Contacts of the helix formed by residues 1531 - 1543 (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 GLN1531 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1529A TYR 3.5 10.3 - - - +
1530A GLU* 1.3 76.6 - - - +
1532A VAL* 1.3 57.0 + - + +
1533A GLU* 2.7 19.2 - - + +
1534A VAL* 2.0 39.3 + - - +
1535A GLN* 3.0 3.3 + - - -
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Residues in contact with VAL1532 (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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1531A GLN* 1.3 70.5 - - + +
1533A GLU* 1.3 67.4 + - - +
1535A GLN* 3.3 23.9 + - + +
1536A LYS* 4.3 3.1 + - - +
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Residues in contact with GLU1533 (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* 6.3 2.7 - - - -
1488A LEU* 5.1 15.7 - - + -
1530A GLU* 4.7 4.7 - - + -
1531A GLN* 2.7 22.3 - - + +
1532A VAL* 1.3 81.0 - - - +
1534A VAL* 1.3 60.5 + - + +
1535A GLN 2.9 3.8 + - - -
1536A LYS 4.4 0.2 + - - -
1537A GLN* 3.7 12.9 + - - +
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Residues in contact with VAL1534 (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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1530A GLU* 4.0 15.5 - - + -
1531A GLN 2.0 37.0 + - - +
1533A GLU* 1.3 71.1 - - - +
1535A GLN* 1.3 52.4 + - - +
1537A GLN* 3.3 9.1 - - + +
1538A VAL* 2.5 37.7 + - + +
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Residues in contact with GLN1535 (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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1531A GLN 3.0 1.7 + - - +
1532A VAL* 3.5 27.4 - - + +
1533A GLU 2.9 5.1 + - - -
1534A VAL* 1.3 73.3 - - - +
1536A LYS* 1.3 54.8 + - - +
1537A GLN 2.9 0.2 - - - -
1538A VAL* 2.7 10.5 + - - +
1539A LEU* 2.4 35.2 + - - +
1572A LYS* 6.4 0.7 - - - -
1575A ARG* 4.6 21.1 - - + -
1622A GLU* 4.9 10.3 - - + -
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Residues in contact with LYS1536 (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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1532A VAL 4.3 4.1 + - - +
1533A GLU 5.6 0.2 - - - +
1535A GLN* 1.3 78.4 - - - +
1537A GLN* 1.3 52.8 + - - +
1539A LEU* 3.0 10.5 - - - +
1540A ASP* 2.3 39.6 + - - +
1622A GLU* 3.2 28.9 + - - +
1623A LEU* 3.5 16.3 - - + +
1624A HIS 4.8 1.1 - - - +
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Residues in contact with GLN1537 (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* 4.8 19.1 - - - -
1533A GLU 3.7 9.7 + - - +
1534A VAL* 3.3 19.3 - - - +
1535A GLN 3.9 0.2 - - - +
1536A LYS* 1.3 75.2 - - - +
1538A VAL* 1.3 54.6 + - - +
1540A ASP* 3.0 6.0 + - - +
1541A LEU* 2.3 39.9 + - - +
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Residues in contact with VAL1538 (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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1534A VAL* 2.5 24.9 + - + +
1535A GLN* 2.7 7.4 + - - +
1537A GLN* 1.3 70.9 - - - +
1539A LEU* 1.3 57.5 + - - +
1541A LEU* 2.6 29.0 + - - +
1542A LEU* 2.9 11.8 + - - +
1562A LEU* 6.5 0.9 - - + -
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Residues in contact with LEU1539 (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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1535A GLN 2.4 22.4 + - - +
1536A LYS* 3.0 21.3 - - - +
1538A VAL* 1.3 68.7 - - - +
1540A ASP* 1.3 66.9 + - - +
1542A LEU* 3.3 15.7 + - - +
1543A LYS* 4.0 2.6 + - - +
1575A ARG 6.0 1.8 - - - +
1578A GLN* 6.3 4.0 - - + -
1622A GLU* 6.3 0.7 - - + -
1623A LEU* 4.0 17.7 - - + -
1627A GLN* 6.2 3.4 - - + -
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Residues in contact with ASP1540 (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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1499A SER* 5.7 9.6 - - - -
1536A LYS 2.3 30.5 + - - +
1537A GLN* 3.3 6.7 - - - +
1539A LEU* 1.3 66.7 - - - +
1541A LEU* 1.3 52.6 + - - +
1542A LEU 2.6 0.5 + - - -
1543A LYS* 2.4 41.9 + - - +
1623A LEU* 5.4 1.2 - - - +
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Residues in contact with LEU1541 (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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1537A GLN 2.3 32.4 + - - +
1538A VAL* 2.6 19.1 + - - +
1540A ASP* 1.3 65.9 - - - +
1542A LEU* 1.3 62.6 + - - +
1543A LYS 3.2 0.5 + - - -
1545A LEU* 3.6 12.0 - - - +
1559A ILE* 5.9 7.9 - - + -
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Residues in contact with LEU1542 (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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1538A VAL 2.9 8.3 + - - +
1539A LEU* 3.3 13.7 - - - +
1540A ASP 2.6 3.2 + - - -
1541A LEU* 1.3 74.3 - - - +
1543A LYS* 1.3 60.6 + - - +
1544A TYR 3.3 0.4 - - - -
1545A LEU* 2.3 39.0 + - - +
1546A VAL 4.4 0.7 + - - -
1559A ILE* 6.1 4.9 - - - +
1582A LYS* 5.6 10.1 - - + -
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Residues in contact with LYS1543 (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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1539A LEU 4.5 3.1 - - - +
1540A ASP* 2.4 30.1 + - - +
1541A LEU 3.1 0.8 + - - -
1542A LEU* 1.3 78.3 - - - +
1544A TYR* 1.3 61.1 + - - +
1627A GLN* 6.5 2.0 - - - -
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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