Contacts of the helix formed by residues 1483 - 1501 (chain A) in PDB entry 5NP1
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 ILE1483 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1479A ARG 2.8 6.3 - - - +
1480A PRO 3.0 4.0 - - - -
1482A CYS* 1.3 80.7 - - - +
1484A MET* 1.3 59.2 + - - +
1485A ASP* 3.3 8.5 - - + +
1486A VAL* 3.1 34.3 - - + +
1487A SER* 2.8 25.1 + - - -
1764A LEU 4.4 2.0 - - - +
1767A PHE* 3.4 21.1 - - + -
1768A ARG* 5.2 0.9 - - - -
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Residues in contact with MET1484 (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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1479A ARG* 2.4 15.3 + - + +
1480A PRO* 2.9 30.3 - - + +
1483A ILE* 1.3 73.9 - - - +
1485A ASP* 1.3 52.0 + - - +
1487A SER* 2.6 10.2 + - - -
1488A LEU* 2.0 48.2 + - + +
1527A LEU* 5.8 7.6 - - + -
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Residues in contact with ASP1485 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1483A ILE* 2.9 9.5 - - + +
1484A MET* 1.3 79.5 - - - +
1486A VAL* 1.3 67.5 + - - +
1488A LEU* 4.1 3.5 - - - +
1489A ARG* 3.2 21.1 + - - +
1533A GLU* 6.3 2.7 - - - -
1763A TYR 5.0 0.7 - - - +
1764A LEU* 3.6 36.1 - - + +
1767A PHE* 5.2 1.1 - - + -
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Residues in contact with VAL1486 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1437A ARG 5.9 1.8 - - - +
1440A LYS* 5.9 8.1 - - + -
1483A ILE* 3.1 17.8 - - + +
1485A ASP* 1.3 80.5 - - - +
1487A SER* 1.3 66.1 + - - +
1489A ARG* 4.1 1.6 - - - +
1490A SER* 2.9 22.6 + - - -
1764A LEU* 4.7 2.7 + - - +
1768A ARG* 4.8 15.3 - - + -
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Residues in contact with SER1487 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1440A LYS* 6.3 2.7 - - - -
1472A LEU* 6.3 2.5 - - - -
1479A ARG* 4.3 4.9 - - - -
1483A ILE 2.8 20.3 + - - -
1484A MET* 2.6 16.8 + - - -
1486A VAL* 1.3 74.6 - - - +
1488A LEU* 1.3 58.2 + - - -
1490A SER* 2.9 8.8 - - - -
1491A PHE* 2.7 27.8 + - - +
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Residues in contact with LEU1488 (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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1484A MET* 2.0 37.9 + - + +
1485A ASP* 4.1 3.6 - - - +
1487A SER* 1.3 68.7 - - - +
1489A ARG* 1.3 51.6 + - - +
1491A PHE* 2.6 13.4 + - - +
1492A SER* 2.3 36.1 + - - -
1530A GLU* 6.4 2.2 - - + -
1533A GLU* 5.1 16.4 - - + -
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Residues in contact with ARG1489 (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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1485A ASP 3.2 13.2 + - - +
1486A VAL* 4.3 1.6 - - - +
1488A LEU* 1.3 77.2 - - - +
1490A SER* 1.3 52.7 + - - +
1492A SER* 3.0 13.8 - - - -
1493A LEU* 2.2 38.0 + - - +
1728A LYS* 5.3 14.1 - - + +
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Residues in contact with SER1490 (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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1440A LYS* 6.0 6.1 - - - -
1486A VAL 2.9 15.9 + - - -
1487A SER* 2.9 17.9 - - - -
1488A LEU 2.9 0.2 + - - -
1489A ARG* 1.3 73.9 - - - +
1491A PHE* 1.3 49.9 - - - -
1493A LEU* 2.8 9.9 + - - +
1494A CYS* 2.2 40.2 + - - +
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Residues in contact with PHE1491 (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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1487A SER 2.7 11.7 + - - +
1488A LEU* 2.6 17.6 + - - +
1490A SER* 1.3 69.9 - - - +
1492A SER* 1.3 48.3 + - - -
1494A CYS* 2.7 12.1 + - + +
1495A CYS* 2.1 41.3 + - - +
1518A HIS* 5.4 6.9 - - + +
1521A VAL* 4.7 19.7 - - + -
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Residues in contact with SER1492 (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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1488A LEU 2.3 22.6 + - - -
1489A ARG* 3.0 25.8 - - - -
1491A PHE* 1.3 66.8 - - - +
1493A LEU* 1.3 48.3 - - - +
1495A CYS* 2.9 10.4 - - - +
1496A ASP* 2.0 40.3 + - - +
1537A GLN* 4.8 18.8 - - - -
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Residues in contact with LEU1493 (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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1489A ARG 2.2 27.7 + - - +
1490A SER* 2.8 12.2 + - - +
1492A SER* 1.3 66.6 - - - +
1494A CYS* 1.3 51.6 + - - +
1496A ASP* 2.5 12.9 + - + +
1497A LEU* 2.1 40.8 + - - +
1729A VAL 5.2 9.4 - - - +
1730A ARG* 6.1 2.2 - - - -
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Residues in contact with CYS1494 (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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1465A LEU* 5.8 8.3 - - + -
1490A SER 2.2 28.6 + - - +
1491A PHE* 2.7 19.6 + - - +
1493A LEU* 1.3 64.7 - - - +
1495A CYS* 1.3 49.9 + - - +
1497A LEU* 3.1 8.6 - - - +
1498A LEU* 2.5 35.5 + - - +
1518A HIS* 5.5 7.2 - - + -
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Residues in contact with CYS1495 (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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1491A PHE 2.1 27.6 + - - +
1492A SER* 3.0 15.9 - - - +
1494A CYS* 1.3 66.4 - - - +
1496A ASP* 1.3 46.7 + - - -
1498A LEU* 2.5 15.0 + - - -
1499A SER* 2.0 43.6 + - - -
1518A HIS* 5.0 12.5 - - + +
1541A LEU* 6.6 0.2 - - - -
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Residues in contact with ASP1496 (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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1492A SER 2.0 29.0 + - - +
1493A LEU* 2.5 19.3 + - + +
1495A CYS* 1.3 65.0 - - - +
1497A LEU* 1.3 49.5 + - - +
1499A SER* 3.1 11.1 - - - -
1500A GLN* 2.2 39.1 + - - +
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Residues in contact with LEU1497 (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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1493A LEU 2.1 25.9 + - - +
1494A CYS* 3.1 12.3 - - - +
1495A CYS 2.8 0.2 + - - -
1496A ASP* 1.3 64.6 - - - +
1498A LEU* 1.3 53.8 + - - +
1500A GLN* 2.8 9.3 + - - +
1501A VAL* 2.3 40.5 + - - +
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Residues in contact with LEU1498 (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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1494A CYS 2.5 14.6 + - - +
1495A CYS* 2.5 17.8 + - - +
1497A LEU* 1.3 71.5 - - - +
1499A SER* 1.3 59.9 + - - +
1501A VAL* 3.0 29.7 - - - +
1512A ALA* 5.1 12.3 - - + +
1515A ASN* 4.2 25.1 - - + -
1518A HIS* 5.6 0.9 - - + -
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Residues in contact with SER1499 (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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1495A CYS* 2.0 31.7 + - - -
1496A ASP* 3.1 14.8 - - - -
1498A LEU* 1.3 63.6 - - - +
1500A GLN* 1.3 60.5 + - - +
1501A VAL 2.7 17.8 - - - +
1540A ASP* 5.7 9.9 - - - -
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Residues in contact with GLN1500 (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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1496A ASP 2.2 31.9 + - - +
1497A LEU* 3.2 8.3 - - - +
1499A SER* 1.3 67.1 - - - +
1501A VAL* 1.3 63.5 + - - +
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Residues in contact with VAL1501 (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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1397A HIS* 5.4 11.0 - - + -
1497A LEU 2.3 29.8 + - - +
1498A LEU* 3.0 23.8 - - - +
1499A SER 2.7 16.7 - - - +
1500A GLN* 1.3 72.1 - - - +
1512A ALA* 5.0 15.7 - - + +
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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