Contacts of the helix formed by residues 1307 - 1319 (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 ASN1307 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1282B ALA 5.2 3.2 + - - -
1305B ASP 3.7 3.0 + - - -
1306B ALA* 1.3 66.9 - - - +
1308B THR* 1.3 60.0 + - - +
1309B GLU* 3.4 8.0 + - - +
1310B LEU* 2.9 58.7 + - + +
1311B VAL* 3.2 10.8 + - - +
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Residues in contact with THR1308 (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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1244B ILE* 4.1 16.6 - - - +
1252B GLU* 2.9 37.9 + - + +
1254B ILE* 4.3 3.1 - - - +
1302B LEU* 3.6 28.1 - - - +
1306B ALA 2.9 10.5 + - - +
1307B ASN* 1.3 73.7 + - - +
1309B GLU* 1.3 60.8 + - - +
1311B VAL* 3.7 4.2 + - - +
1312B LEU* 3.3 22.3 + - - +
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Residues in contact with GLU1309 (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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1307B ASN* 3.2 7.2 + - - +
1308B THR* 1.3 78.6 + - - +
1310B LEU* 1.3 65.4 + - - +
1312B LEU* 4.0 7.8 - - + +
1313B ASN* 3.1 36.0 + - - +
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Residues in contact with LEU1310 (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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1281B VAL* 4.2 18.3 - - + +
1282B ALA* 5.7 6.3 - - + +
1307B ASN* 2.9 41.2 + - + +
1309B GLU* 1.3 78.3 - - - +
1311B VAL* 1.3 61.1 + - + +
1313B ASN* 3.6 7.6 + - + +
1314B TYR* 3.1 22.3 + - + +
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Residues in contact with VAL1311 (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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1254B ILE* 4.4 7.0 - - + -
1281B VAL* 4.2 12.6 - - + -
1282B ALA 3.5 23.8 - - - +
1283B GLY* 4.9 0.7 - - - -
1284B ILE* 4.1 15.5 - - + -
1300B ILE* 5.2 1.1 - - + -
1302B LEU* 3.5 34.3 - - + -
1306B ALA* 5.1 0.9 - - + -
1307B ASN 3.2 11.3 + - - +
1308B THR 3.8 6.1 - - - +
1310B LEU* 1.3 73.7 - - + +
1312B LEU* 1.3 69.3 + - - +
1313B ASN 3.0 1.3 - - - -
1314B TYR* 3.0 5.0 + - - +
1315B LEU* 2.9 43.6 + - + +
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Residues in contact with LEU1312 (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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1242B THR* 4.3 18.6 - - + +
1244B ILE* 5.1 11.7 - - + -
1254B ILE* 3.3 35.9 - - + +
1308B THR 3.3 15.4 + - - +
1309B GLU* 4.0 7.2 - - + +
1310B LEU 3.6 0.2 - - - -
1311B VAL* 1.3 79.4 - - - +
1313B ASN* 1.3 63.8 + - - +
1315B LEU* 3.3 6.7 + - + +
1316B PHE* 3.1 55.9 + - + -
1321B LEU* 4.8 8.3 - - + -
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Residues in contact with ASN1313 (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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1239B ARG* 5.2 2.3 + - - -
1309B GLU* 3.1 25.5 + - - +
1310B LEU* 3.7 9.8 - - + +
1311B VAL 3.0 0.4 - - - -
1312B LEU* 1.3 79.8 - - - +
1314B TYR* 1.3 65.5 + - - +
1316B PHE* 3.2 17.5 + - - +
1317B LYS* 3.1 22.5 + - - +
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Residues in contact with TYR1314 (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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1275B VAL* 3.9 17.2 - - + +
1280B LYS* 3.3 44.7 - - + +
1281B VAL* 3.8 30.5 - - + -
1310B LEU* 3.1 13.3 + - + +
1311B VAL 3.0 8.5 + - - +
1313B ASN* 1.3 77.3 - - - +
1315B LEU* 1.3 61.6 + - + +
1317B LYS* 3.3 1.7 + - - -
1318B TYR* 2.9 77.0 + + + +
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Residues in contact with LEU1315 (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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1254B ILE* 5.1 2.0 - - + -
1272B ILE* 3.9 21.1 - - + -
1275B VAL* 4.3 22.4 - - + -
1281B VAL* 5.3 0.7 - - + -
1284B ILE* 4.4 5.2 - - + -
1300B ILE* 3.5 32.1 - - + -
1311B VAL* 2.9 35.8 + - + +
1312B LEU* 3.7 9.6 - - - +
1314B TYR* 1.3 74.7 - - + +
1316B PHE* 1.3 67.0 + - - +
1319B THR* 2.8 47.9 + - + +
1321B LEU* 3.8 19.3 - - + +
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Residues in contact with PHE1316 (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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1239B ARG* 2.6 54.3 - - + +
1240B SER 4.1 11.7 - - - -
1242B THR* 4.6 7.4 - - + -
1312B LEU* 3.1 51.7 + - + -
1313B ASN* 3.2 15.2 + - - +
1315B LEU* 1.3 77.2 - - - +
1317B LYS* 1.3 62.3 + - - +
1319B THR 3.2 13.2 - - - +
1321B LEU* 3.8 27.4 - - + -
1322B GLN* 3.5 46.8 + - + +
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Residues in contact with LYS1317 (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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1313B ASN 3.1 15.2 + - - +
1314B TYR* 3.3 1.5 + - - -
1316B PHE* 1.3 79.2 - - + +
1318B TYR* 1.3 96.8 + - + +
1319B THR 3.7 1.3 + - - +
1322B GLN* 5.7 2.2 - - - +
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Residues in contact with TYR1318 (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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1275B VAL* 5.5 1.2 - - + +
1314B TYR* 2.9 64.4 + + + +
1317B LYS* 1.3 115.1 - - + +
1319B THR* 1.3 64.8 + - + +
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Residues in contact with THR1319 (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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1268B LEU* 4.1 10.8 - - - +
1271B LYS* 4.2 19.1 - - + +
1272B ILE* 4.3 7.2 - - + +
1275B VAL* 4.0 24.9 - - + -
1315B LEU* 2.8 31.7 + - + +
1316B PHE 3.2 9.5 - - - +
1317B LYS 4.5 0.9 - - - +
1318B TYR* 1.3 83.7 - - + +
1320B ASP* 1.3 63.4 + - - +
1321B LEU* 3.1 18.7 + - - +
1322B GLN 3.2 15.6 - - - +
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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