Contacts of the helix formed by residues 1514 - 1529 (chain B) in PDB entry 1XTB
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 VAL1514 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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387A GLN 3.9 22.0 - - - +
388A HIS* 5.5 0.9 - - - -
391A TYR* 6.1 1.3 - - + -
392A GLN* 4.6 12.3 - - + +
395A HIS* 5.6 1.1 - - - -
431A GLN* 5.3 2.0 + - - +
1357B GLU* 4.3 15.9 - - - +
1511B GLN* 3.4 25.8 - - + +
1513B GLY* 1.3 79.6 - - - +
1515B GLU* 1.3 73.2 + - + +
1516B LEU 3.6 0.6 + - - -
1517B GLY* 3.7 4.2 + - - -
1518B LYS* 3.4 47.4 + - + +
2001B S6P 6.4 0.7 - - - -
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Residues in contact with GLU1515 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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439A LYS* 5.1 5.3 + - - +
465A LYS* 2.9 33.6 + - - +
467A PHE* 4.8 3.4 - - + -
1512B TRP* 3.2 42.1 + - + +
1514B VAL* 1.3 83.3 - - + +
1516B LEU* 1.3 67.1 + - - +
1518B LYS* 3.2 10.2 + - + +
1519B GLN* 3.1 31.0 + - - +
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Residues in contact with LEU1516 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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434A ALA* 3.7 25.4 - - + +
437A LYS* 5.7 1.6 - - + -
438A GLY* 3.5 42.6 - - - +
439A LYS* 4.2 12.3 - - + +
467A PHE* 3.8 40.8 - - + -
1514B VAL 3.6 0.8 - - - -
1515B GLU* 1.3 76.1 - - - +
1517B GLY* 1.3 63.6 + - - +
1519B GLN* 3.0 36.2 + - - +
1520B LEU* 3.1 34.5 + - + +
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Residues in contact with GLY1517 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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395A HIS* 5.3 3.3 + - - -
427A ASN* 5.5 0.9 - - - -
430A ALA* 3.7 9.2 - - - +
431A GLN* 3.5 29.2 + - - -
434A ALA* 4.2 14.6 - - - +
1513B GLY 5.3 1.8 + - - -
1514B VAL 3.7 5.3 + - - -
1515B GLU 3.3 0.4 - - - -
1516B LEU* 1.3 78.7 - - - +
1518B LYS* 1.3 62.1 + - - +
1520B LEU* 3.5 0.4 + - - -
1521B ALA* 3.1 24.4 + - - +
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Residues in contact with LYS1518 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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387A GLN* 6.0 1.6 - - - +
388A HIS* 4.6 17.9 - - - -
427A ASN* 5.5 4.3 - - - +
431A GLN* 4.6 1.3 - - - +
1214B THR* 5.4 9.0 + - - +
1514B VAL* 3.4 37.5 + - + +
1515B GLU* 3.2 11.3 + - + +
1517B GLY* 1.3 76.4 - - - +
1519B GLN* 1.3 62.4 + - - +
1521B ALA* 3.3 7.5 + - - +
1522B LYS* 3.2 27.6 + - + +
2001B S6P 4.3 13.7 + - - -
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Residues in contact with GLN1519 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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439A LYS* 3.0 25.5 + - - +
447A GLU* 4.0 16.4 + - - -
1515B GLU* 3.1 13.9 + - - +
1516B LEU* 3.0 38.9 + - + +
1518B LYS* 1.3 77.7 - - - +
1520B LEU* 1.3 66.5 + - + +
1522B LYS* 3.3 18.2 + - - +
1523B LYS* 3.3 25.8 + - + +
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Residues in contact with LEU1520 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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430A ALA* 3.6 14.1 - - + +
433A GLU* 3.6 27.5 - - + +
434A ALA* 3.6 40.8 - - + +
437A LYS* 4.6 18.2 - - + +
1516B LEU* 3.1 34.0 + - + +
1517B GLY 4.0 0.2 - - - +
1519B GLN* 1.3 80.8 - - + +
1521B ALA* 1.3 61.1 + - - +
1523B LYS* 3.3 30.2 + - + +
1524B ILE* 3.3 27.4 + - - +
1537B HIS* 5.4 0.6 - - + -
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Residues in contact with ALA1521 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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426A ALA* 3.8 15.7 - - + +
427A ASN* 3.9 24.9 - - - +
430A ALA* 3.3 15.7 - - + +
1215B GLN* 5.7 2.9 - - - +
1517B GLY 3.1 17.7 + - - +
1518B LYS* 3.5 7.0 - - - +
1519B GLN 3.2 0.2 - - - -
1520B LEU* 1.3 75.8 - - - +
1522B LYS* 1.3 67.3 + - + +
1524B ILE* 4.6 0.7 - - - +
1525B GLU* 3.1 28.8 + - - +
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Residues in contact with LYS1522 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1215B GLN* 3.5 22.3 + - + +
1518B LYS* 3.2 17.3 + - + +
1519B GLN* 3.3 10.7 + - - +
1521B ALA* 1.3 78.0 - - + +
1523B LYS* 1.3 58.4 + - + +
1525B GLU* 3.2 31.1 + - - +
1526B PRO* 3.2 21.8 - - - +
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Residues in contact with LYS1523 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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437A LYS* 4.7 10.5 - - - +
1519B GLN* 3.3 21.4 + - - +
1520B LEU* 3.6 29.6 - - + +
1521B ALA 3.2 0.6 - - - -
1522B LYS* 1.3 78.9 - - + +
1524B ILE* 1.3 63.4 + - + +
1526B PRO* 3.4 13.7 - - - +
1527B GLU* 3.4 19.4 - - - +
1537B HIS* 5.0 11.7 - - + -
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Residues in contact with ILE1524 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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426A ALA* 4.1 9.4 - - + +
429A LEU* 3.8 31.9 - - + -
430A ALA* 3.7 25.8 - - + +
433A GLU* 3.6 21.5 - - - +
1520B LEU 3.3 13.7 + - - +
1521B ALA 3.4 3.5 + - - +
1523B LYS* 1.3 75.0 - - - +
1525B GLU* 1.3 68.5 + - - +
1527B GLU* 2.8 19.4 + - - +
1528B LEU* 3.2 20.2 + - + +
1537B HIS* 3.8 22.0 - - + +
1541B THR* 4.3 8.3 - - + -
1545B ILE* 4.2 8.1 - - + -
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Residues in contact with GLU1525 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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419A LEU* 5.4 2.6 - - - +
422A LYS* 3.7 38.7 - - + +
423A ILE* 4.1 18.2 - - + +
426A ALA* 4.0 15.7 - - + +
1215B GLN* 3.0 33.7 + - - +
1521B ALA* 3.1 20.7 + - - +
1522B LYS* 3.2 24.3 + - - +
1524B ILE* 1.3 76.3 - - - +
1526B PRO* 1.3 69.2 - - + +
1528B LEU* 3.4 10.3 + - - +
1529B ASP* 4.2 0.9 + - - +
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Residues in contact with PRO1526 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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422A LYS* 5.7 0.4 - - - +
1522B LYS 3.2 19.1 - - - +
1523B LYS* 3.4 11.9 - - - +
1525B GLU* 1.3 94.0 - - + +
1527B GLU* 1.3 63.3 + - + +
1528B LEU 3.2 0.7 + - - -
1529B ASP* 3.5 26.7 + - - +
1530B GLY 4.6 1.4 + - - -
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Residues in contact with GLU1527 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1523B LYS* 3.4 19.2 - - - +
1524B ILE* 2.8 18.0 + - + +
1526B PRO* 1.3 77.5 - - + +
1528B LEU* 1.3 59.8 + - - +
1529B ASP 3.3 0.2 - - - -
1530B GLY 4.2 1.5 + - - -
1534B VAL* 3.7 22.2 - - + +
1536B SER* 3.2 20.3 + - - -
1537B HIS* 2.8 30.3 + - - -
1545B ILE* 4.3 2.8 - - + +
1549B LYS* 2.9 26.7 + - - -
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Residues in contact with LEU1528 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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422A LYS* 3.4 41.1 - - + +
425A LEU* 4.1 11.4 - - + -
426A ALA* 4.0 19.7 - - + +
429A LEU* 4.0 21.1 - - + -
1524B ILE* 3.2 17.0 + - + +
1525B GLU 3.7 5.6 - - - +
1526B PRO 3.2 0.8 - - - -
1527B GLU* 1.3 78.3 - - - +
1529B ASP* 1.3 63.3 + - - +
1530B GLY 3.3 4.0 - - - +
1545B ILE* 4.1 21.3 - - + +
1548B ILE* 5.0 10.1 - - + -
1549B LYS* 3.6 2.8 - - - +
1552B ARG* 2.6 36.0 + - - +
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Residues in contact with ASP1529 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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422A LYS* 3.1 34.6 + - - +
1525B GLU 4.6 1.1 - - - -
1526B PRO* 3.6 20.7 - - - +
1527B GLU 3.3 0.2 - - - -
1528B LEU* 1.3 78.8 - - - +
1530B GLY* 1.3 65.9 + - - +
1552B ARG* 3.6 9.1 + - - +
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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