Contacts of the helix formed by residues 2394 - 2410 (chain B) in PDB entry 5WBY
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 GLY2394 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1427B GLU 3.9 7.9 - - - -
1428B ALA 4.5 0.7 - - - -
1431B GLY* 3.6 17.5 - - - -
2388B GLU* 4.0 6.1 - - - -
2390B THR 2.9 13.1 + - - -
2391B GLY 3.0 3.1 + - - -
2393B ASP* 1.3 82.7 - - - +
2395B ASN* 1.3 64.9 + - - -
2396B TYR 3.3 2.7 + - - -
2397B ARG 3.6 0.3 + - - -
2398B ILE* 3.2 27.2 + - - +
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Residues in contact with ASN2395 (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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1425B GLN* 4.0 5.7 + - - +
1427B GLU* 2.9 37.4 + - - +
1428B ALA* 3.2 18.8 - - - +
2314B PHE* 6.2 0.2 - - - -
2318B THR* 4.9 9.4 - - - +
2321B THR* 3.6 20.8 - - + -
2322B ARG* 3.5 18.9 + - + +
2388B GLU* 3.0 33.0 + - - +
2391B GLY 3.6 1.4 + - - -
2394B GLY* 1.3 72.3 - - - -
2396B TYR* 1.3 56.6 + - - +
2398B ILE* 3.9 2.8 - - - +
2399B THR* 2.7 39.3 + - - +
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Residues in contact with TYR2396 (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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2321B THR* 3.5 15.1 - - + +
2324B LEU* 4.1 7.6 - - + -
2325B ALA* 3.6 34.4 - - + +
2328B SER* 2.8 22.2 + - - -
2377B PHE* 3.2 22.5 - - - -
2379B LEU* 3.7 31.4 - - + +
2387B MET* 3.6 26.2 - - + -
2391B GLY 3.4 14.8 + - - +
2392B LEU* 4.0 14.1 - - + -
2394B GLY 3.3 1.0 - - - -
2395B ASN* 1.3 79.6 - - - +
2397B ARG* 1.3 55.4 + - - +
2400B CYS* 2.8 56.6 + - - -
2529B ILE* 4.0 13.0 - - + -
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Residues in contact with ARG2397 (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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1438B LYS* 5.4 8.5 - - - +
2392B LEU* 2.8 53.7 + - - +
2393B ASP* 4.1 22.7 + - - +
2394B GLY 3.6 1.4 + - - -
2395B ASN 3.5 0.4 - - - -
2396B TYR* 1.3 80.0 - - - +
2398B ILE* 1.3 59.9 + - + +
2400B CYS* 3.2 7.7 + - - +
2401B HIS* 2.8 60.3 + - + +
2522B PRO 5.2 1.0 + - - -
2525B VAL* 4.1 8.7 - - + -
2526B GLU* 2.6 47.1 + - - +
2529B ILE* 4.0 17.5 - - + +
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Residues in contact with ILE2398 (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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1427B GLU* 3.4 42.8 - - + +
1430B ALA* 4.7 9.4 - - + -
1431B GLY 5.3 0.4 - - - +
2218B LYS* 3.7 18.6 - - - +
2393B ASP 4.3 8.1 - - - +
2394B GLY 3.2 20.7 + - - +
2395B ASN* 4.0 4.3 - - - +
2397B ARG* 1.3 76.5 - - + +
2399B THR* 1.3 52.8 + - - +
2401B HIS* 3.5 14.9 + - + +
2402B THR* 2.7 35.7 + - - +
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Residues in contact with THR2399 (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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1427B GLU* 4.4 7.6 + - - -
2218B LYS* 4.4 4.3 + - - +
2220B LEU* 3.7 32.4 - - + +
2322B ARG* 3.5 37.1 - - - +
2325B ALA* 3.9 8.5 - - + -
2326B VAL* 4.2 0.4 - - + -
2395B ASN 2.7 22.4 + - - -
2396B TYR 3.7 3.1 - - - -
2398B ILE* 1.3 74.8 - - - +
2400B CYS* 1.3 58.8 + - - +
2402B THR* 3.3 5.9 + - - -
2403B VAL* 2.9 42.1 + - + +
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Residues in contact with CYS2400 (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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2325B ALA* 3.7 11.6 - - - +
2329B MET* 3.6 33.6 - - - +
2396B TYR* 2.8 58.1 + - - +
2397B ARG* 3.4 9.6 - - - +
2399B THR* 1.3 73.8 - - - +
2401B HIS* 1.3 62.2 + - - +
2404B MET* 3.1 28.1 + - - +
2525B VAL* 3.6 21.3 - - + -
2529B ILE* 5.0 0.4 - - - -
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Residues in contact with HIS2401 (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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2397B ARG* 2.8 48.9 + - + +
2398B ILE* 3.5 16.7 - - + +
2399B THR 3.2 0.2 - - - -
2400B CYS* 1.3 70.2 - - - +
2402B THR* 1.3 55.9 + - - +
2404B MET* 3.2 1.9 + - - -
2405B GLU* 2.8 41.1 + - - +
2521B VAL* 3.7 12.9 - - + +
2522B PRO* 3.5 45.5 + - + +
2525B VAL* 3.8 16.8 - - + +
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Residues in contact with THR2402 (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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2212B ASP* 4.0 9.4 - - - +
2214B THR* 4.0 22.9 - - + +
2215B SER* 3.6 22.4 - - - +
2218B LYS* 3.3 15.4 + - - +
2220B LEU* 4.4 8.7 - - + -
2398B ILE* 2.7 22.5 + - - +
2399B THR* 3.7 5.4 - - - -
2401B HIS* 1.3 76.9 - - - +
2403B VAL* 1.3 63.6 + - - +
2405B GLU* 3.3 8.0 + - - +
2406B VAL* 3.1 26.6 + - - +
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Residues in contact with VAL2403 (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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2205B VAL* 5.7 0.4 - - + -
2209B LEU* 4.2 18.6 - - + -
2220B LEU* 3.8 16.6 - - + -
2326B VAL* 3.8 50.7 - - + +
2329B MET* 4.0 8.5 - - + -
2330B VAL* 4.1 6.5 - - + -
2399B THR* 2.9 21.1 + - + +
2400B CYS 4.2 2.0 - - - +
2402B THR* 1.3 74.1 - - - +
2404B MET* 1.3 64.2 + - - +
2406B VAL* 3.0 6.6 + - - +
2407B LEU* 3.0 39.6 + - + +
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Residues in contact with MET2404 (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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2329B MET* 3.6 44.9 - - + +
2332B TYR* 4.3 18.4 - - + -
2333B ILE* 4.1 17.7 - - + -
2400B CYS 3.1 21.0 + - - +
2401B HIS 3.8 2.5 - - - +
2403B VAL* 1.3 76.4 - - - +
2405B GLU* 1.3 60.8 + - - +
2407B LEU* 3.4 7.8 + - - +
2408B ARG* 3.1 37.1 + - - -
2507B LYS 4.6 4.9 - - - +
2508B LEU* 5.7 0.7 - - - -
2521B VAL* 4.0 12.1 - - + -
2524B GLN* 3.6 28.9 - - - +
2525B VAL* 4.4 3.4 - - + -
2528B LEU* 4.4 5.4 - - + -
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Residues in contact with GLU2405 (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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2401B HIS* 2.8 21.4 + - - +
2402B THR* 3.4 8.3 - - - +
2404B MET* 1.3 69.9 - - - +
2406B VAL* 1.3 64.8 + - + +
2408B ARG* 3.5 5.1 + - - +
2409B GLU* 3.0 24.8 + - - +
2521B VAL* 3.4 38.5 - - - +
2522B PRO* 5.1 1.6 - - - +
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Residues in contact with VAL2406 (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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2205B VAL* 6.2 1.1 - - + -
2208B LEU* 3.8 38.6 - - + +
2209B LEU* 4.2 12.6 - - + -
2212B ASP* 3.3 37.2 - - + +
2215B SER* 3.7 10.3 - - - +
2402B THR 3.1 16.4 + - - +
2403B VAL 3.0 9.5 + - - +
2405B GLU* 1.3 75.7 - - + +
2407B LEU* 1.3 65.0 + - + +
2409B GLU* 3.5 6.6 + - - +
2410B HIS* 3.1 31.6 + - + +
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Residues in contact with LEU2407 (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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2205B VAL* 4.2 23.8 - - + -
2208B LEU* 5.4 3.8 - - + -
2329B MET* 4.6 2.2 - - + -
2330B VAL* 4.0 16.4 - - + +
2333B ILE* 3.5 35.0 - - + -
2403B VAL* 3.0 42.0 + - + +
2404B MET* 3.7 11.0 - - - +
2405B GLU 3.3 0.4 - - - -
2406B VAL* 1.3 80.5 - - + +
2408B ARG* 1.3 55.9 + - - +
2410B HIS* 3.2 5.1 - - - +
2411B LYS* 3.0 28.1 + - - +
2414B VAL* 4.0 26.4 - - + +
2508B LEU* 3.8 8.9 - - + +
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Residues in contact with ARG2408 (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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2404B MET* 3.1 32.4 + - - +
2405B GLU* 3.9 5.6 + - - +
2407B LEU* 1.3 72.7 - - - +
2409B GLU* 1.3 66.1 + - - +
2411B LYS* 3.3 23.5 + - - +
2507B LYS 4.2 4.2 + - - -
2508B LEU* 3.0 30.3 + - - +
2509B THR* 3.5 11.6 + - - +
2510B GLY* 3.2 21.8 - - - +
2519B LEU 2.7 29.9 + - - -
2520B ASP* 4.2 4.2 - - - +
2521B VAL* 3.5 27.5 - - - +
2524B GLN* 3.2 21.4 + - - -
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Residues in contact with GLU2409 (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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2212B ASP* 5.0 8.9 - - - +
2405B GLU 3.0 18.2 + - - +
2406B VAL* 3.7 7.8 - - - +
2408B ARG* 1.3 78.3 - - - +
2410B HIS* 1.3 89.4 + - + +
2411B LYS* 3.5 4.0 + - - +
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Residues in contact with HIS2410 (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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2208B LEU* 3.6 46.0 + - + +
2211B ASN* 5.9 4.6 - - + +
2212B ASP* 6.0 1.8 - - - +
2406B VAL* 3.1 28.9 + - + +
2407B LEU 3.2 4.5 - - - -
2409B GLU* 1.3 108.8 + - + +
2411B LYS* 1.3 63.1 - - - +
2412B ASP* 3.3 3.3 + - - +
2413B SER* 3.6 12.0 + - - +
2414B VAL* 3.4 23.0 + - - +
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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