Contacts of the helix formed by residues 1583 - 1599 (chain B) in PDB entry 3PT6
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 PRO1583 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1304B ALA* 4.0 16.4 - - + -
1309B VAL* 4.7 7.0 - - + -
1311B GLN* 4.4 2.9 - - - +
1313B ARG* 3.7 21.8 - - - +
1315B ARG* 4.9 2.2 - - - -
1559B GLN* 3.1 26.0 - - + +
1560B GLY 4.2 9.4 - - - +
1581B ALA 3.6 7.1 - - - +
1582B VAL* 1.3 88.9 - - + +
1584B PRO* 1.3 74.3 - - + +
1585B PRO* 3.3 2.5 - - + -
1586B LEU* 2.9 31.0 + - + +
1587B ALA 3.0 9.5 + - - -
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Residues in contact with PRO1584 (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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1153B GLY 3.9 18.6 - - - +
1156B GLU* 4.0 21.3 - - + -
1157B GLY* 3.5 7.8 - - - +
1160B GLN* 4.3 9.4 - - - +
1559B GLN* 4.7 0.2 - - + -
1560B GLY 3.5 27.4 - - - +
1561B PHE* 4.0 27.4 - - + +
1582B VAL 3.1 5.8 - - - +
1583B PRO* 1.3 81.5 - - + +
1585B PRO* 1.3 64.7 - - + +
1587B ALA* 2.8 2.5 + - - +
1588B LYS* 2.6 37.3 + - - +
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Residues in contact with PRO1585 (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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1160B GLN* 5.1 2.0 - - - +
1304B ALA 5.9 0.4 - - - +
1307B TYR* 3.5 30.5 - - + +
1308B GLY* 4.3 7.9 - - - +
1309B VAL* 4.2 12.3 - - + -
1334B LEU* 6.0 0.5 - - - +
1399B PHE* 5.5 2.7 - - + -
1403B LEU* 6.1 0.9 - - + -
1560B GLY* 3.1 34.3 - - - +
1583B PRO* 3.5 4.0 - - + -
1584B PRO* 1.3 91.4 - - + +
1586B LEU* 1.3 59.1 + - - +
1588B LYS* 3.6 10.6 + - + +
1589B ALA* 3.3 21.1 + - - +
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Residues in contact with LEU1586 (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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1302B LEU* 4.1 27.8 - - + +
1304B ALA* 4.3 25.8 + - + +
1307B TYR* 3.8 35.4 - - + +
1315B ARG* 4.6 22.2 - - + -
1317B ILE* 5.8 2.7 - - + -
1582B VAL* 4.4 14.4 - - + -
1583B PRO* 2.9 21.4 + - + +
1585B PRO* 1.3 75.1 - - - +
1587B ALA* 1.3 67.0 + - - +
1588B LYS 3.1 2.0 - - - -
1589B ALA* 3.1 12.4 + - + +
1590B ILE* 3.2 22.3 + - + +
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Residues in contact with ALA1587 (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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1153B GLY 4.1 0.7 - - - +
1154B LEU* 3.3 50.3 - - + +
1157B GLY* 3.5 11.9 - - - +
1158B PHE* 3.3 15.3 - - - -
1582B VAL* 4.2 5.5 - - + +
1583B PRO 3.0 9.9 + - - +
1584B PRO 2.8 6.4 + - - +
1586B LEU* 1.3 74.2 - - - +
1588B LYS* 1.3 57.4 + - - +
1590B ILE* 3.5 5.5 + - - -
1591B GLY 3.0 22.5 + - - -
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Residues in contact with LYS1588 (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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1157B GLY* 3.3 22.4 - - - +
1160B GLN* 3.7 35.4 + - + +
1161B ALA* 3.7 4.6 - - - +
1584B PRO 2.6 18.4 + - - +
1585B PRO* 3.8 8.7 - - + +
1586B LEU 3.1 0.2 - - - -
1587B ALA* 1.3 72.2 - - - +
1589B ALA* 1.3 59.2 + - - +
1591B GLY* 3.3 1.2 + - - -
1592B LEU* 2.9 57.3 + - + +
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Residues in contact with ALA1589 (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 TYR* 3.6 32.5 - - + -
1331B PRO* 3.6 15.2 - - + +
1334B LEU* 5.4 6.1 - - + -
1585B PRO 3.3 8.9 + - - +
1586B LEU* 3.1 9.7 + - + +
1588B LYS* 1.3 76.1 - - - +
1590B ILE* 1.3 66.2 + - - +
1592B LEU* 3.5 9.6 + - - +
1593B GLU* 3.3 23.6 + - - +
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Residues in contact with ILE1590 (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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1154B LEU* 5.6 1.8 - - + -
1158B PHE* 4.2 12.8 - - + -
1267B LEU* 4.4 20.0 - - + -
1269B GLU* 6.2 0.2 - - + -
1302B LEU* 4.3 18.6 - - + -
1317B ILE* 3.9 32.1 - - + -
1319B LEU* 4.7 16.6 - - + -
1331B PRO* 4.4 8.3 - - + -
1586B LEU* 3.2 21.7 + - + +
1587B ALA* 3.8 10.8 - - - +
1589B ALA* 1.3 75.1 - - - +
1591B GLY* 1.3 67.6 + - - +
1593B GLU* 2.8 25.1 + - + +
1594B ILE* 3.2 13.1 + - + +
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Residues in contact with GLY1591 (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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1158B PHE* 4.0 13.2 - - - -
1161B ALA* 3.7 15.9 - - - -
1163B ILE* 3.4 16.2 - - - +
1587B ALA 3.0 15.6 + - - -
1588B LYS 3.3 3.1 + - - -
1590B ILE* 1.3 77.7 - - - +
1592B LEU* 1.3 56.1 + - - +
1594B ILE* 2.9 22.6 + - - +
1595B LYS 2.9 9.5 + - - -
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Residues in contact with LEU1592 (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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1160B GLN 5.2 0.4 - - - +
1161B ALA* 3.6 22.6 - - + +
1588B LYS* 2.9 44.5 + - + +
1589B ALA* 4.0 8.7 - - - +
1590B ILE 3.2 0.2 - - - -
1591B GLY* 1.3 75.3 - - - +
1593B GLU* 1.3 64.6 + - - +
1595B LYS* 3.2 44.6 + - + +
1596B LEU* 3.5 15.1 + - - +
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Residues in contact with GLU1593 (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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1328B PRO* 4.1 6.4 - - + +
1329B LEU* 3.6 34.0 + - - +
1330B PHE 4.0 5.7 - - - +
1331B PRO* 3.5 37.8 - - + +
1332B GLU* 4.3 3.3 + - - +
1589B ALA 3.3 14.5 + - - +
1590B ILE* 2.8 13.7 + - + +
1592B LEU* 1.3 79.8 - - - +
1594B ILE* 1.3 59.3 + - + +
1596B LEU* 3.4 30.6 + - - +
1597B CYS* 3.5 14.0 - - - -
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Residues in contact with ILE1594 (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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1142B LEU* 4.7 3.8 - - + -
1158B PHE* 4.7 7.2 - - + -
1163B ILE* 4.2 17.9 - - + -
1222B MET* 3.5 31.2 - - + -
1265B PHE* 4.5 27.8 - - + -
1267B LEU* 5.9 0.7 - - + -
1319B LEU* 5.8 6.7 - - + -
1328B PRO* 4.1 16.6 - - + -
1590B ILE* 3.2 16.5 + - + +
1591B GLY* 2.9 10.1 + - - +
1593B GLU* 1.3 74.3 - - + +
1595B LYS* 1.3 60.6 + - - +
1596B LEU 3.1 0.4 - - - -
1597B CYS* 2.8 24.5 + - - +
1598B LEU* 3.2 24.3 + - + +
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Residues in contact with LYS1595 (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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1139B LEU* 5.6 14.8 - - + -
1161B ALA 3.4 25.2 + - - +
1162B GLY 5.3 3.6 - - - +
1163B ILE* 3.6 19.7 - - + +
1591B GLY 2.9 6.1 + - - +
1592B LEU* 3.3 29.8 - - + +
1593B GLU 3.2 0.4 - - - -
1594B ILE* 1.3 77.2 - - - +
1596B LEU* 1.3 58.1 + - + +
1598B LEU* 3.4 8.5 + - + +
1599B LEU* 3.2 31.1 + - + +
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Residues in contact with LEU1596 (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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1326B LYS* 5.5 1.6 + - - -
1329B LEU* 6.4 1.1 - - + -
1592B LEU 3.8 13.9 - - - +
1593B GLU* 3.4 26.8 + - - +
1594B ILE 3.1 0.6 - - - -
1595B LYS* 1.3 78.1 - - + +
1597B CYS* 1.3 61.7 + - - +
1599B LEU* 3.5 17.2 + - + +
1600B SER* 3.4 20.3 + - - -
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Residues in contact with CYS1597 (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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1265B PHE* 4.1 16.9 - - + -
1325B GLU* 5.2 3.8 - - - +
1326B LYS* 3.2 42.3 + - + +
1327B LEU 4.6 0.4 - - - -
1328B PRO* 3.5 31.9 - - - -
1593B GLU 3.5 9.9 - - - -
1594B ILE 2.8 9.5 + - - +
1596B LEU* 1.3 80.3 - - - +
1598B LEU* 1.3 62.8 + - - +
1599B LEU 3.4 0.2 - - - -
1600B SER* 3.9 15.3 - - - -
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Residues in contact with LEU1598 (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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1139B LEU* 5.7 10.5 - - + -
1140B PRO 4.5 13.0 - - - +
1142B LEU* 4.0 23.8 - - + -
1163B ILE* 4.3 20.4 - - + +
1264B ARG* 3.7 21.1 - - - +
1265B PHE* 3.6 34.3 - - + -
1594B ILE* 3.2 17.6 + - + +
1595B LYS* 3.4 8.0 + - + +
1596B LEU 3.3 0.2 - - - -
1597B CYS* 1.3 76.5 - - - +
1599B LEU* 1.3 57.6 + - - +
1600B SER 3.2 7.3 + - - -
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Residues in contact with LEU1599 (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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1139B LEU* 5.6 9.6 - - + -
1595B LYS* 3.2 20.5 + - + +
1596B LEU* 3.5 19.9 + - + +
1597B CYS 3.4 0.2 - - - -
1598B LEU* 1.3 78.0 - - - +
1600B SER* 1.3 63.2 + - - +
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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