Contacts of the helix formed by residues 1578 - 1590 (chain A) in PDB entry 5M64
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 SER1578 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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661A THR 3.2 11.0 + - - -
662A SER* 4.4 4.1 - - - +
1057A ILE* 3.6 11.9 - - - +
1577A VAL* 1.3 73.1 - - - +
1579A PHE* 1.3 64.0 + - - +
1580A ARG* 2.8 34.0 + - - -
1581A HIS* 3.3 31.1 + - - -
1582A LEU* 3.2 18.4 - - - +
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Residues in contact with PHE1579 (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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1563A VAL* 4.9 5.3 - - + +
1567A ASN* 3.1 39.7 - - - -
1577A VAL* 3.6 16.6 - - + -
1578A SER* 1.3 72.9 + - - +
1580A ARG* 1.3 59.5 + - - +
1581A HIS 3.3 0.2 - - - -
1582A LEU* 3.3 13.5 + - + +
1583A ASP* 2.9 40.0 + - - +
202E SER* 5.5 2.2 - - - +
203E GLU* 3.2 48.2 - - + -
204E THR* 4.8 14.1 - - + -
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Residues in contact with ARG1580 (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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1050A TYR* 3.4 30.5 + - + +
1051A GLY* 3.6 26.0 - - - -
1053A ASP* 4.0 12.7 - - - +
1055A ILE* 2.7 57.8 + - - +
1056A ASP 4.3 0.4 - - - -
1057A ILE* 3.3 24.0 - - - +
1060A GLU* 4.9 2.5 - - - +
1578A SER* 2.8 19.1 + - - -
1579A PHE* 1.3 77.0 - - - +
1581A HIS* 1.3 60.0 + - - +
1583A ASP* 3.2 9.8 + - - +
1584A LEU* 2.9 34.3 + - - +
204E THR* 3.6 36.9 + - + -
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Residues in contact with HIS1581 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
660A PRO 3.3 12.9 + - - -
661A THR 4.3 2.9 + - - -
1050A TYR* 3.3 24.4 + + - -
1057A ILE* 3.4 30.6 - - + +
1185A VAL 5.1 0.4 - - - -
1188A ILE* 3.4 16.2 - - + +
1189A ALA* 3.5 28.7 - - + +
1192A SER* 3.2 35.8 + - - -
1578A SER* 3.3 21.5 + - - +
1579A PHE 3.3 0.2 - - - -
1580A ARG* 1.3 77.5 - - - +
1582A LEU* 1.3 60.8 + - + +
1584A LEU* 3.0 17.6 + - - +
1585A ILE* 3.0 22.1 + - - +
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Residues in contact with LEU1582 (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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1192A SER* 5.8 0.9 - - - -
1193A VAL* 4.3 17.3 - - + -
1563A VAL* 4.2 8.6 - - + +
1566A ILE* 3.6 34.7 - - + +
1567A ASN* 6.0 2.2 - - + -
1570A PHE* 3.9 19.3 - - + -
1577A VAL* 3.7 32.5 - - + -
1578A SER 3.2 20.2 - - - +
1579A PHE* 3.3 12.0 + - + +
1581A HIS* 1.3 81.3 - - + +
1583A ASP* 1.3 57.9 + - - +
1585A ILE* 3.9 12.3 - - + +
1586A ALA* 2.9 29.3 + - - +
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Residues in contact with ASP1583 (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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1047A GLN* 5.1 9.1 + - + +
1051A GLY* 5.0 9.4 - - - -
1559A ARG* 3.5 23.4 + - - +
1563A VAL* 3.4 21.7 - - - +
1579A PHE* 2.9 26.8 + - - +
1580A ARG* 3.4 14.6 - - - +
1581A HIS 3.1 0.2 - - - -
1582A LEU* 1.3 75.5 - - - +
1584A LEU* 1.3 62.3 + - + +
1586A ALA* 3.8 3.5 - - - +
1587A ASP* 3.0 32.7 + - - +
202E SER* 4.5 10.7 + - - -
204E THR* 5.2 0.9 - - - +
208E TYR* 5.1 4.1 + - - -
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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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1027A LEU* 5.4 5.2 - - + -
1030A VAL* 5.0 15.7 - - + -
1038A ILE* 3.7 37.7 - - + -
1046A VAL* 4.4 13.2 - - + +
1047A GLN* 5.9 2.9 - - + -
1050A TYR* 3.8 25.6 - - + -
1051A GLY 5.0 5.6 - - - +
1185A VAL* 4.7 11.0 - - + +
1186A GLY* 5.7 1.6 - - - -
1189A ALA* 4.1 18.4 - - + -
1580A ARG 2.9 22.9 + - - +
1581A HIS 3.0 8.9 + - - +
1583A ASP* 1.3 78.8 - - + +
1585A ILE* 1.3 62.8 + - + +
1587A ASP* 4.3 0.2 - - - -
1588A MET* 3.1 27.5 + - + +
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Residues in contact with ILE1585 (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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1023A LEU* 5.3 6.5 - - + -
1027A LEU* 4.8 13.2 - - + -
1189A ALA* 3.7 35.4 - - + +
1190A SER* 4.3 2.7 - - - +
1193A VAL* 4.7 21.1 - - + -
1226A VAL* 5.6 9.2 - - + -
1562A ILE* 6.3 0.7 - - + -
1566A ILE* 6.5 0.7 - - + -
1581A HIS 3.0 29.2 + - - +
1582A LEU* 4.0 13.5 - - + +
1584A LEU* 1.3 76.9 - - - +
1586A ALA* 1.3 59.3 + - - +
1588A MET* 3.7 3.7 - - - -
1589A MET* 2.8 35.3 + - + +
1598A PHE* 3.8 23.2 - - + -
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Residues in contact with ALA1586 (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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1559A ARG* 3.6 28.8 - - + +
1562A ILE* 3.7 24.0 - - + +
1563A VAL* 4.7 5.4 - - + -
1582A LEU 2.9 19.8 + - - +
1583A ASP* 3.8 4.9 - - - +
1584A LEU 3.3 0.2 - - - -
1585A ILE* 1.3 79.1 - - - +
1587A ASP* 1.3 63.2 + - - +
1589A MET* 3.1 5.4 + - - +
1590A THR* 3.0 27.0 + - - -
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Residues in contact with ASP1587 (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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1046A VAL* 2.9 34.1 - - + +
1047A GLN* 2.4 36.3 + - + +
1559A ARG* 4.3 9.6 - - + +
1583A ASP 3.0 17.2 + - - +
1586A ALA* 1.3 75.2 - - - +
1588A MET* 1.3 58.2 + - - +
1590A THR* 3.2 3.8 - - - +
1591A ARG* 2.9 39.3 + - - +
176E PRO* 4.9 2.3 - - - +
212E ARG* 3.6 22.3 + - - -
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Residues in contact with MET1588 (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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1026A GLN 3.3 26.9 - - - +
1027A LEU* 3.5 21.3 - - + -
1030A VAL* 4.1 15.5 - - + -
1040A ASP* 4.5 5.8 - - - +
1046A VAL* 3.8 9.9 - - + +
1584A LEU* 3.1 21.6 + - + +
1585A ILE* 3.9 3.4 - - - +
1587A ASP* 1.3 77.0 - - - +
1589A MET* 1.3 57.0 + - - +
1591A ARG* 3.2 50.1 - - - +
1596A LEU* 3.2 22.9 - - - +
1598A PHE* 4.2 6.5 - - + -
1603A MET* 3.5 27.3 - - + +
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Residues in contact with MET1589 (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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1225A ILE* 3.5 24.0 - - + +
1226A VAL* 4.4 5.8 - - - +
1230A SER* 5.0 0.4 - - - +
1546A VAL* 5.7 2.2 - - + -
1562A ILE* 5.5 9.9 - - + -
1585A ILE* 2.8 21.4 + - + +
1586A ALA* 3.1 7.1 + - - +
1588A MET* 1.3 78.2 - - - +
1590A THR* 1.3 68.0 + - - +
1591A ARG 3.7 0.7 - - - -
1595A TYR* 3.4 36.8 - - + +
1596A LEU* 3.1 49.8 + - - +
1598A PHE* 3.5 29.1 - - + -
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Residues in contact with THR1590 (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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1550A LEU* 5.1 2.2 - - + -
1555A VAL* 3.6 40.4 - - + +
1558A ALA* 5.5 5.5 - - + +
1559A ARG* 5.4 7.8 - - - +
1562A ILE* 5.2 6.2 - - - +
1586A ALA 3.0 14.3 + - - -
1587A ASP* 3.2 8.6 - - - +
1589A MET* 1.3 92.3 + - - +
1591A ARG* 1.3 58.9 + - - +
1592A GLN 3.6 2.0 - - - +
1593A GLY 4.6 1.1 + - - -
1594A THR 3.5 27.1 - - - +
1595A TYR* 4.6 4.0 - - + +
1596A LEU* 4.9 1.8 - - - +
177E ARG 5.7 0.2 - - - +
212E ARG* 4.8 5.0 + - - -
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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