Contacts of the helix formed by residues 1385 - 1407 (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 GLU1385 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1386B ARG* 1.3 69.6 + - + +
1387B ALA* 3.3 5.2 - - - +
1388B ALA* 3.1 21.6 + - - +
1389B LYS* 3.2 37.3 + - - +
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Residues in contact with ARG1386 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1385B GLU* 1.3 78.6 - - + +
1387B ALA* 1.3 63.8 + - - +
1389B LYS* 3.5 38.5 + - + +
1390B CYS* 3.7 9.0 + - - +
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Residues in contact with ALA1387 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1385B GLU 3.3 3.5 - - - +
1386B ARG* 1.3 76.9 - - - +
1388B ALA* 1.3 59.5 + - - +
1390B CYS* 3.2 27.8 - - - -
1391B ARG* 3.7 6.1 + - - +
2311B GLU* 5.2 3.5 - - - +
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Residues in contact with ALA1388 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1385B GLU* 3.1 15.1 + - - +
1387B ALA* 1.3 76.3 - - - +
1389B LYS* 1.3 61.9 + - - +
1390B CYS 3.5 0.2 - - - -
1391B ARG* 3.5 21.6 - - + +
1392B ALA* 3.4 19.6 + - - +
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Residues in contact with LYS1389 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1385B GLU* 3.2 32.8 + - - +
1386B ARG* 3.7 34.6 - - + +
1387B ALA 3.3 0.8 - - - -
1388B ALA* 1.3 76.2 - - - +
1390B CYS* 1.3 63.5 + - - +
1392B ALA* 3.4 14.9 + - - +
1393B TYR* 3.1 30.2 + - + -
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Residues in contact with CYS1390 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1386B ARG 3.7 7.6 + - - +
1387B ALA* 3.2 27.1 - - - -
1389B LYS* 1.3 75.6 - - - +
1391B ARG* 1.3 59.2 + - - +
1393B TYR* 3.5 6.1 + - - -
1394B ALA* 3.0 26.4 + - - +
1422B LYS 6.1 0.2 - - - +
1423B LEU* 3.4 28.1 - - + +
2311B GLU* 4.5 17.5 - - - -
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Residues in contact with ARG1391 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1387B ALA 3.7 5.4 + - - +
1388B ALA* 3.5 24.4 + - - +
1390B CYS* 1.3 80.3 - - - +
1392B ALA* 1.3 64.8 + - - +
1394B ALA* 3.3 2.4 + - - -
1395B LYS* 3.1 13.8 + - + +
2308B PRO 4.9 2.8 + - - -
2309B SER* 3.7 22.6 - - - -
2310B SER* 2.8 31.8 + - - +
2311B GLU* 3.3 31.0 + - - +
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Residues in contact with ALA1392 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1388B ALA 3.4 9.7 + - - +
1389B LYS* 3.6 11.2 - - - +
1390B CYS 3.4 0.2 - - - -
1391B ARG* 1.3 78.3 - - - +
1393B TYR* 1.3 65.6 + - + +
1395B LYS* 4.1 4.8 - - - +
1396B ALA* 3.2 23.2 + - - +
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Residues in contact with TYR1393 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1389B LYS* 3.1 33.1 + - + -
1390B CYS* 3.5 10.2 + - - +
1391B ARG 3.3 0.4 - - - -
1392B ALA* 1.3 79.2 - - + +
1394B ALA* 1.3 59.3 + - - +
1396B ALA* 3.4 4.7 + - + -
1397B LEU* 2.8 29.6 + - - +
1419B ILE* 3.4 25.5 - - + +
1422B LYS* 4.0 47.9 - - + +
1423B LEU* 4.1 11.4 - - + -
1578B MET* 3.7 26.3 - - - +
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Residues in contact with ALA1394 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1390B CYS 3.0 18.3 + - - +
1391B ARG 3.3 0.2 + - - -
1393B TYR* 1.3 76.4 - - - +
1395B LYS* 1.3 59.8 + - - +
1397B LEU* 3.4 5.7 + - - +
1398B HIS* 3.3 17.0 + - - +
1423B LEU* 4.1 18.8 - - + +
2310B SER* 3.6 34.7 - - - +
2311B GLU* 4.0 6.7 - - - +
2313B TRP* 3.9 11.4 - - - -
2314B PHE* 4.6 6.5 - - + -
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Residues in contact with LYS1395 (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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1391B ARG* 3.1 16.1 + - + +
1392B ALA* 4.1 4.7 - - - +
1394B ALA* 1.3 74.0 - - - +
1396B ALA* 1.3 64.2 - - - +
1398B HIS* 3.4 13.8 + - - +
1399B TYR* 3.2 54.5 + - + -
2304B TRP* 4.7 12.1 - - + -
2310B SER* 3.4 15.4 - - - +
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Residues in contact with ALA1396 (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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1392B ALA 3.2 17.7 + - - +
1393B TYR* 3.6 3.8 - - + +
1394B ALA 3.3 0.2 - - - -
1395B LYS* 1.3 75.5 - - - +
1397B LEU* 1.3 61.0 + - - +
1399B TYR* 3.6 7.0 + - - +
1400B LYS* 3.0 30.1 + - - +
1419B ILE* 3.5 18.3 - - + +
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Residues in contact with LEU1397 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1393B TYR 2.8 17.6 + - - +
1394B ALA* 3.5 7.2 - - - +
1395B LYS 3.3 0.2 - - - -
1396B ALA* 1.3 73.9 - - - +
1398B HIS* 1.3 56.0 + - - +
1400B LYS* 3.2 2.0 + - - -
1401B GLU* 2.7 64.3 + - + +
1416B LEU* 4.0 16.4 - - + -
1419B ILE* 3.3 20.3 - - + +
1420B ASN* 3.4 31.4 - - - +
1423B LEU* 4.0 9.0 - - + -
2313B TRP* 4.9 2.2 - - + -
2314B PHE* 3.5 31.0 - - + -
2317B ARG* 4.3 7.2 - - - +
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Residues in contact with HIS1398 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1394B ALA 3.3 8.1 + - - +
1395B LYS 3.4 8.9 + - - +
1397B LEU* 1.3 78.2 - - - +
1399B TYR* 1.3 76.2 + + - +
1401B GLU* 3.5 5.4 + - - +
1402B LEU* 3.0 46.1 + - + +
2301B LYS* 6.4 2.0 - - + -
2304B TRP* 3.3 77.1 + + + -
2313B TRP* 3.8 23.6 - + + -
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Residues in contact with TYR1399 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1395B LYS* 3.2 56.2 + - + -
1396B ALA* 4.1 6.3 - - - +
1397B LEU 3.3 0.2 - - - -
1398B HIS* 1.3 93.1 - + - +
1400B LYS* 1.3 60.2 + - - +
1402B LEU* 3.2 15.2 + - + +
1403B GLU* 2.8 29.3 + - - +
2304B TRP* 4.5 8.8 + + - -
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Residues in contact with LYS1400 (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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1396B ALA 3.0 20.1 + - - +
1397B LEU* 3.6 7.4 - - - +
1399B TYR* 1.3 75.2 - - - +
1401B GLU* 1.3 59.0 + - - +
1403B GLU* 3.4 27.4 + - - +
1404B PHE* 3.1 19.9 + - - +
1412B ILE* 3.6 16.7 - - + +
1415B SER* 3.2 44.1 + - - +
1416B LEU* 3.7 19.2 - - + +
1419B ILE* 4.8 7.9 - - + -
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Residues in contact with GLU1401 (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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1397B LEU* 2.7 43.1 + - + +
1398B HIS* 3.7 4.8 + - - +
1400B LYS* 1.3 71.2 - - - +
1402B LEU* 1.3 59.5 + - - +
1403B GLU 3.1 0.2 - - - -
1404B PHE* 3.1 10.8 + - - +
1405B GLN* 2.9 31.2 + - - +
1416B LEU* 4.1 5.0 - - + +
1420B ASN* 5.4 1.2 + - - -
2313B TRP* 4.0 6.8 - - - -
2317B ARG* 2.7 44.0 + - - -
2388B GLU* 3.6 12.3 - - - +
2389B VAL* 3.6 33.9 + - + +
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Residues in contact with LEU1402 (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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1398B HIS* 3.0 41.1 + - + +
1399B TYR* 3.2 16.6 + - + +
1401B GLU* 1.3 72.6 - - - +
1403B GLU* 1.3 62.0 + - - +
1405B GLN* 3.6 22.5 - - + +
1406B LYS* 3.5 29.4 + - - +
2297B ASP* 5.9 2.0 - - - +
2301B LYS* 5.3 20.0 - - - +
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Residues in contact with GLU1403 (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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1399B TYR 2.8 12.6 + - - +
1400B LYS* 3.4 38.3 + - - +
1402B LEU* 1.3 75.6 - - - +
1404B PHE* 1.3 64.8 + - - +
1406B LYS* 3.1 19.3 + - + +
1407B GLY 3.2 12.1 + - - +
1412B ILE* 3.7 22.7 - - + +
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Residues in contact with PHE1404 (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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1400B LYS 3.1 10.5 + - - +
1401B GLU* 3.1 11.4 + - - +
1403B GLU* 1.3 77.6 - - - +
1405B GLN* 1.3 70.0 + - - +
1407B GLY 4.4 0.4 - - - -
1408B PRO* 3.2 45.3 - - + +
1412B ILE* 3.9 21.2 - - + +
1413B LEU* 3.8 19.3 - - + -
1416B LEU* 4.2 16.4 - - + -
1435B TYR* 3.6 42.8 - + - -
2389B VAL* 3.7 33.7 - - + -
2390B THR* 4.9 8.5 - - - -
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Residues in contact with GLN1405 (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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1401B GLU 2.9 17.9 + - - +
1402B LEU* 3.6 29.0 - - + +
1404B PHE* 1.3 82.9 - - - +
1406B LYS* 1.3 61.1 + - + +
1407B GLY* 3.4 1.0 + - - -
1408B PRO* 4.9 2.6 - - - +
2297B ASP* 5.4 3.0 - - - +
2385B ASN* 3.5 33.2 + - - +
2389B VAL* 3.9 22.7 - - + +
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Residues in contact with LYS1406 (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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1402B LEU* 3.6 17.0 - - - +
1403B GLU* 3.1 12.1 + - + +
1405B GLN* 1.3 79.5 - - + +
1407B GLY* 1.3 57.8 + - - +
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Residues in contact with GLY1407 (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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1403B GLU 3.2 5.1 + - - +
1404B PHE 3.5 2.7 - - - -
1405B GLN 3.3 2.6 - - - -
1406B LYS* 1.3 79.7 - - - +
1408B PRO* 1.4 72.7 - - - +
1409B THR* 3.2 13.1 + - - +
1412B ILE* 3.3 18.5 - - - +
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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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
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