Contacts of the helix formed by residues 1583 - 1596 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1304A ALA* 4.2 15.5 - - + -
1309A VAL* 4.7 6.1 - - + -
1311A GLN* 4.5 2.5 - - - +
1313A ARG* 3.6 23.8 - - - +
1315A ARG* 4.7 1.3 - - - -
1559A GLN* 3.1 25.8 - - + +
1560A GLY 4.1 11.2 - - - +
1581A ALA 3.4 6.7 - - - +
1582A VAL* 1.3 88.7 - - + +
1584A PRO* 1.3 74.0 - - + +
1585A PRO* 3.2 5.2 - - + -
1586A LEU* 2.9 28.8 + - + +
1587A ALA 3.0 8.7 + - - -
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Residues in contact with PRO1584 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1153A GLY 4.0 7.0 - - - +
1156A GLU* 4.0 29.2 - - + -
1157A GLY* 3.5 12.3 - - - +
1160A GLN* 4.2 11.0 - - - +
1560A GLY 3.5 34.5 - - - +
1561A PHE* 4.0 22.0 - - + +
1562A PRO* 4.7 0.2 - - + -
1582A VAL 3.3 8.5 - - - +
1583A PRO* 1.3 81.4 - - + +
1585A PRO* 1.3 55.5 - - + +
1587A ALA* 2.9 2.1 + - + -
1588A LYS* 2.6 38.2 + - - +
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Residues in contact with PRO1585 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1160A GLN* 5.0 2.0 - - - +
1304A ALA 5.7 0.7 - - - +
1307A TYR* 3.6 26.7 - - + +
1308A GLY 4.4 5.2 - - - +
1309A VAL* 3.7 20.2 - - + -
1399A PHE* 5.5 2.7 - - + -
1403A LEU* 6.5 0.2 - - + -
1560A GLY* 3.2 31.4 - - - +
1583A PRO* 3.3 4.9 - - + -
1584A PRO* 1.3 91.4 - - + +
1586A LEU* 1.3 56.0 + - - +
1588A LYS* 3.5 10.6 + - + +
1589A ALA* 3.0 27.0 + - - +
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Residues in contact with LEU1586 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1302A LEU* 4.2 19.7 - - + +
1304A ALA* 4.0 25.1 + - + +
1307A TYR* 3.3 37.6 - - + +
1315A ARG* 4.5 26.2 - - + -
1317A ILE* 5.2 8.7 - - + -
1331A PRO* 6.0 0.2 - - + -
1582A VAL* 4.1 16.6 - - + -
1583A PRO* 2.9 20.1 + - + +
1585A PRO* 1.3 75.9 - - - +
1587A ALA* 1.3 66.7 + - - +
1588A LYS 3.1 0.2 - - - -
1589A ALA* 3.3 5.2 + - + +
1590A ILE* 3.1 34.4 + - + +
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Residues in contact with ALA1587 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1153A GLY 4.2 1.3 - - - +
1154A LEU* 3.4 51.4 - - + +
1157A GLY* 3.6 6.1 - - - +
1158A PHE* 3.3 13.4 - - + +
1582A VAL* 4.0 5.8 - - + +
1583A PRO 3.0 9.6 + - - +
1584A PRO 2.9 6.8 + - - +
1586A LEU* 1.3 78.1 - - - +
1588A LYS* 1.3 57.5 + - - +
1590A ILE* 3.5 5.7 + - - +
1591A GLY 2.9 22.2 + - - -
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Residues in contact with LYS1588 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1157A GLY* 3.3 19.9 - - - +
1160A GLN* 3.7 35.9 - - + +
1161A ALA* 3.8 7.7 - - + +
1584A PRO 2.6 20.8 + - - +
1585A PRO* 3.6 9.2 - - + +
1587A ALA* 1.3 71.3 - - - +
1589A ALA* 1.3 65.8 + - - +
1591A GLY* 2.9 2.3 + - - +
1592A LEU* 2.8 41.5 + - + +
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Residues in contact with ALA1589 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1307A TYR* 3.7 30.7 - - + -
1331A PRO* 3.8 15.1 - - + +
1334A LEU* 5.7 4.7 - - + -
1585A PRO 3.0 17.8 + - - +
1586A LEU 3.5 5.6 - - - +
1588A LYS* 1.3 76.8 - - - +
1590A ILE* 1.3 65.4 + - - +
1592A LEU* 3.4 10.9 + - - +
1593A GLU* 3.4 20.8 + - - +
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Residues in contact with ILE1590 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1154A LEU* 5.7 2.2 - - + -
1158A PHE* 4.5 7.0 - - + -
1267A LEU* 4.7 12.6 - - + -
1302A LEU* 4.3 11.7 - - + -
1317A ILE* 4.1 34.3 - - + -
1319A LEU* 4.6 20.4 - - + -
1329A LEU 5.8 0.4 - - - +
1331A PRO* 4.0 19.5 - - + -
1586A LEU* 3.1 22.5 + - + +
1587A ALA* 3.8 8.7 - - - +
1589A ALA* 1.3 72.8 - - - +
1591A GLY* 1.3 69.0 + - - +
1593A GLU* 2.7 20.6 + - + +
1594A ILE* 3.1 26.0 + - + +
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Residues in contact with GLY1591 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1158A PHE* 3.8 16.1 - - - -
1161A ALA* 3.7 16.6 - - - -
1163A ILE* 3.6 14.6 - - - +
1587A ALA 2.9 16.3 + - - -
1588A LYS 2.9 4.6 + - - -
1590A ILE* 1.3 75.7 - - - +
1592A LEU* 1.3 56.3 - - - +
1594A ILE* 3.0 20.1 + - - +
1595A LYS 3.0 9.7 + - - -
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Residues in contact with LEU1592 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1161A ALA* 3.7 29.8 - - + +
1588A LYS* 2.8 40.7 + - + +
1589A ALA* 3.8 8.5 - - - +
1590A ILE 3.1 0.2 - - - -
1591A GLY* 1.3 72.0 - - - +
1593A GLU* 1.3 66.9 + - + +
1595A LYS* 3.3 34.0 + - + +
1596A LEU* 3.4 13.7 + - - +
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Residues in contact with GLU1593 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1328A PRO* 4.0 6.3 - - + +
1329A LEU* 3.5 37.8 + - - +
1330A PHE 3.8 10.4 - - - +
1331A PRO* 3.5 27.6 - - + +
1332A GLU* 4.3 3.5 + - - +
1589A ALA 3.4 13.0 + - - +
1590A ILE* 2.7 17.2 + - + +
1592A LEU* 1.3 75.6 - - - +
1594A ILE* 1.3 61.2 + - + +
1596A LEU* 3.5 28.3 + - - +
1597A CYS* 3.5 17.0 - - - -
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Residues in contact with ILE1594 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1142A LEU* 4.7 10.8 - - + -
1158A PHE* 4.3 9.4 - - + -
1163A ILE* 3.9 18.4 - - + -
1222A MET* 3.4 29.4 - - + -
1265A PHE* 4.0 31.9 - - + -
1267A LEU* 5.6 1.1 - - + -
1319A LEU* 5.3 7.9 - - + -
1328A PRO* 4.1 14.6 - - + -
1590A ILE* 3.5 22.7 - - + +
1591A GLY 3.0 7.1 + - - +
1593A GLU* 1.3 75.2 - - + +
1595A LYS* 1.3 56.0 + - - +
1596A LEU 3.1 2.0 - - - -
1597A CYS* 2.8 32.0 + - - +
1598A LEU* 3.5 8.1 + - + +
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Residues in contact with LYS1595 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1139A LEU* 5.6 8.7 - - - -
1161A ALA 3.0 27.2 + - - +
1162A GLY* 4.2 12.2 + - - -
1163A ILE* 3.6 19.8 - - + +
1591A GLY 3.0 7.8 + - - +
1592A LEU* 3.3 26.4 - - + +
1594A ILE* 1.3 76.0 - - - +
1596A LEU* 1.3 62.0 + - + +
1597A CYS 3.1 1.4 + - - -
1598A LEU* 3.1 19.4 + - + +
1599A LEU* 3.3 17.7 + - + +
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Residues in contact with LEU1596 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1326A LYS* 5.0 3.6 + - - +
1592A LEU 3.4 10.8 + - - +
1593A GLU* 3.7 30.7 - - - +
1594A ILE 3.1 1.2 - - - -
1595A LYS* 1.3 80.1 - - + +
1597A CYS* 1.3 60.5 + - - +
1598A LEU 3.4 0.2 - - - -
1599A LEU* 4.1 17.3 - - + +
1600A SER* 3.7 15.8 + - - -
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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