Contacts of the helix formed by residues 1542 - 1554 (chain r) in PDB entry 6FF7
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 MET1542 (chain r).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1538r ARG 3.0 13.4 + - - +
1539r LEU* 3.5 7.6 + - - +
1540r LEU 3.1 0.8 - - - -
1541r SER* 1.3 78.9 - - - +
1543r ALA* 1.3 63.9 + - - +
1544r LYS 3.6 0.9 - - - -
1545r PRO* 3.6 12.8 - - + +
1546r VAL* 3.3 18.2 + - - +
1664r MET* 6.0 5.4 - - + -
1665r ASP* 6.2 1.6 - - + +
1705r MET* 4.6 20.6 - - + -
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Residues in contact with ALA1543 (chain r).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1539r LEU 3.8 3.9 + - - +
1540r LEU* 3.1 20.0 + - - +
1541r SER 3.3 0.4 - - - -
1542r MET* 1.3 77.2 - - - +
1544r LYS* 1.3 65.3 + - - +
1546r VAL* 3.1 21.8 + - - +
1547r TYR* 3.6 4.0 + - - +
1575r ASP* 4.7 21.0 - - + +
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Residues in contact with LYS1544 (chain r).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
907r LEU 6.1 0.9 - - - +
908r GLY* 5.3 10.1 - - - +
1541r SER 4.8 3.4 + - - +
1542r MET 3.6 0.4 - - - -
1543r ALA* 1.3 79.2 - - - +
1545r PRO* 1.4 63.6 - - - +
1546r VAL 3.1 1.0 + - - -
1547r TYR* 3.1 10.1 + - - +
1548r HIS* 3.1 20.9 + - - +
1579r THR* 5.6 9.9 - - - -
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Residues in contact with PRO1545 (chain r).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1541r SER 5.0 3.4 - - - +
1542r MET* 3.6 20.9 - - + +
1543r ALA 3.3 0.6 - - - -
1544r LYS* 1.4 76.8 - - - +
1546r VAL* 1.3 52.3 + - - +
1548r HIS* 3.6 8.2 - - + +
1549r ALA* 2.7 36.1 + - - +
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Residues in contact with VAL1546 (chain r).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1542r MET 3.3 9.1 + - - +
1543r ALA* 3.1 14.2 + - - +
1544r LYS 3.1 1.2 + - - -
1545r PRO* 1.3 78.0 - - - +
1547r TYR* 1.3 65.1 + - - +
1549r ALA* 3.0 9.0 + - - +
1550r ILE* 3.0 20.4 + - - +
1576r ILE* 6.4 1.8 - - + -
1662r ILE* 5.8 8.3 - - + -
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Residues in contact with TYR1547 (chain r).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1543r ALA 3.6 3.2 + - - +
1544r LYS* 3.1 10.6 + - - +
1546r VAL* 1.3 78.0 - - - +
1548r HIS* 1.3 63.9 + - - +
1550r ILE* 3.0 11.2 + - - +
1551r THR* 3.0 22.2 + - - -
1576r ILE* 5.4 13.5 - - + +
1579r THR* 4.9 21.3 - - - +
1580r CYS* 6.4 0.2 - - - -
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Residues in contact with HIS1548 (chain r).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1544r LYS 3.1 12.5 + - - +
1545r PRO* 3.8 11.2 - - + +
1547r TYR* 1.3 76.2 - - - +
1549r ALA* 1.3 57.5 + - - +
1551r THR* 3.3 7.9 + - - +
1552r LYS* 2.9 32.6 + - - +
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Residues in contact with ALA1549 (chain r).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1545r PRO 2.7 22.3 + - - +
1546r VAL* 3.0 8.3 + - - +
1548r HIS* 1.3 72.9 - - - +
1550r ILE* 1.3 58.1 + - - +
1552r LYS* 4.5 3.6 - - - -
1553r HIS* 3.0 33.9 + - + +
1554r SER 4.0 0.2 + - - -
1662r ILE* 5.3 7.9 - - + -
1703r VAL* 4.6 21.5 - - + -
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Residues in contact with ILE1550 (chain r).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1546r VAL 3.0 9.2 + - - +
1547r TYR* 3.0 13.2 + - - +
1549r ALA* 1.3 72.4 - - - +
1551r THR* 1.3 65.6 + - - +
1552r LYS 3.0 1.6 - - - -
1554r SER* 2.9 43.2 + - - +
1555r PRO* 4.4 1.6 - - + +
1559r VAL* 5.5 9.9 - - + -
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Residues in contact with THR1551 (chain r).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1547r TYR 3.0 15.3 + - - -
1548r HIS* 3.9 7.4 - - - -
1550r ILE* 1.3 75.7 - - - +
1552r LYS* 1.3 60.9 + - - +
1555r PRO* 3.8 21.1 - - - +
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Residues in contact with LYS1552 (chain r).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1548r HIS 2.9 18.1 + - - +
1549r ALA* 4.0 4.5 - - - +
1550r ILE 3.0 0.4 + - - -
1551r THR* 1.3 81.2 - - - +
1553r HIS* 1.3 67.1 + - + +
1554r SER 3.6 0.5 + - - -
1555r PRO* 4.5 2.9 - - - +
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Residues in contact with HIS1553 (chain r).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1549r ALA* 3.0 16.6 + - + +
1552r LYS* 1.3 79.9 - - + +
1554r SER* 1.3 62.6 + - - +
1555r PRO 4.0 0.2 - - - -
1660r LEU* 5.1 3.8 - - + -
1701r ARG* 4.5 22.3 - - + +
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Residues in contact with SER1554 (chain r).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1549r ALA 4.0 0.8 + - - -
1550r ILE* 2.9 18.8 + - - +
1553r HIS* 1.3 81.2 - - - +
1555r PRO* 1.3 64.9 - - - +
1556r LYS 3.4 2.6 + - - -
1557r LYS* 3.7 29.9 - - - +
1559r VAL* 5.5 1.3 - - - -
1659r HIS* 4.9 1.6 - - - -
1660r LEU* 3.5 33.4 - - - -
1701r ARG* 5.8 0.7 - - - -
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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