Contacts of the helix formed by residues 1469 - 1480 (chain C) in PDB entry 1TH1
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 GLN1469 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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660A PHE* 4.1 1.8 - - - -
1468C LYS* 1.3 75.1 - - - +
1470C ALA* 1.3 60.6 + - - +
1471C ALA* 3.3 7.9 - - + +
1472C VAL* 3.4 15.8 - - + +
1473C ASN* 3.0 31.5 + - - +
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Residues in contact with ALA1470 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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660A PHE* 4.0 23.6 - - + -
664A GLU 5.7 1.3 - - - +
1469C GLN* 1.3 74.2 - - - +
1471C ALA* 1.3 58.3 + - - +
1472C VAL 3.4 0.2 - - - -
1473C ASN* 4.1 1.0 - - - +
1474C ALA* 3.3 27.9 + - - +
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Residues in contact with ALA1471 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1469C GLN* 3.3 5.0 - - + +
1470C ALA* 1.3 78.9 - - - +
1472C VAL* 1.3 59.4 + - - +
1474C ALA* 4.2 3.8 - - - +
1475C ALA* 3.4 21.0 + - - +
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Residues in contact with VAL1472 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1468C LYS* 4.1 11.9 - - + -
1469C GLN* 3.4 31.3 - - + +
1471C ALA* 1.3 78.0 - - - +
1473C ASN* 1.3 62.0 + - - +
1474C ALA 3.3 1.6 - - - -
1475C ALA* 3.1 9.2 + - + +
1476C VAL* 3.0 39.1 + - + +
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Residues in contact with ASN1473 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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653A THR* 5.9 0.5 - - - +
657A ALA* 4.9 13.3 - - + +
660A PHE* 3.9 31.9 - - + -
661A ARG* 5.0 4.2 + - - +
1468C LYS* 4.9 7.4 - - + -
1469C GLN 3.0 18.9 + - - +
1470C ALA 4.4 1.3 - - - +
1472C VAL* 1.3 79.2 - - + +
1474C ALA* 1.3 59.6 + - - +
1475C ALA 3.2 0.8 + - - -
1476C VAL* 3.8 10.2 + - - +
1477C GLN* 3.8 17.7 + - - +
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Residues in contact with ALA1474 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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661A ARG* 4.3 19.9 - - - +
1470C ALA 3.3 18.4 + - - +
1471C ALA* 4.4 4.7 - - - +
1472C VAL 3.3 0.4 - - - -
1473C ASN* 1.3 76.7 - - - +
1475C ALA* 1.3 58.2 + - - +
1477C GLN* 4.1 10.2 - - - +
1478C ARG* 3.5 21.1 + - - +
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Residues in contact with ALA1475 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1471C ALA 3.4 15.4 + - - +
1472C VAL* 3.1 15.3 + - + +
1474C ALA* 1.3 78.5 - - - +
1476C VAL* 1.3 59.3 + - - +
1477C GLN 3.2 1.6 - - - -
1478C ARG* 3.2 5.8 + - - +
1479C VAL* 3.0 38.4 + - + +
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Residues in contact with VAL1476 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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653A THR* 3.7 28.5 - - + +
1472C VAL* 3.0 26.0 - - + +
1473C ASN* 3.8 9.4 + - - +
1475C ALA* 1.3 75.8 - - - +
1477C GLN* 1.3 60.3 + - - +
1479C VAL* 3.8 8.4 + - + +
1480C GLN* 3.6 17.0 + - - +
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Residues in contact with GLN1477 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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578A HIS* 4.4 7.3 - - - -
619A CYS* 3.5 30.4 - - - -
620A GLU* 3.6 26.8 + - - +
653A THR* 4.2 10.0 - - + +
654A TYR* 3.4 31.7 + - + -
657A ALA* 4.8 4.5 - - + -
661A ARG* 5.1 7.3 + - - +
1473C ASN 3.8 14.8 + - - +
1474C ALA* 4.1 9.5 - - - +
1476C VAL* 1.3 78.9 - - - +
1478C ARG* 1.3 65.1 + - - +
1480C GLN* 3.4 22.5 + - - +
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Residues in contact with ARG1478 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1474C ALA 3.5 16.7 + - - +
1475C ALA* 3.2 8.4 + - - +
1477C GLN* 1.3 81.3 + - - +
1479C VAL* 1.3 63.9 + - + +
1480C GLN 3.2 7.9 + - - +
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Residues in contact with VAL1479 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1475C ALA* 3.0 28.3 + - + +
1476C VAL* 4.0 9.4 - - + +
1477C GLN 3.4 0.2 - - - -
1478C ARG* 1.3 77.2 - - + +
1480C GLN* 1.3 61.6 + - - +
1481C VAL* 3.7 4.7 + - - +
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Residues in contact with GLN1480 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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612A ARG* 2.9 28.7 + - - +
649A GLU 5.5 0.4 - - - +
650A GLY* 3.5 24.2 + - - -
653A THR* 3.7 18.1 - - + +
654A TYR* 3.1 52.8 + - - -
1476C VAL 3.6 8.6 + - - +
1477C GLN 3.4 17.1 + - - +
1478C ARG 3.2 6.3 - - - +
1479C VAL* 1.3 81.6 - - - +
1481C VAL* 1.3 61.7 + - - +
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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