Contacts of the helix formed by residues 1679 - 1689 (chain D) in PDB entry 6X34
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 ASN1679 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1677D GLY* 3.9 7.2 + - - +
1678D ASN* 1.3 74.1 - - - +
1680D ARG* 1.3 64.3 + - - +
1681D VAL 3.4 0.7 - - - -
1682D ALA* 3.3 15.0 + - + +
1683D HIS* 3.3 21.1 + - - +
1721D GLU* 6.1 0.8 - - - +
1722D SER* 3.3 27.2 + - - +
1797D ALA* 6.0 1.3 - - + -
1798D ARG* 3.4 25.3 - - + +
1799D LEU 2.9 24.9 + - - +
1800D SER* 3.6 18.4 - - - +
1801D PRO* 4.2 6.7 - - - +
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Residues in contact with ARG1680 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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88C PRO* 5.4 16.4 - - + -
619D ASP* 3.9 31.9 + - - +
1678D ASN* 3.5 9.5 + - - +
1679D ASN* 1.3 79.2 - - - +
1681D VAL* 1.3 61.5 + - - +
1682D ALA 3.4 0.5 + - - -
1683D HIS* 3.8 9.7 + - - +
1684D ALA* 4.0 8.3 + - - +
1797D ALA* 5.0 14.6 - - - +
1798D ARG* 5.1 18.4 + - - +
2174D GLN* 5.4 13.3 - - - +
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Residues in contact with VAL1681 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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618D GLN* 4.3 4.7 - - + +
619D ASP* 5.6 5.1 + - - +
622D THR* 3.2 35.2 - - + +
626D LEU* 5.6 2.7 - - + -
1673D VAL* 3.3 42.4 - - + +
1674D CYS* 3.7 9.9 - - + -
1678D ASN* 3.6 26.3 + - - +
1680D ARG* 1.3 77.3 - - - +
1682D ALA* 1.3 62.0 + - - +
1683D HIS 3.3 0.4 - - - -
1684D ALA* 3.3 5.8 + - + -
1685D LEU* 2.9 29.4 + - + +
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Residues in contact with ALA1682 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1674D CYS* 4.4 8.5 - - + -
1678D ASN 4.0 4.3 - - - +
1679D ASN* 3.3 26.4 + - - +
1680D ARG 3.2 0.6 - - - -
1681D VAL* 1.3 82.7 - - - +
1683D HIS* 1.3 58.8 + - - +
1685D LEU* 3.3 1.7 + - - -
1686D CYS* 2.9 25.2 + - - +
1717D SER 5.4 3.4 - - - +
1718D ILE* 3.1 27.9 - - + +
1801D PRO* 4.3 16.6 - - + -
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Residues in contact with HIS1683 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87C HIS* 6.3 1.6 - - - +
90C VAL* 4.8 1.3 - - - +
1679D ASN* 3.3 14.2 + - + -
1680D ARG 3.8 6.3 + - - +
1681D VAL 3.3 0.4 - - - -
1682D ALA* 1.3 76.3 - - - +
1684D ALA* 1.3 58.5 + - - +
1686D CYS* 3.3 7.4 + - - +
1687D SER* 2.9 29.8 + - - -
1779D SER* 4.1 3.8 + - - -
1780D ALA 3.2 26.7 + - - -
1781D PRO* 5.1 7.9 - - + -
1782D CYS 5.4 4.7 - - - -
1783D PHE* 6.3 4.5 - - + -
1798D ARG* 3.4 48.0 - - + +
1800D SER* 4.4 3.1 - - - -
1801D PRO* 3.7 34.0 - - + +
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Residues in contact with ALA1684 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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87C HIS* 6.3 0.2 - - + -
88C PRO 3.3 26.2 - - - +
89C GLY* 4.6 0.2 - - - -
90C VAL* 3.9 16.5 - - + +
622D THR* 4.1 15.7 - - + -
626D LEU* 4.3 6.1 - - + -
1680D ARG 4.0 4.3 + - - +
1681D VAL* 3.3 12.6 + - - +
1682D ALA 3.3 0.6 - - - -
1683D HIS* 1.3 78.4 - - - +
1685D LEU* 1.3 59.5 + - - +
1687D SER* 2.9 19.8 + - - -
1688D HIS* 3.1 13.9 + - - -
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Residues in contact with LEU1685 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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626D LEU* 4.8 5.6 - - + +
1670D TYR* 5.2 14.1 - - + +
1673D VAL* 5.4 4.3 - - + -
1674D CYS* 5.0 9.2 - - + -
1681D VAL* 2.9 20.3 + - + +
1682D ALA* 3.7 5.2 - - - +
1683D HIS 3.3 0.2 - - - -
1684D ALA* 1.3 75.5 - - - +
1686D CYS* 1.3 63.0 + - - +
1688D HIS* 3.4 16.7 + - - +
1689D VAL* 3.4 14.9 + - - +
1714D LEU* 5.7 6.5 - - + -
1718D ILE* 4.6 8.5 - - + -
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Residues in contact with CYS1686 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1682D ALA 2.9 16.8 + - - +
1683D HIS* 3.3 7.2 + - - +
1685D LEU* 1.3 74.7 - - - +
1687D SER* 1.3 64.4 + - - +
1688D HIS 3.2 0.2 - - - -
1689D VAL 2.8 30.2 - - - +
1690D ASP* 3.9 3.9 + - - -
1691D GLN* 4.9 12.3 - - - -
1718D ILE* 3.9 22.4 - - + +
1719D HIS* 5.3 10.1 - - - -
1781D PRO* 4.9 17.3 - - - +
1801D PRO* 5.5 9.0 - - + -
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Residues in contact with SER1687 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35C LYS 3.8 9.2 - - - +
36C PHE* 3.5 29.2 + - - +
37C ASP* 5.0 1.0 - - - -
90C VAL* 3.4 26.9 - - - +
629D ARG* 4.9 2.3 + - - -
1683D HIS 2.9 16.7 + - - -
1684D ALA 2.9 15.0 + - - -
1686D CYS* 1.3 78.0 - - - +
1688D HIS* 1.3 68.2 + - - +
1689D VAL 5.0 0.3 - - - -
1690D ASP* 5.1 1.4 + - - +
1783D PHE* 6.2 3.6 - - - -
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Residues in contact with HIS1688 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35C LYS 4.8 6.1 - - - +
89C GLY 3.3 19.0 + - - -
626D LEU* 3.6 36.0 - - + +
629D ARG* 3.3 41.4 + - + +
634D GLN* 5.3 10.4 - - + +
635D THR 4.6 10.9 - - - +
1670D TYR* 5.7 6.9 + + + -
1684D ALA 3.1 24.9 - - - -
1685D LEU* 3.4 8.6 + - - +
1686D CYS 3.2 0.6 - - - -
1687D SER* 1.3 86.5 + - - +
1689D VAL* 1.3 67.9 + - + +
1690D ASP* 3.5 3.6 + - - +
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Residues in contact with VAL1689 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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635D THR* 4.4 18.8 - - + +
1667D LEU* 6.3 2.5 - - + -
1670D TYR* 5.5 12.8 - - + -
1685D LEU 3.4 8.8 + - - +
1686D CYS* 2.8 23.7 - - - +
1688D HIS* 1.3 80.6 - - + +
1690D ASP* 1.3 71.9 + - - +
1693D GLN* 4.3 13.9 - - + -
1694D LEU* 4.9 8.7 - - + +
1711D TYR* 5.7 13.2 - - + -
1714D LEU* 6.1 10.1 - - + -
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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