Contacts of the helix formed by residues 1679 - 1689 (chain F) 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 F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1677F GLY* 3.9 7.0 + - - +
1678F ASN* 1.3 73.2 - - - +
1680F ARG* 1.3 64.8 + - - +
1681F VAL 3.4 0.9 - - - -
1682F ALA* 3.3 14.9 + - + +
1683F HIS* 3.3 21.7 + - - +
1721F GLU* 6.1 1.2 - - - +
1722F SER* 3.3 26.7 + - - +
1797F ALA* 6.0 2.0 - - + -
1798F ARG* 3.4 22.9 - - + +
1799F LEU 2.9 24.2 + - - +
1800F SER* 3.6 18.0 - - - +
1801F PRO* 4.2 6.3 - - - +
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Residues in contact with ARG1680 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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88E PRO* 5.4 17.0 - - + +
619F ASP* 3.9 31.6 + - - +
1678F ASN* 3.5 9.3 + - - +
1679F ASN* 1.3 78.9 - - - +
1681F VAL* 1.3 62.1 + - - +
1682F ALA 3.4 0.3 + - - -
1683F HIS* 3.8 9.4 + - - +
1684F ALA* 4.0 7.6 + - - +
1797F ALA* 5.0 14.3 - - - +
1798F ARG* 5.1 18.4 + - - +
2174F GLN* 5.4 13.7 - - - +
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Residues in contact with VAL1681 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
618F GLN* 4.3 4.0 - - + +
619F ASP* 5.6 5.1 + - - +
622F THR* 3.2 35.9 - - + +
626F LEU* 5.6 2.7 - - + -
1673F VAL* 3.3 41.5 - - + +
1674F CYS* 3.7 10.5 - - + -
1678F ASN* 3.6 25.6 + - - +
1680F ARG* 1.3 77.9 - - - +
1682F ALA* 1.3 61.0 + - - +
1683F HIS 3.3 0.2 - - - -
1684F ALA* 3.3 6.0 + - + -
1685F LEU* 2.9 30.3 + - + +
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Residues in contact with ALA1682 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1674F CYS* 4.4 8.7 - - + -
1678F ASN 4.0 3.8 - - - +
1679F ASN* 3.3 25.7 + - - +
1680F ARG 3.2 1.0 - - - -
1681F VAL* 1.3 83.0 - - - +
1683F HIS* 1.3 59.0 + - - +
1685F LEU* 3.3 1.3 + - - -
1686F CYS* 2.9 24.5 + - - +
1717F SER 5.4 3.1 - - - +
1718F ILE* 3.1 28.7 - - + +
1801F PRO* 4.3 17.3 - - + -
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Residues in contact with HIS1683 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87E HIS* 6.3 1.8 - - - +
90E VAL* 4.8 1.1 - - - +
1679F ASN* 3.3 14.8 + - + -
1680F ARG 3.8 6.0 + - - +
1681F VAL 3.3 0.2 - - - -
1682F ALA* 1.3 76.0 - - - +
1684F ALA* 1.3 57.4 + - - +
1686F CYS* 3.3 6.5 + - - +
1687F SER* 2.9 29.5 + - - -
1779F SER* 4.1 4.2 + - - -
1780F ALA 3.2 25.8 + - - -
1781F PRO* 5.1 7.9 - - + -
1782F CYS 5.4 4.7 - - - -
1783F PHE* 6.3 4.5 - - + -
1798F ARG* 3.4 50.3 - - + +
1800F SER* 4.4 2.2 - - - -
1801F PRO* 3.7 34.0 - - + +
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Residues in contact with ALA1684 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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88E PRO 3.3 26.7 - - - +
90E VAL* 3.9 16.1 - - + +
622F THR* 4.1 15.0 - - + -
626F LEU* 4.3 6.3 - - + -
1680F ARG 4.0 4.3 + - - +
1681F VAL* 3.3 13.3 + - + +
1682F ALA 3.3 0.2 - - - -
1683F HIS* 1.3 78.4 - - - +
1685F LEU* 1.3 59.0 + - - +
1687F SER* 2.9 19.8 + - - -
1688F HIS* 3.1 14.0 - - - -
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Residues in contact with LEU1685 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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626F LEU* 4.8 4.4 - - + +
1670F TYR* 5.2 13.7 - - + +
1673F VAL* 5.4 4.9 - - + -
1674F CYS* 5.0 9.2 - - + -
1681F VAL* 2.9 20.3 + - + +
1682F ALA* 3.7 4.7 - - - +
1684F ALA* 1.3 75.9 - - - +
1686F CYS* 1.3 62.5 + - - +
1688F HIS* 3.4 17.0 + - - +
1689F VAL* 3.4 14.9 + - - +
1714F LEU* 5.7 7.2 - - + -
1718F ILE* 4.6 8.5 - - + -
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Residues in contact with CYS1686 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1682F ALA 2.9 17.2 + - - +
1683F HIS* 3.3 6.9 + - - +
1685F LEU* 1.3 75.1 - - - +
1687F SER* 1.3 65.2 + - - +
1689F VAL 2.8 30.5 - - - +
1690F ASP* 3.9 3.5 + - - -
1691F GLN* 4.9 12.8 - - - -
1718F ILE* 3.9 22.4 - - + +
1719F HIS* 5.3 10.1 - - - -
1781F PRO* 4.9 16.4 - - - +
1801F PRO* 5.5 9.2 - - + -
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Residues in contact with SER1687 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35E LYS 3.8 10.2 - - - +
36E PHE* 3.5 28.6 + - - +
37E ASP* 5.0 1.6 - - - +
90E VAL* 3.4 27.0 - - - +
629F ARG* 4.9 2.1 + - - -
1683F HIS 2.9 16.3 + - - -
1684F ALA 2.9 15.2 + - - -
1686F CYS* 1.3 77.2 - - - +
1688F HIS* 1.3 68.6 + - - +
1689F VAL 5.0 0.2 - - - -
1690F ASP* 5.1 1.7 + - - +
1783F PHE* 6.2 3.4 - - - -
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Residues in contact with HIS1688 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35E LYS 4.8 6.5 - - - +
89E GLY 3.3 19.1 + - - -
626F LEU* 3.6 37.4 - - + +
629F ARG* 3.3 40.7 + - + +
634F GLN* 5.3 10.8 - - + +
635F THR 4.6 10.4 - - - +
1670F TYR* 5.7 7.1 + + + -
1684F ALA 3.1 24.9 - - - -
1685F LEU* 3.4 8.6 + - - +
1686F CYS 3.2 0.4 - - - -
1687F SER* 1.3 86.5 + - - +
1689F VAL* 1.3 68.2 + - + +
1690F ASP* 3.5 3.3 + - - +
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Residues in contact with VAL1689 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
635F THR* 4.4 18.2 - - + +
1667F LEU* 6.3 2.9 - - + -
1670F TYR* 5.5 12.6 - - + -
1685F LEU 3.4 8.8 + - - +
1686F CYS* 2.8 23.7 - - - +
1688F HIS* 1.3 81.7 - - + +
1690F ASP* 1.3 73.8 + - - +
1691F GLN 3.9 0.2 + - - -
1693F GLN* 4.3 13.5 - - + -
1694F LEU* 4.9 9.0 - - + +
1711F TYR* 5.7 12.3 - - + -
1714F LEU* 6.1 11.2 - - + -
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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