Contacts of the helix formed by residues 1440 - 1451 (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 SER1440 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1026B ARG* 4.6 4.7 - - - +
1439B LYS* 1.3 75.7 - - - +
1441B THR* 1.3 60.2 + - - +
1442B GLU* 3.7 7.6 + - - +
1443B GLU* 2.9 37.5 + - - +
1444B ALA* 2.8 28.1 + - - +
1466B VAL* 4.1 4.3 - - - -
1467B PHE 4.9 0.4 - - - -
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Residues in contact with THR1441 (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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1440B SER* 1.3 73.6 - - - +
1442B GLU* 1.3 63.1 + - - +
1444B ALA* 3.2 2.6 + - - +
1445B ARG* 2.8 51.7 + - - +
1462B LEU* 3.6 19.1 - - + +
1466B VAL* 3.6 24.7 - - + +
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Residues in contact with GLU1442 (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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1440B SER* 3.2 7.0 + - - +
1441B THR* 1.3 79.7 - - - +
1443B GLU* 1.3 66.4 + - + +
1445B ARG* 3.3 39.1 + - - +
1446B LYS* 3.1 24.4 + - - +
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Residues in contact with GLU1443 (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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1026B ARG* 2.9 39.6 + - - -
1437B LYS* 4.6 5.1 + - - -
1438B GLY 4.3 1.2 - - - +
1439B LYS* 3.3 17.2 - - + -
1440B SER* 2.9 39.4 + - - +
1442B GLU* 1.3 78.8 - - + +
1444B ALA* 1.3 64.0 + - - +
1446B LYS* 3.4 6.4 + - - +
1447B GLU* 3.2 27.1 + - - +
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Residues in contact with ALA1444 (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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1439B LYS* 4.0 20.1 - - + +
1440B SER 2.8 16.6 + - - +
1441B THR 3.5 4.0 - - - +
1443B GLU* 1.3 77.1 - - - +
1445B ARG* 1.3 64.2 + - - +
1447B GLU* 3.1 8.2 + - - +
1448B LEU* 3.0 24.9 + - - +
1462B LEU* 3.7 15.3 - - + -
1465B LYS* 4.1 22.1 - - + +
1466B VAL* 4.2 6.7 - - + -
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Residues in contact with ARG1445 (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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1441B THR* 2.8 36.0 + - - +
1442B GLU* 3.3 39.3 + - - +
1444B ALA* 1.3 73.6 - - - +
1446B LYS* 1.3 62.9 + - - +
1448B LEU* 3.1 6.9 + - - +
1449B GLN* 2.9 50.2 + - + +
1458B LEU* 4.4 14.8 - - + +
1462B LEU* 3.6 26.3 - - + +
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Residues in contact with LYS1446 (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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1442B GLU 3.1 15.0 + - - +
1443B GLU* 3.7 7.6 - - - +
1444B ALA 3.3 0.2 - - - -
1445B ARG* 1.3 79.8 - - - +
1447B GLU* 1.3 58.8 + - + +
1449B GLN* 3.4 16.0 + - - +
1450B ALA* 3.0 30.0 + - + +
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Residues in contact with GLU1447 (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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519A GLN* 3.9 10.9 + - - +
1439B LYS* 2.7 43.1 + - - +
1443B GLU* 3.2 14.0 + - - +
1444B ALA* 3.1 9.8 + - - +
1446B LYS* 1.3 79.4 - - + +
1448B LEU* 1.3 59.1 + - + +
1450B ALA* 3.3 6.5 + - - +
1451B ALA* 2.9 29.2 + - - +
1465B LYS* 5.9 3.8 - - + +
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Residues in contact with LEU1448 (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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1444B ALA 3.0 16.8 + - - +
1445B ARG 3.6 6.1 - - - +
1447B GLU* 1.3 76.8 - - + +
1449B GLN* 1.3 61.4 + - - +
1451B ALA* 3.2 8.7 + - + -
1453B LYS* 3.2 51.9 + - + +
1458B LEU* 3.7 39.9 - - + +
1461B LEU* 4.5 5.2 - - + -
1462B LEU* 3.7 27.4 - - + +
1465B LYS* 3.4 38.1 - - + -
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Residues in contact with GLN1449 (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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1445B ARG* 2.9 39.5 + - - +
1446B LYS* 3.7 19.7 + - - +
1448B LEU* 1.3 77.1 - - - +
1450B ALA* 1.3 62.5 + - - +
1452B GLY* 3.1 14.4 + - - -
1453B LYS 4.4 4.5 + - - +
1458B LEU* 3.5 19.1 - - + +
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Residues in contact with ALA1450 (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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1446B LYS* 3.0 19.5 + - + +
1447B GLU* 3.7 7.0 - - - +
1449B GLN* 1.3 76.2 - - - +
1451B ALA* 1.3 58.5 + - - +
1452B GLY* 3.1 4.5 + - - -
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Residues in contact with ALA1451 (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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1447B GLU 2.9 17.2 + - - +
1448B LEU* 3.6 12.1 - - + +
1449B GLN 3.2 0.8 - - - -
1450B ALA* 1.3 76.1 - - - +
1452B GLY* 1.3 61.5 + - - +
1453B LYS* 3.4 14.5 + - + +
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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