Contacts of the helix formed by residues 1656 - 1674 (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 ARG1656 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1237D TRP* 5.1 13.2 - - - -
1604D SER* 5.7 0.6 + - - -
1605D TRP* 4.1 19.0 + - - +
1606D SER* 5.4 2.4 - - - +
1648D MET* 3.4 43.2 - - - +
1649D ASP 5.3 0.6 + - - +
1652D GLU 4.2 8.9 + - - -
1653D LEU* 3.2 48.0 + - + +
1654D SER 4.5 0.4 - - - -
1655D GLU* 1.3 75.7 - - + +
1657D LEU* 1.3 62.8 + - - +
1658D ASP* 3.3 3.1 - - + +
1659D LEU* 3.9 20.7 + - + +
1660D GLN* 3.6 14.0 + - - +
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Residues in contact with LEU1657 (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 SER 5.0 3.1 - - - +
1655D GLU 3.0 11.1 + - - +
1656D ARG* 1.3 71.0 - - - +
1658D ASP* 1.3 63.8 + - - +
1659D LEU 3.5 0.2 - - - -
1660D GLN* 3.6 20.5 + - - +
1661D GLN* 3.7 13.9 + - - +
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Residues in contact with ASP1658 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1656D ARG* 3.3 1.6 - - + -
1657D LEU* 1.3 80.1 - - - +
1659D LEU* 1.3 71.2 + - + +
1660D GLN 3.5 0.3 + - - -
1661D GLN* 3.9 3.7 + - - +
1662D PHE* 3.7 17.2 + - - +
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Residues in contact with LEU1659 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
595D ARG* 6.5 0.9 - - - -
633D LEU* 4.3 27.6 - - + +
1639D LEU* 6.3 0.9 - - + -
1641D ILE* 4.9 14.4 - - + -
1648D MET* 5.1 12.8 - - + -
1653D LEU* 4.5 19.7 - - + +
1656D ARG* 3.9 20.1 + - + +
1658D ASP* 1.3 86.0 - - + +
1660D GLN* 1.3 60.3 + - - +
1662D PHE* 3.9 10.6 - - + +
1663D HIS* 3.0 30.0 + - - +
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Residues in contact with GLN1660 (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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1653D LEU* 4.4 18.1 - - + +
1654D SER* 4.5 10.3 - - - +
1656D ARG 3.6 14.4 + - - +
1657D LEU* 3.9 16.5 - - - +
1658D ASP 3.3 1.2 - - - -
1659D LEU* 1.3 75.8 - - - +
1661D GLN* 1.3 61.0 + - - +
1663D HIS* 3.3 5.5 + - - +
1664D SER* 2.9 28.9 + - - -
1704D PRO* 4.3 16.0 - - + +
1706D PRO* 4.0 29.9 - - + +
1707D LEU* 4.5 14.9 - - + +
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Residues in contact with GLN1661 (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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597D HIS* 3.5 17.1 - - + +
598D LYS* 4.1 10.8 + - - +
1657D LEU 3.7 11.3 + - - +
1658D ASP 3.9 3.6 + - - +
1660D GLN* 1.3 79.5 - - - +
1662D PHE* 1.3 58.2 + - - +
1664D SER* 3.3 5.2 + - - -
1665D HIS* 2.9 60.4 + - + +
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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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590D LEU* 5.6 6.1 - - + -
595D ARG* 3.6 48.7 - - + -
596D ASN 4.5 9.2 - - - -
597D HIS* 5.0 4.9 - - + +
600D LEU* 3.7 25.6 - - + -
631D LEU 4.3 4.0 - - - -
632D LEU* 3.6 30.1 - - + -
633D LEU* 3.4 33.7 - - + -
1658D ASP 3.7 14.0 + - - +
1659D LEU* 3.6 10.5 + - + +
1660D GLN 3.3 0.4 - - - -
1661D GLN* 1.3 79.6 - - - +
1663D HIS* 1.3 52.3 + - - +
1665D HIS* 3.3 6.6 + - - +
1666D THR* 2.6 39.2 + - - -
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Residues in contact with HIS1663 (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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633D LEU* 4.8 24.8 - - + +
635D THR* 4.3 17.0 - - + -
1639D LEU* 6.0 4.5 - - + -
1650D ILE* 6.1 2.6 - - - +
1653D LEU* 5.5 8.3 - - + -
1659D LEU 3.0 20.2 + - - +
1660D GLN* 3.7 5.6 - - - +
1662D PHE* 1.3 75.4 - - - +
1664D SER* 1.3 60.8 + - - +
1666D THR* 3.3 8.5 + - + +
1667D LEU* 2.9 60.3 + - + +
1707D LEU* 3.8 32.8 - - + -
1711D TYR* 3.4 22.4 + + - -
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Residues in contact with SER1664 (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 GLN* 2.9 17.8 + - - -
1661D GLN* 3.7 8.1 - - - -
1663D HIS* 1.3 77.0 - - - +
1665D HIS* 1.3 64.1 + - - +
1667D LEU* 3.3 7.3 + - - +
1668D ARG* 2.9 34.2 + - - +
1706D PRO* 3.9 30.0 + - - +
1707D LEU* 4.9 6.2 - - - +
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Residues in contact with HIS1665 (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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597D HIS* 2.8 39.3 + - + +
598D LYS* 5.4 1.6 - - + -
600D LEU* 3.5 23.7 - - + +
601D ASP* 5.3 4.9 + - + -
1661D GLN* 2.9 50.3 + - + +
1662D PHE* 3.8 4.5 - - - +
1664D SER* 1.3 79.9 - - - +
1666D THR* 1.3 60.1 + - - +
1668D ARG* 3.6 25.7 + - - +
1669D LEU* 2.9 30.1 + - - +
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Residues in contact with THR1666 (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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600D LEU* 3.5 10.3 - - + +
632D LEU* 3.6 34.8 - - + +
633D LEU* 5.0 7.4 - - + +
1662D PHE* 2.6 30.7 + - - -
1663D HIS* 3.3 11.5 + - + +
1665D HIS* 1.3 77.2 - - - +
1667D LEU* 1.3 62.6 + - + +
1669D LEU* 3.3 4.7 + - + +
1670D TYR* 2.9 55.5 + - + +
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Residues in contact with LEU1667 (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 HIS* 2.9 60.4 + - + +
1664D SER* 3.7 7.4 - - - +
1666D THR* 1.3 79.0 - - + +
1668D ARG* 1.3 58.2 + - - +
1670D TYR* 3.3 10.6 + - + -
1671D ARG* 2.9 24.6 + - - +
1689D VAL* 6.3 2.7 - - + -
1707D LEU* 5.2 4.5 - - - +
1710D GLY* 3.9 21.8 - - - +
1711D TYR* 3.7 32.1 - - + -
1714D LEU* 3.1 37.4 - - + +
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Residues in contact with ARG1668 (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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604D CYS* 4.8 21.1 - - + -
1664D SER* 2.9 23.6 + - - +
1665D HIS* 3.6 25.8 + - - +
1667D LEU* 1.3 76.8 - - - +
1669D LEU* 1.3 57.2 + - - +
1671D ARG* 3.2 7.3 + - + +
1672D ALA* 2.9 29.2 + - + +
1710D GLY* 5.8 0.2 - - - -
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Residues in contact with LEU1669 (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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600D LEU* 4.3 24.0 - - + +
603D LEU* 3.8 36.1 - - + +
604D CYS* 4.0 18.4 - - - +
607D CYS* 5.4 4.0 - - + -
621D ILE* 6.5 0.4 - - + -
625D LEU* 4.2 25.6 - - + -
632D LEU* 6.2 2.0 - - + -
1665D HIS 2.9 17.0 + - - +
1666D THR* 3.7 6.3 - - + +
1667D LEU 3.3 0.2 - - - -
1668D ARG* 1.3 78.4 - - - +
1670D TYR* 1.3 65.8 + - + +
1672D ALA* 3.3 3.5 + - + +
1673D VAL* 2.9 38.0 + - + +
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Residues in contact with TYR1670 (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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625D LEU* 4.0 16.8 - - + +
626D LEU* 3.7 30.5 - - + +
632D LEU* 4.2 14.6 - - + +
633D LEU 4.8 8.8 + - - -
1666D THR* 2.9 39.3 + - + +
1667D LEU* 3.3 13.7 + - + +
1669D LEU* 1.3 84.8 - - + +
1671D ARG* 1.3 61.8 + - - +
1673D VAL* 3.2 22.9 - - + +
1674D CYS* 3.9 8.0 + - - +
1685D LEU* 5.2 9.9 - - + +
1688D HIS* 5.7 6.4 + + + -
1689D VAL* 5.5 12.6 - - + -
1714D LEU* 3.7 23.4 - - + +
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Residues in contact with ARG1671 (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 LEU 2.9 16.8 + - - +
1668D ARG* 3.6 7.9 - - + +
1670D TYR* 1.3 77.9 - - - +
1672D ALA* 1.3 61.1 + - - +
1674D CYS 3.2 20.4 - - - +
1675D ALA* 4.0 4.2 - - - +
1713D ASP* 4.3 22.9 - - + +
1714D LEU* 3.6 19.2 - - + +
1717D SER* 3.5 9.8 + - - -
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Residues in contact with ALA1672 (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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604D CYS* 4.1 28.0 - - + +
607D CYS* 3.4 17.6 - - + -
608D VAL* 5.4 9.9 - - + +
618D GLN* 4.5 2.1 + - - -
1668D ARG* 2.9 18.0 + - + +
1669D LEU* 4.0 4.3 - - + +
1671D ARG* 1.3 75.0 - - - +
1673D VAL* 1.3 63.3 + - - +
1674D CYS 3.2 1.2 + - - -
1675D ALA* 4.1 13.7 + - - +
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Residues in contact with VAL1673 (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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607D CYS* 3.6 15.9 - - - -
618D GLN* 2.9 39.1 + - + +
621D ILE* 5.1 8.3 - - + -
622D THR* 4.4 7.9 - - - +
1669D LEU* 2.9 21.6 + - + +
1670D TYR* 3.2 32.1 - - + +
1672D ALA* 1.3 77.2 - - - +
1674D CYS* 1.3 60.1 + - + +
1675D ALA 3.8 0.4 - - - -
1681D VAL* 3.3 25.4 - - + +
1685D LEU* 5.4 5.6 - - + -
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Residues in contact with CYS1674 (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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1670D TYR 3.9 8.0 + - - +
1671D ARG 3.2 3.5 + - - +
1672D ALA 3.2 0.2 - - - -
1673D VAL* 1.3 81.3 - - + +
1675D ALA* 1.3 61.7 + - - +
1678D ASN* 4.4 8.3 - - - +
1681D VAL* 3.7 21.8 - - + +
1682D ALA* 4.4 13.0 - - + -
1685D LEU* 5.0 5.8 - - + -
1717D SER* 2.3 46.0 + - - +
1718D ILE* 5.5 2.7 - - + -
1721D GLU* 4.8 1.1 - - - +
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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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
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