Contacts of the helix formed by residues 1307 - 1319 (chain B) in PDB entry 4DM8
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 LEU1307 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1272B ILE* 5.6 2.9 - - + -
1304B PHE* 3.0 21.8 + - + +
1306B PRO* 1.3 80.8 - - + +
1308B THR* 1.3 64.4 + - - +
1309B ASP 3.4 0.9 - - - -
1310B LEU* 3.1 22.6 + - + +
1311B VAL* 3.0 28.7 + - + +
1389B ILE* 4.1 14.4 - - + +
1392B LYS* 3.2 38.1 - - + +
1393B GLY* 3.3 28.9 - - - +
1396B ARG* 4.2 9.4 - - + -
1501B REA 3.9 16.8 - - + -
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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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1219B ARG* 4.0 6.7 - - - +
1296B ARG* 3.5 40.4 - - + +
1299B MET* 4.4 2.2 - - + -
1300B HIS* 3.2 28.3 - - + +
1304B PHE* 3.4 12.6 + - + +
1305B GLY 2.5 24.0 + - - -
1306B PRO 3.3 0.8 - - - -
1307B LEU* 1.3 77.8 - - - +
1309B ASP* 1.3 66.3 + - - +
1311B VAL* 3.2 4.4 + - - +
1312B PHE* 3.1 36.3 + - + -
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Residues in contact with ASP1309 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1219B ARG* 3.3 30.9 + - - -
1296B ARG* 3.7 23.5 + - - +
1306B PRO 4.6 4.5 + - - +
1307B LEU 3.4 0.6 - - - -
1308B THR* 1.3 75.2 - - - +
1310B LEU* 1.3 59.9 + - + +
1312B PHE* 4.0 1.1 - - - +
1313B THR* 2.8 36.7 + - - +
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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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342A GLN* 5.4 14.4 - - + -
1306B PRO 4.6 8.0 + - - +
1307B LEU* 3.1 25.2 + - + +
1309B ASP* 1.3 78.8 - - + +
1311B VAL* 1.3 57.9 + - - +
1313B THR* 3.6 6.1 - - + +
1314B PHE* 3.0 28.2 + - - +
1389B ILE* 3.9 24.4 - - + +
1392B LYS* 3.3 37.9 - - + -
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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
----------------------------------------------------------
1272B ILE* 4.8 7.6 - - + -
1275B ILE* 4.4 9.2 - - + -
1276B CYS* 3.6 21.8 - - - -
1286B MET* 4.0 16.8 - - + -
1304B PHE* 3.8 30.5 - - + -
1307B LEU* 3.0 23.1 + - + +
1308B THR* 3.6 5.8 - - - +
1310B LEU* 1.3 75.2 - - - +
1312B PHE* 1.3 63.3 + - + +
1314B PHE* 3.3 6.4 + - - +
1315B ALA* 2.9 27.4 + - - +
1389B ILE* 4.5 16.6 - - + -
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Residues in contact with PHE1312 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1279B TYR* 3.6 17.9 - + - -
1284B ASP* 3.4 33.4 - - - -
1285B THR* 4.4 1.6 - - - -
1286B MET* 3.7 26.0 - - + -
1295B ASN 4.5 0.4 - - - -
1296B ARG* 3.3 64.2 - - + +
1299B MET* 3.9 31.2 - - + -
1308B THR* 3.1 28.6 + - + +
1309B ASP 4.0 0.9 - - - +
1311B VAL* 1.3 79.4 - - + +
1313B THR* 1.3 60.4 + - - +
1315B ALA* 3.2 2.6 + - - +
1316B ASN* 2.7 33.4 + - - +
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Residues in contact with THR1313 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
342A GLN* 3.3 40.4 + - - +
1296B ARG* 5.7 1.4 + - - -
1309B ASP* 2.8 26.5 + - - +
1310B LEU* 3.6 7.4 - - + +
1312B PHE* 1.3 76.8 - - - +
1314B PHE* 1.3 63.0 + - - +
1316B ASN* 3.1 9.3 + - - +
1317B GLN* 3.0 36.6 + - + +
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Residues in contact with PHE1314 (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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1272B ILE* 4.5 0.9 - - + -
1273B LEU* 4.5 9.0 - - + -
1276B CYS* 3.7 20.4 - - + -
1310B LEU 3.0 18.1 + - - +
1311B VAL* 3.6 4.5 - - - +
1313B THR* 1.3 77.2 - - - +
1315B ALA* 1.3 61.8 + - - +
1317B GLN* 3.1 27.4 + - - +
1318B LEU* 3.1 42.5 + - + +
1382B LYS* 3.8 37.5 - - + -
1385B ASP* 3.9 21.8 - - + -
1386B LEU* 3.6 32.1 - - + -
1389B ILE* 3.6 17.5 - - + -
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Residues in contact with ALA1315 (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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1276B CYS* 4.0 20.9 - - + +
1279B TYR* 3.8 23.3 - - + -
1286B MET* 3.7 20.6 - - + -
1311B VAL 2.9 14.5 + - - +
1312B PHE 3.4 9.9 - - - +
1313B THR 3.2 0.2 - - - -
1314B PHE* 1.3 78.6 - - - +
1316B ASN* 1.3 59.2 + - - +
1318B LEU* 3.4 10.2 + - - +
1319B LEU* 3.1 21.5 + - - +
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Residues in contact with ASN1316 (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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1279B TYR* 3.2 31.9 + - - -
1281B PRO* 4.9 3.2 - - - +
1296B ARG* 4.7 3.6 + - - -
1312B PHE* 2.7 28.3 + - - +
1313B THR* 3.1 9.7 + - - +
1315B ALA* 1.3 72.1 - - - +
1317B GLN* 1.3 63.6 + - + +
1318B LEU 3.0 5.6 + - - -
1319B LEU* 3.2 21.9 + - - +
1320B PRO* 3.2 18.9 - - - +
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Residues in contact with GLN1317 (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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340A ASP* 3.3 33.5 + - - +
342A GLN* 3.5 24.1 + - - -
1313B THR* 3.0 22.0 + - + +
1314B PHE* 3.1 19.2 + - - +
1316B ASN* 1.3 75.2 - - + +
1318B LEU* 1.3 61.1 + - - +
1320B PRO* 3.7 7.6 - - - +
1321B LEU* 3.5 19.6 - - - +
1382B LYS* 3.8 16.6 - - - +
1385B ASP* 4.0 15.2 + - - +
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Residues in contact with LEU1318 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1273B LEU* 4.1 9.4 - - + -
1276B CYS* 3.8 24.5 - - + +
1277B THR* 4.5 7.2 - - + -
1314B PHE* 3.1 53.7 + - + +
1315B ALA 3.5 9.0 - - - +
1316B ASN 3.0 0.6 - - - -
1317B GLN* 1.3 79.9 - - - +
1319B LEU* 1.3 68.3 + - + +
1321B LEU* 3.0 22.8 + - + +
1322B GLU 3.7 2.3 + - - -
1323B MET* 3.2 36.6 + - + +
1382B LYS* 4.2 19.3 - - + -
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Residues in contact with LEU1319 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1276B CYS 5.5 1.6 - - - +
1279B TYR* 4.0 21.8 - - + +
1281B PRO* 4.0 31.9 - - + -
1315B ALA 3.1 20.0 - - - +
1316B ASN* 3.2 26.6 + - - +
1318B LEU* 1.3 78.9 - - + +
1320B PRO* 1.3 70.4 - - + +
1322B GLU* 3.0 21.0 + - - +
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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