Contacts of the helix formed by residues 1658 - 1672 (chain D) in PDB entry 3COJ
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 THR1658 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1656D GLY 5.4 1.3 - - - +
1657D LEU* 1.3 77.1 - - - +
1659D PRO* 1.3 74.5 - - - +
1660D GLU* 3.6 17.4 + - - +
1661D GLU* 2.8 43.0 + - - +
1662D PHE* 3.0 19.8 + - - +
1690D LYS* 5.8 1.3 - - + -
1262L GLN* 5.7 4.9 - - - +
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Residues in contact with PRO1659 (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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1657D LEU 4.4 1.8 - - - +
1658D THR* 1.3 85.8 - - - +
1660D GLU* 1.3 73.7 + - + +
1662D PHE* 3.1 22.5 + - + +
1663D MET* 3.4 15.9 + - - +
1262L GLN* 5.4 8.5 - - - +
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Residues in contact with GLU1660 (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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1658D THR* 3.2 16.6 + - - +
1659D PRO* 1.3 90.1 - - + +
1661D GLU* 1.3 62.9 + - + +
1663D MET* 3.4 20.7 + - - +
1664D LEU* 3.8 9.5 + - - +
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Residues in contact with GLU1661 (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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1656D GLY 4.2 0.2 - - - +
1657D LEU* 3.4 23.2 - - + +
1658D THR* 2.8 43.0 + - - +
1660D GLU* 1.3 75.3 - - + +
1662D PHE* 1.3 66.9 + - - +
1663D MET 3.2 0.9 + - - -
1664D LEU* 3.2 17.9 + - + +
1665D VAL* 3.4 13.5 + - - +
1690D LYS* 3.1 37.3 + - - +
1716D TYR* 3.8 26.8 - - + +
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Residues in contact with PHE1662 (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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1654D VAL* 3.4 34.5 - - + -
1657D LEU* 3.7 12.3 - - + +
1658D THR 3.0 11.0 + - - +
1659D PRO* 3.1 13.4 + - + +
1661D GLU* 1.3 76.3 - - - +
1663D MET* 1.3 78.9 + - + +
1665D VAL* 3.1 5.6 + - + +
1666D TYR* 2.9 27.1 + + + -
1676D LEU* 3.7 33.9 - - + -
1677D THR 5.2 4.5 - - - -
1678D ASN* 5.9 4.3 - - - -
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Residues in contact with MET1663 (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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1659D PRO 3.4 16.0 + - - +
1660D GLU* 3.5 12.8 - - - +
1661D GLU 3.1 0.8 - - - -
1662D PHE* 1.3 93.6 - - + +
1664D LEU* 1.3 59.4 + - + +
1666D TYR* 3.2 35.3 + - + +
1667D LYS* 2.9 29.8 + - - +
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Residues in contact with LEU1664 (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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1660D GLU 3.8 8.9 + - - +
1661D GLU* 3.2 10.3 + - + +
1663D MET* 1.3 77.6 - - + +
1665D VAL* 1.3 59.6 + - + +
1667D LYS* 3.9 8.7 - - + +
1668D PHE* 3.0 26.9 + - - +
1716D TYR* 3.4 24.9 - - + +
1719D VAL* 4.1 6.2 - - + +
1720D THR* 4.8 9.9 - - + -
1723D ILE* 4.2 27.3 - - + +
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Residues in contact with VAL1665 (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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1652D MET* 3.9 25.7 - - + +
1654D VAL* 4.1 18.4 - - + -
1657D LEU* 3.7 19.7 - - + -
1661D GLU 3.5 14.8 - - - +
1662D PHE* 3.1 10.0 + - + +
1663D MET 3.1 0.4 - - - -
1664D LEU* 1.3 77.2 - - - +
1666D TYR* 1.3 59.0 + - - +
1668D PHE* 3.6 7.7 - - + +
1669D ALA* 2.9 28.2 + - - +
1676D LEU* 4.1 10.1 - - + -
1688D VAL* 5.6 1.3 - - + -
1716D TYR* 4.2 12.3 - - + -
1719D VAL* 4.3 18.6 - - + -
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Residues in contact with TYR1666 (chain D).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1662D PHE* 2.9 17.5 + + + +
1663D MET* 3.2 33.4 + - + +
1665D VAL* 1.3 74.5 - - - +
1667D LYS* 1.3 64.5 + - - +
1669D ALA* 3.5 13.9 + - + +
1670D ARG* 3.8 39.3 + - + +
1676D LEU* 4.1 20.8 - - + +
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Residues in contact with LYS1667 (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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1663D MET 2.9 16.1 + - - +
1664D LEU* 4.0 10.1 - - + +
1666D TYR* 1.3 77.3 - - - +
1668D PHE* 1.3 59.6 + - - +
1670D ARG* 4.3 4.6 + - - +
1671D LYS* 3.2 41.9 + - + +
1723D ILE* 4.7 23.5 - - + +
1726D ARG* 6.1 0.6 - - - +
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Residues in contact with PHE1668 (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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1652D MET* 5.2 5.2 - - + -
1664D LEU 3.0 19.3 + - - +
1665D VAL* 3.6 7.0 - - + +
1666D TYR 3.3 0.2 - - - -
1667D LYS* 1.3 78.9 - - - +
1669D ALA* 1.3 66.0 + - - +
1671D LYS* 3.8 4.9 - - + +
1672D HIS* 3.3 46.5 + + - +
1674D ILE* 4.0 24.1 - - + +
1718D TRP* 4.3 23.1 - + - -
1719D VAL* 3.6 29.2 - - + -
1722D SER* 3.6 32.5 - - - -
1723D ILE* 4.2 18.4 - - + -
1728D MET* 4.4 12.6 - - + -
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Residues in contact with ALA1669 (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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1652D MET* 4.1 12.3 - - + -
1665D VAL 2.9 16.9 + - - +
1666D TYR* 3.8 12.6 - - + +
1667D LYS 3.4 0.6 - - - -
1668D PHE* 1.3 77.9 - - - +
1670D ARG* 1.3 55.8 + - + +
1673D HIS 2.9 6.4 + - - -
1674D ILE* 2.7 59.7 + - - +
1676D LEU* 4.1 12.3 - - + -
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Residues in contact with ARG1670 (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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1666D TYR* 3.8 38.5 + - + +
1667D LYS* 4.8 3.9 - - - +
1669D ALA* 1.3 74.2 - - + +
1671D LYS* 1.3 64.0 + - - +
1672D HIS 3.3 1.6 - - - -
1673D HIS* 3.5 24.3 + - - +
1674D ILE 4.9 0.4 - - - +
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Residues in contact with LYS1671 (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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1667D LYS* 3.2 38.3 + - + +
1668D PHE* 3.8 7.0 - - + +
1669D ALA 3.3 0.6 - - - -
1670D ARG* 1.3 78.8 - - - +
1672D HIS* 1.3 91.0 + - + +
1673D HIS* 3.5 9.2 + - - -
1726D ARG* 3.6 36.2 - - - +
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Residues in contact with HIS1672 (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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1668D PHE* 3.3 50.0 + + - +
1669D ALA 4.5 0.4 - - - +
1671D LYS* 1.3 109.5 + - + +
1673D HIS* 1.3 70.6 + - - +
1674D ILE* 3.0 28.9 + - + +
1722D SER* 5.0 1.2 + - - -
1726D ARG* 5.4 7.4 - - - -
1727D LYS* 5.2 3.7 - - + -
1728D MET* 4.5 30.2 + - + +
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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