Contacts of the helix formed by residues 1397 - 1410 (chain B) in PDB entry 4Z4Q
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 ASN1397 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1428A THR* 3.5 19.0 - - - +
1395B SER 3.5 0.8 - - - -
1396B GLU* 1.3 94.5 - - - +
1398B LYS* 1.3 66.0 + - - +
1399B ALA* 2.9 31.4 + - - +
1400B ASP* 3.2 13.4 + - - +
1401B ALA* 3.0 22.5 + - - +
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Residues in contact with LYS1398 (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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1423A GLN* 5.2 1.8 + - - -
1425A TYR* 3.5 62.2 + - + -
1428A THR* 4.5 1.2 + - - -
1397B ASN* 1.3 75.9 - - - +
1399B ALA* 1.3 65.1 + - - +
1401B ALA* 2.9 14.5 + - + +
1402B LYS* 3.1 26.9 + - + +
1417B GLU* 3.1 38.1 + - - -
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Residues in contact with ALA1399 (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 ASN* 2.9 12.7 + - - +
1398B LYS* 1.3 74.7 - - - +
1400B ASP* 1.3 64.9 + - - +
1402B LYS* 3.0 17.4 + - - +
1403B GLU* 3.0 22.1 + - - +
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Residues in contact with ASP1400 (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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1394B ALA 4.8 0.5 - - - +
1395B SER* 3.3 9.2 - - - -
1396B GLU* 2.9 31.9 + - - +
1397B ASN* 3.2 26.2 + - - +
1398B LYS 3.2 0.2 - - - -
1399B ALA* 1.3 80.5 - - - +
1401B ALA* 1.3 60.8 + - - +
1403B GLU* 3.5 7.9 + - - +
1404B ASN* 3.0 40.6 + - - +
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Residues in contact with ALA1401 (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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1425A TYR* 5.3 4.7 - - + -
1428A THR* 4.5 3.1 - - + -
1391B LEU* 4.2 1.4 - - - +
1392B ILE* 4.5 24.9 - - + -
1395B SER* 3.4 21.0 - - - +
1397B ASN 3.0 12.9 + - - +
1398B LYS* 2.9 12.4 + - - +
1400B ASP* 1.3 76.8 - - - +
1402B LYS* 1.3 58.6 + - + +
1404B ASN* 3.3 3.6 + - - +
1405B LEU* 2.9 33.8 + - + +
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Residues in contact with LYS1402 (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 LYS* 3.6 20.5 - - + +
1399B ALA* 3.0 15.1 + - - +
1401B ALA* 1.3 73.5 - - + +
1403B GLU* 1.3 67.1 + - - +
1405B LEU* 2.9 10.3 + - + +
1406B LYS* 2.8 31.0 + - - +
1413B GLU* 2.9 37.0 + - - +
1416B ALA* 3.9 15.7 - - + +
1417B GLU* 2.5 51.0 + - - +
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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 ALA 3.0 15.2 + - - +
1400B ASP* 4.0 9.0 - - - +
1402B LYS* 1.3 75.5 - - - +
1404B ASN* 1.3 59.6 + - - +
1406B LYS* 3.6 10.0 - - - +
1407B VAL* 2.8 41.4 + - + +
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Residues in contact with ASN1404 (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 LEU* 3.6 26.1 + - + +
1394B ALA 5.4 0.8 + - - -
1395B SER* 3.3 18.2 + - - +
1400B ASP* 3.0 41.1 + - - +
1401B ALA 3.7 0.9 - - - +
1402B LYS 3.2 0.2 - - - -
1403B GLU* 1.3 78.1 - - - +
1405B LEU* 1.3 58.2 + - - +
1407B VAL* 4.6 4.7 - - - +
1408B SER* 2.9 39.8 + - - +
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Residues in contact with LEU1405 (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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1381B VAL* 6.3 0.4 - - + -
1388B VAL* 4.1 28.0 - - + -
1391B LEU* 4.2 19.7 - - + -
1392B ILE* 4.9 14.4 - - + -
1401B ALA* 2.9 16.9 + - + +
1402B LYS* 2.9 12.0 + - + +
1404B ASN* 1.3 73.7 - - - +
1406B LYS* 1.3 65.4 + - - +
1409B TYR* 3.1 26.4 + - + +
1410B ASP 3.6 3.5 + - - -
1411B PHE* 3.7 27.1 + - + -
1416B ALA* 4.2 32.8 - - + +
1419B ILE* 5.3 8.7 - - - -
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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 LYS* 2.8 20.5 + - - +
1403B GLU* 3.6 11.9 - - - +
1405B LEU* 1.3 75.4 - - - +
1407B VAL* 1.3 59.8 + - + +
1410B ASP* 2.7 34.0 + - - +
1411B PHE 3.5 23.1 - - - +
1413B GLU* 3.1 52.6 + - - +
1416B ALA* 4.5 10.1 - - + -
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Residues in contact with VAL1407 (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* 2.8 29.3 + - + +
1404B ASN* 4.3 4.7 - - - +
1406B LYS* 1.3 77.9 - - + +
1408B SER* 1.3 64.5 + - - +
1410B ASP* 4.6 4.0 + - - +
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Residues in contact with SER1408 (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 LEU* 3.8 9.5 - - - +
1404B ASN* 2.9 27.1 + - - +
1407B VAL* 1.3 80.4 - - - +
1409B TYR* 1.3 89.1 + - - +
1410B ASP* 3.8 1.8 - - - +
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Residues in contact with TYR1409 (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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1380B ARG* 2.5 45.8 + - - +
1384B ILE* 3.4 34.8 - - + -
1387B GLU* 3.4 30.0 + - + +
1388B VAL* 4.9 4.5 - - + -
1391B LEU* 3.6 27.4 - - + -
1405B LEU* 3.1 13.4 + - + +
1408B SER* 1.3 94.5 - - - +
1410B ASP* 1.3 60.3 + - - +
1411B PHE* 3.2 24.5 - + + -
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Residues in contact with ASP1410 (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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1380B ARG* 3.5 7.0 + - - +
1406B LYS 2.7 24.7 + - - +
1407B VAL 5.2 3.5 - - - +
1408B SER 3.8 1.3 - - - +
1409B TYR* 1.3 74.6 - - - +
1411B PHE* 1.3 64.6 + - - +
1412B THR* 3.8 3.1 + - - +
1415B GLN* 4.8 0.9 - - - +
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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