Contacts of the helix formed by residues 1514 - 1521 (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 GLU1514 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1462A ALA* 5.3 13.7 - - + -
1463A PHE* 5.9 0.7 - - - +
1466A ARG* 4.8 15.3 - - + -
1512A ALA 3.0 1.0 - - - -
1513A LEU* 1.3 75.5 - - - +
1515A ASN* 1.3 54.0 + - - +
1516A HIS* 2.8 7.6 - - - +
1517A LEU* 2.4 41.9 + - + +
1518A HIS 3.3 0.9 + - - -
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Residues in contact with ASN1515 (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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1498A LEU* 4.2 21.5 - - + -
1512A ALA* 2.5 27.7 + - + +
1514A GLU* 1.3 70.7 - - - +
1516A HIS* 1.3 49.3 - - - +
1517A LEU 3.2 0.2 - - - -
1518A HIS* 2.8 19.1 + - + +
1519A VAL* 2.2 37.0 + - - +
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Residues in contact with HIS1516 (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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1513A LEU 3.5 14.9 + - - +
1514A GLU* 4.1 1.8 - - - +
1515A ASN* 1.3 74.1 - - - +
1517A LEU* 1.3 53.9 + - - +
1519A VAL* 2.8 12.4 + - - +
1520A ILE* 2.2 39.6 + - - +
1555A LEU* 5.0 15.5 - - + -
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Residues in contact with LEU1517 (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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1466A ARG* 5.1 10.1 - - + -
1469A ILE* 4.7 20.6 - - + -
1514A GLU* 2.4 22.9 + - + +
1516A HIS* 1.3 72.8 - - - +
1518A HIS* 1.3 51.9 + - - +
1520A ILE* 2.3 34.5 + - + +
1521A VAL* 2.5 17.7 + - - +
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Residues in contact with HIS1518 (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* 5.4 7.6 - - + +
1494A CYS* 5.5 5.6 - - + -
1495A CYS* 5.0 22.2 - - + +
1498A LEU* 5.6 0.9 - - + -
1514A GLU 3.3 2.2 + - - -
1515A ASN* 2.8 26.8 + - + +
1517A LEU* 1.3 76.5 - - - +
1519A VAL* 1.3 63.8 + - - +
1521A VAL* 2.9 20.6 - - - +
1522A GLY 4.0 0.2 + - - -
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Residues in contact with VAL1519 (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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1515A ASN 2.2 26.5 + - - +
1516A HIS* 2.8 17.9 + - - +
1518A HIS* 1.3 65.6 - - - +
1520A ILE* 1.3 46.7 - - - -
1521A VAL 2.7 4.0 - - - -
1522A GLY* 2.1 38.8 + - - -
1555A LEU* 5.6 6.1 - - + -
1558A THR* 4.9 17.7 - - - -
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Residues in contact with ILE1520 (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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1516A HIS 2.2 26.8 + - - +
1517A LEU* 2.3 21.2 + - + +
1519A VAL* 1.3 66.1 - - - +
1521A VAL* 1.3 48.9 + - - -
1522A GLY 5.2 0.2 - - - -
1523A THR* 2.5 38.5 + - - -
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Residues in contact with VAL1521 (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* 4.7 16.6 - - + -
1517A LEU 2.5 11.2 + - - +
1518A HIS* 2.9 21.3 - - - +
1519A VAL 2.5 3.8 + - - -
1520A ILE* 1.3 65.0 - - - +
1522A GLY* 1.3 56.3 + - - -
1523A THR* 2.8 11.8 + - - -
1524A LEU* 3.8 12.0 + - - +
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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