Contacts of the helix formed by residues 1581 - 1599 (chain A) in PDB entry 4YOC
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 PRO1581 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1301A ALA* 4.0 17.3 - - + -
1306A VAL* 4.8 6.3 - - + -
1308A GLN* 4.5 1.8 - - - +
1310A ARG* 3.7 20.9 - - - +
1312A ARG* 5.5 2.2 - - + -
1557A GLN* 3.2 36.6 - - - +
1579A ALA 3.6 5.8 - - - +
1580A VAL* 1.3 90.1 - - + +
1582A PRO* 1.3 71.2 - - + +
1583A PRO* 3.2 7.0 - - + -
1584A LEU* 2.9 27.0 + - + +
1585A ALA 3.3 8.5 + - - -
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Residues in contact with PRO1582 (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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1150A GLY 3.8 23.8 - - - +
1153A GLU* 4.1 12.6 - - + -
1154A GLY* 3.3 14.5 - - - +
1157A GLN* 4.3 10.9 - - - +
1557A GLN 3.1 15.3 - - - +
1558A GLY 3.9 13.5 - - - +
1559A PHE* 4.1 28.5 - - + -
1580A VAL 3.1 8.7 - - - +
1581A PRO* 1.3 81.4 - - + +
1583A PRO* 1.3 61.2 - - + +
1585A ALA* 4.4 1.3 - - + -
1586A LYS* 2.9 29.3 + - - +
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Residues in contact with PRO1583 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1157A GLN* 5.3 1.6 - - - +
1301A ALA 5.9 0.2 - - - +
1304A TYR* 3.3 28.4 - - + +
1305A GLY* 4.7 4.0 - - - +
1306A VAL* 3.7 20.9 - - + -
1396A PHE* 5.7 1.6 - - + -
1400A LEU* 6.3 0.9 - - + -
1557A GLN 3.8 8.3 - - - +
1558A GLY* 3.8 11.7 - - - +
1581A PRO* 3.3 6.5 - - + -
1582A PRO* 1.3 97.2 - - + +
1584A LEU* 1.3 56.2 + - - +
1586A LYS* 3.1 12.4 + - + +
1587A ALA* 2.9 27.7 + - - +
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Residues in contact with LEU1584 (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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1299A LEU* 3.8 28.7 - - + -
1301A ALA* 4.3 18.6 + - + +
1304A TYR* 3.7 33.7 - - + +
1312A ARG* 4.2 26.9 - - + -
1314A ILE* 5.2 3.1 - - + -
1328A PRO* 5.4 0.4 - - + -
1580A VAL* 3.9 21.3 - - + -
1581A PRO* 2.9 20.9 + - + +
1583A PRO* 1.3 78.7 - - - +
1585A ALA* 1.3 62.2 + - - +
1587A ALA* 3.0 6.2 + - - +
1588A ILE* 3.0 36.6 + - + +
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Residues in contact with ALA1585 (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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1151A LEU* 3.6 48.9 - - + +
1154A GLY* 3.9 4.5 - - - -
1155A PHE* 3.1 19.8 - - + +
1580A VAL* 4.4 2.7 - - + -
1581A PRO 3.3 7.4 + - - +
1582A PRO* 3.9 8.1 - - + +
1584A LEU* 1.3 80.4 - - - +
1586A LYS* 1.3 56.0 + - - +
1588A ILE* 4.4 8.3 - - - -
1589A GLY 2.9 22.5 + - - -
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Residues in contact with LYS1586 (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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1077A MET* 3.7 26.5 - - - +
1154A GLY 3.4 19.5 + - - +
1157A GLN* 3.8 34.7 + - + +
1158A ALA* 3.8 7.5 - - - +
1582A PRO 2.9 15.2 + - - +
1583A PRO* 3.2 13.5 - - + +
1584A LEU 3.1 0.2 - - - -
1585A ALA* 1.3 74.2 - - - +
1587A ALA* 1.3 59.7 + - - +
1589A GLY* 3.2 1.4 + - - -
1590A LEU* 2.9 51.6 + - + +
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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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1304A TYR* 3.8 20.2 - - + -
1328A PRO* 3.5 24.6 - - + +
1331A LEU* 5.4 7.4 - - + -
1583A PRO 2.9 11.8 + - - +
1584A LEU 3.0 8.7 + - - +
1586A LYS* 1.3 76.5 - - - +
1588A ILE* 1.3 62.9 + - - +
1590A LEU* 3.1 13.3 + - - +
1591A GLU* 3.0 24.6 + - - +
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Residues in contact with ILE1588 (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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1151A LEU* 5.7 2.5 - - + -
1155A PHE* 4.4 1.8 - - + -
1264A LEU* 3.6 30.1 - - + -
1299A LEU* 4.1 22.2 - - + -
1314A ILE* 4.0 29.8 - - + -
1316A LEU* 4.2 18.8 - - + -
1325A PRO* 6.3 0.4 - - + -
1326A LEU 5.8 0.2 - - - +
1327A PHE* 6.3 0.4 - - + -
1328A PRO* 4.2 9.9 - - + -
1580A VAL* 6.0 0.9 - - + -
1584A LEU* 3.0 26.5 + - + +
1585A ALA* 3.9 8.1 - - - +
1587A ALA* 1.3 74.5 - - - +
1589A GLY* 1.3 58.8 + - - +
1591A GLU* 3.1 12.3 + - + +
1592A ILE* 2.9 31.9 + - + +
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Residues in contact with GLY1589 (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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1155A PHE* 3.8 6.1 - - - -
1158A ALA* 3.6 11.7 - - - -
1160A ILE* 3.4 32.3 - - - +
1585A ALA 2.9 18.8 + - - -
1586A LYS 3.5 2.0 - - - -
1587A ALA 3.2 0.2 - - - -
1588A ILE* 1.3 77.7 - - - +
1590A LEU* 1.3 56.6 + - - +
1592A ILE* 3.2 2.3 + - - -
1593A LYS 2.9 21.5 + - - -
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Residues in contact with LEU1590 (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 GLN 5.4 0.2 - - - +
1158A ALA* 3.7 27.6 - - + +
1586A LYS* 2.9 38.1 + - + +
1587A ALA* 3.1 10.9 + - - +
1589A GLY* 1.3 71.5 - - - +
1591A GLU* 1.3 65.5 + - - +
1592A ILE 3.1 0.2 - - - -
1593A LYS* 2.9 33.1 + - + +
1594A LEU* 3.0 18.5 + - - +
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Residues in contact with GLU1591 (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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1325A PRO* 4.0 5.1 - - + +
1326A LEU* 3.5 36.8 + - - +
1327A PHE 4.3 3.4 - - - -
1328A PRO* 3.6 36.4 - - + +
1329A GLU* 4.5 3.6 + - - +
1587A ALA 3.0 15.9 + - - +
1588A ILE* 3.1 11.4 + - + +
1590A LEU* 1.3 78.2 - - - +
1592A ILE* 1.3 61.0 + - - +
1594A LEU* 3.7 30.2 - - - +
1595A CYS* 3.7 16.6 - - - -
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Residues in contact with ILE1592 (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* 4.9 0.4 - - + -
1155A PHE* 4.4 10.3 - - + -
1160A ILE* 4.0 15.7 - - + -
1219A MET* 3.5 25.4 - - + -
1262A PHE* 4.2 31.9 - - + -
1263A PHE 6.6 0.2 - - - -
1264A LEU* 4.9 2.0 - - + -
1316A LEU* 4.9 8.3 - - + -
1325A PRO* 3.8 26.0 - - + -
1588A ILE* 2.9 31.6 + - + +
1589A GLY 3.4 6.1 - - - +
1591A GLU* 1.3 76.5 - - - +
1593A LYS* 1.3 65.8 + - - +
1594A LEU 3.2 0.4 - - - -
1595A CYS* 2.9 6.1 + - - +
1596A MET* 2.9 26.1 + - + +
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Residues in contact with LYS1593 (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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1134A ILE 5.5 6.3 - - - -
1136A LEU* 4.3 20.9 - - + +
1158A ALA 3.5 25.0 + - - +
1159A GLY* 4.6 12.6 + - - -
1160A ILE* 3.5 20.8 - - + +
1589A GLY 2.9 7.4 + - - +
1590A LEU* 2.9 22.9 + - + +
1592A ILE* 1.3 76.3 - - - +
1594A LEU* 1.3 64.3 + - + +
1596A MET* 3.1 7.8 + - - +
1597A LEU* 2.9 34.7 + - + +
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Residues in contact with LEU1594 (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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1323A LYS* 4.4 13.2 + - - +
1326A LEU* 6.2 2.2 - - + -
1590A LEU 3.0 15.4 + - - +
1591A GLU* 3.7 33.7 - - - +
1592A ILE 3.2 0.2 - - - -
1593A LYS* 1.3 79.0 - - + +
1595A CYS* 1.3 57.1 + - - +
1597A LEU* 3.2 18.9 + - + +
1598A ALA* 2.9 28.2 + - - +
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Residues in contact with CYS1595 (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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1262A PHE* 4.0 12.6 - - + -
1322A GLU* 4.7 2.6 - - - +
1323A LYS* 3.1 56.3 - - + +
1324A LEU 3.8 3.4 - - - -
1325A PRO* 3.4 29.8 - - - -
1326A LEU 4.9 0.7 - - - -
1591A GLU 3.7 8.3 - - - -
1592A ILE 2.9 8.8 + - - +
1594A LEU* 1.3 76.4 - - - +
1596A MET* 1.3 66.0 + - - +
1598A ALA* 3.8 1.4 - - - +
1599A LYS* 3.3 23.2 + - - +
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Residues in contact with MET1596 (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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1136A LEU* 3.6 33.1 - - + +
1137A PRO* 3.7 22.9 - - + +
1139A LEU* 3.9 27.8 - - + -
1160A ILE* 3.8 37.0 - - + +
1261A ARG* 4.2 14.2 + - - +
1262A PHE* 4.1 20.8 - - + -
1322A GLU* 5.4 1.1 - - - -
1592A ILE* 2.9 16.8 + - + +
1593A LYS* 3.1 8.0 + - - +
1595A CYS* 1.3 77.4 - - - +
1597A LEU* 1.3 62.5 + - - +
1599A LYS* 3.6 16.7 + - - +
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Residues in contact with LEU1597 (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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1134A ILE* 4.3 31.6 - - + +
1136A LEU* 3.6 31.0 - - + -
1593A LYS* 2.9 31.2 + - + +
1594A LEU* 3.5 20.2 - - + +
1596A MET* 1.3 79.0 - - - +
1598A ALA* 1.3 61.2 + - - +
1599A LYS 3.4 5.7 + - - +
1600A ALA* 4.7 5.2 + - - +
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Residues in contact with ALA1598 (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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1323A LYS* 3.7 34.3 - - + +
1594A LEU 2.9 17.2 + - - +
1595A CYS 3.3 3.1 + - - +
1597A LEU* 1.3 77.5 - - - +
1599A LYS* 1.3 57.2 + - - +
1600A ALA* 3.1 12.3 + - - +
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Residues in contact with LYS1599 (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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1261A ARG* 3.3 22.8 - - - +
1321A GLY* 3.4 24.0 - - - +
1322A GLU* 3.2 33.9 - - - +
1323A LYS* 5.6 2.8 - - + +
1595A CYS 3.3 14.3 + - - +
1596A MET 3.8 12.5 - - - +
1597A LEU 3.3 3.9 - - - +
1598A ALA* 1.3 72.9 - - - +
1600A ALA* 1.3 62.2 + - - +
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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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
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