0 - - + +
303A VAL* 3.0 13.0 + - + +
305A LEU* 1.4 75.9 - - + +
307A ILE* 1.4 60.6 + - + +
310A LEU* 2.8 58.3 + - + +
311A ILE* 3.5 10.2 + - + +
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Residues in contact with ILE 307 (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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137A LEU* 3.8 28.3 - - + -
141A LEU* 3.8 31.4 - - + -
303A VAL* 3.1 33.8 + - + +
304A GLY 4.0 0.7 - - - +
306A VAL* 1.4 76.4 - - + +
308A HIS* 1.3 52.2 + - - +
311A ILE* 3.2 25.9 - - + +
312A VAL* 2.8 34.3 + - + +
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Residues in contact with HIS 308 (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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130A THR* 3.8 8.3 - - + -
133A ILE* 4.3 4.3 - - + +
134A ALA* 3.6 36.7 + - + -
137A LEU* 3.8 9.3 - - + +
304A GLY 3.3 18.8 + - - +
305A LEU* 4.2 2.7 - - - +
307A ILE* 1.3 76.0 - - - +
309A GLY* 1.3 57.7 + - - +
312A VAL* 3.2 33.9 + - + +
313A LEU* 2.8 61.3 + - + +
316A ILE* 5.7 0.2 - - + -
380A ASP* 3.5 22.3 - - + +
384A LEU* 4.0 7.4 - - + -
462A VAL* 3.9 15.9 - - + -
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Residues in contact with GLY 309 (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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305A LEU 2.8 21.9 + - - -
308A HIS* 1.3 75.3 - - - +
310A LEU* 1.3 62.9 + - - +
311A ILE 3.6 0.2 - - - -
313A LEU* 4.2 6.5 - - - +
314A PRO* 3.4 15.6 - - - +
329A ILE* 4.8 1.2 - - - +
462A VAL* 4.5 7.9 - - - -
465A LEU* 3.3 33.2 - - - +
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Residues in contact with LEU 310 (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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306A VAL* 2.8 44.4 + - + +
309A GLY* 1.3 76.8 - - - +
311A ILE* 1.3 68.9 + - + +
314A PRO* 3.5 8.2 - - - +
326A PHE* 3.2 45.4 - - + -
329A ILE* 5.3 8.5 - - + -
465A LEU* 6.2 0.9 - - + -
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Residues in contact with ILE 311 (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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306A VAL* 3.8 18.8 - - + +
307A ILE* 3.2 27.7 + - + +
310A LEU* 1.3 90.7 - - + +
312A VAL* 1.4 69.4 + - + +
314A PRO* 3.6 4.3 - - - +
315A LEU* 3.3 22.6 + - + +
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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