Contacts of the helix formed by residues 1506 - 1516 (chain A) in PDB entry 3UVD
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 ASP1506 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1485A PHE 3.2 11.7 - - - +
1486A ILE 3.1 17.5 - - - +
1487A GLN* 3.6 3.6 - - - +
1488A LEU* 2.7 33.3 + - + +
1505A VAL* 1.3 76.2 - - - +
1507A PHE* 1.3 60.5 + - - +
1508A LYS* 3.4 6.4 + - - +
1509A LYS* 2.9 56.2 + - - +
1510A ILE* 3.1 28.2 + - - +
1532A LEU* 3.6 7.2 - - - -
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Residues in contact with PHE1507 (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 VAL* 4.0 15.9 - - + -
1469A VAL* 3.8 28.9 - - + -
1470A ILE* 3.9 21.5 - - + -
1482A SER* 4.1 15.7 - - - -
1485A PHE* 3.0 45.1 + - + -
1486A ILE* 3.9 24.9 - - + -
1506A ASP* 1.3 72.5 - - - +
1508A LYS* 1.3 60.6 + - - +
1510A ILE* 3.8 17.3 - - + +
1511A LYS* 2.9 35.5 + - - +
1529A VAL* 4.6 14.6 - - + -
1532A LEU* 3.9 18.2 - - + -
1533A CYS* 6.2 0.2 - - - -
1553A LEU* 4.5 8.7 - - + -
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Residues in contact with LYS1508 (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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1486A ILE* 3.1 25.0 + - + +
1487A GLN* 3.8 43.7 + - + +
1506A ASP* 3.3 9.6 - - - +
1507A PHE* 1.3 76.3 - - - +
1509A LYS* 1.3 58.6 + - + +
1511A LYS* 3.5 7.2 + - - +
1512A GLU* 3.0 25.9 + - - +
1515A ARG* 4.2 4.3 + - - -
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Residues in contact with LYS1509 (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* 4.1 19.4 - - - +
1498A TYR* 5.2 4.4 + - - -
1504A PRO* 4.3 19.7 + - - +
1505A VAL* 4.4 2.6 - - + +
1506A ASP* 2.9 46.8 + - - +
1508A LYS* 1.3 74.2 - - + +
1510A ILE* 1.3 61.9 + - - +
1512A GLU* 3.2 15.4 + - - +
1513A ARG* 2.8 57.3 + - - +
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Residues in contact with ILE1510 (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 VAL* 4.0 18.4 - - + -
1505A VAL* 3.5 15.5 - - + -
1506A ASP 3.1 14.4 + - - +
1507A PHE* 3.3 11.6 + - + +
1509A LYS* 1.3 74.6 - - - +
1511A LYS* 1.3 63.5 + - - +
1513A ARG* 3.0 2.9 + - - -
1514A ILE* 2.9 24.1 + - + +
1519A TYR* 3.4 19.8 - - - +
1525A LEU* 3.5 30.3 - - + -
1528A ASP* 4.0 2.5 - - + +
1529A VAL* 3.9 28.5 - - + +
1532A LEU* 3.5 31.2 - - + -
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Residues in contact with LYS1511 (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 VAL* 4.2 13.5 - - + -
1467A ASP* 3.7 18.9 + - - -
1470A ILE* 3.1 37.7 - - - +
1471A LYS* 6.2 1.0 - - - +
1486A ILE* 6.1 0.2 - - - +
1507A PHE* 2.9 18.6 + - - +
1508A LYS* 3.7 7.0 - - - +
1510A ILE* 1.3 76.0 - - - +
1512A GLU* 1.3 63.0 + - - +
1514A ILE* 3.2 14.4 + - + +
1515A ARG* 3.0 38.6 + - - +
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Residues in contact with GLU1512 (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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1508A LYS 3.0 15.3 + - - +
1509A LYS* 3.2 18.7 + - - +
1511A LYS* 1.3 75.8 - - - +
1513A ARG* 1.3 62.8 + - - +
1515A ARG* 3.2 25.0 + - - +
1516A ASN* 2.9 50.5 + - - +
1518A LYS* 2.7 27.0 + - - -
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Residues in contact with ARG1513 (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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1504A PRO 4.9 4.8 + - - -
1505A VAL* 4.4 17.6 - - - +
1509A LYS* 2.8 41.7 + - - +
1510A ILE 3.0 0.4 + - - -
1512A GLU* 1.3 77.9 + - - +
1514A ILE* 1.3 60.1 + - - +
1516A ASN 3.6 0.2 + - - -
1517A HIS 3.3 2.1 + - - -
1518A LYS* 2.9 63.1 + - + +
1519A TYR* 3.5 28.6 + - + -
1528A ASP* 2.7 41.0 + - - -
1531A LEU* 6.2 0.2 - - - +
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Residues in contact with ILE1514 (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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1454A ASN* 5.1 1.9 + - - -
1459A THR* 3.8 24.9 + - + +
1462A MET* 3.7 42.0 - - + +
1463A LYS* 3.9 17.5 - - + +
1466A VAL* 3.7 32.5 - - + -
1510A ILE* 2.9 20.4 + - + +
1511A LYS* 3.2 15.9 + - + +
1513A ARG* 1.3 74.0 - - - +
1515A ARG* 1.3 65.9 + - + +
1517A HIS* 3.0 19.6 + - - +
1519A TYR* 3.8 19.5 - - + -
1525A LEU* 4.5 1.3 - - + -
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Residues in contact with ARG1515 (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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1459A THR* 5.5 3.6 - - + -
1463A LYS* 5.2 13.2 - - + +
1508A LYS 4.2 5.5 + - - -
1511A LYS* 3.0 23.1 + - - +
1512A GLU* 3.2 42.4 + - - +
1514A ILE* 1.3 77.8 - - + +
1516A ASN* 1.3 70.2 + - - +
1517A HIS* 3.3 18.9 + - - -
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Residues in contact with ASN1516 (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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1451A LEU* 3.7 16.8 + - - +
1512A GLU* 2.9 39.8 + - - +
1514A ILE 3.2 0.2 - - - -
1515A ARG* 1.3 85.8 + - - +
1517A HIS* 1.3 76.7 + - - +
1518A LYS* 3.4 28.7 + - + +
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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