Contacts of the helix formed by residues 1625 - 1638 (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 SER1625 (chain r).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1623r GLY 3.5 3.4 + - - -
1624r LEU* 1.3 72.9 - - - +
1626r PRO* 1.3 57.9 - - - +
1627r MET* 3.0 9.0 - - - -
1628r GLU* 2.8 33.2 + - - +
1629r ARG* 3.0 10.0 + - - +
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Residues in contact with PRO1626 (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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1624r LEU 3.6 3.1 - - - +
1625r SER* 1.3 70.3 - - - +
1627r MET* 1.3 57.2 + - - +
1629r ARG* 3.8 8.6 - - + +
1630r ARG* 2.9 29.5 + - - +
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Residues in contact with MET1627 (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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1603r LYS* 5.7 11.9 - - + +
1625r SER* 3.0 6.4 - - - -
1626r PRO* 1.3 78.6 - - - +
1628r GLU* 1.3 64.4 + - - +
1630r ARG* 3.4 6.2 + - - +
1631r LEU* 2.9 25.3 + - - +
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Residues in contact with GLU1628 (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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1603r LYS* 5.6 8.0 + - - +
1604r LEU* 6.1 4.9 - - + -
1624r LEU* 4.3 9.4 - - + -
1625r SER* 2.8 30.8 + - - +
1627r MET* 1.3 73.3 - - - +
1629r ARG* 1.3 56.0 + - - +
1631r LEU* 3.3 8.0 + - - +
1632r VAL* 3.0 28.6 + - - +
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Residues in contact with ARG1629 (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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1619r TYR 6.1 0.7 - - - -
1620r LEU* 5.6 11.9 - - + +
1621r HIS 6.0 1.1 - - - +
1624r LEU* 4.7 11.6 - - + +
1625r SER 3.0 10.1 + - - +
1626r PRO* 3.8 11.2 - - + +
1628r GLU* 1.3 74.2 - - - +
1630r ARG* 1.3 66.7 + - - +
1632r VAL* 3.1 7.2 + - - +
1633r GLU* 2.9 25.3 + - - +
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Residues in contact with ARG1630 (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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1626r PRO 2.9 19.1 + - - +
1627r MET* 3.7 7.0 - - - +
1629r ARG* 1.3 74.8 - - - +
1631r LEU* 1.3 56.4 + - - +
1633r GLU* 3.5 6.6 + - - +
1634r GLN* 2.9 29.5 + - - +
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Residues in contact with LEU1631 (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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1600r TYR* 5.2 18.4 - - + +
1603r LYS* 6.1 4.0 - - + -
1627r MET 2.9 14.5 + - - +
1628r GLU* 3.3 11.4 - - - +
1629r ARG 3.2 0.2 - - - -
1630r ARG* 1.3 76.1 - - - +
1632r VAL* 1.3 63.7 + - - +
1634r GLN* 3.1 8.9 + - - +
1635r LEU* 2.9 24.1 + - - +
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Residues in contact with VAL1632 (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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1618r GLY* 5.8 3.1 - - - -
1619r TYR 4.5 20.9 - - - +
1620r LEU* 5.7 4.3 - - + -
1628r GLU 3.0 13.5 + - - +
1629r ARG* 3.7 9.2 - - - +
1631r LEU* 1.3 73.6 - - - +
1633r GLU* 1.3 58.3 + - - +
1635r LEU* 3.3 8.5 + - - +
1636r PHE* 2.9 30.1 + - - +
1641r ILE* 6.0 0.2 - - - +
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Residues in contact with GLU1633 (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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1629r ARG 2.9 17.7 + - - +
1630r ARG* 3.6 8.1 - - - +
1632r VAL* 1.3 76.5 - - - +
1634r GLN* 1.3 55.1 + - - +
1636r PHE* 3.2 7.0 + - - +
1637r SER* 2.9 32.4 + - - -
1656r VAL* 4.6 17.7 - - + +
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Residues in contact with GLN1634 (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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1630r ARG 2.9 15.5 + - - +
1631r LEU* 3.1 11.6 + - - +
1633r GLU* 1.3 75.6 - - - +
1635r LEU* 1.3 56.9 + - - +
1637r SER* 4.2 2.8 - - - -
1638r SER* 2.9 36.2 + - - -
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Residues in contact with LEU1635 (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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1631r LEU 2.9 13.4 + - - +
1632r VAL* 3.5 11.2 - - - +
1634r GLN* 1.3 76.5 - - - +
1636r PHE* 1.3 59.1 + - - +
1638r SER* 4.2 2.4 - - - -
1639r GLY 3.3 1.9 + - - -
1640r ALA* 2.9 42.8 + - + +
1641r ILE* 3.3 13.6 + - + -
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Residues in contact with PHE1636 (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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1558r PRO* 5.7 5.0 - - - +
1632r VAL 2.9 17.2 + - - +
1633r GLU* 3.6 7.0 - - - +
1635r LEU* 1.3 76.7 - - - +
1637r SER* 1.3 58.8 + - - +
1639r GLY* 3.0 21.1 + - - -
1641r ILE* 3.8 20.4 - - + +
1643r VAL 6.3 0.7 - - - -
1644r VAL* 5.2 15.0 - - + -
1656r VAL* 5.4 6.7 - - + -
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Residues in contact with SER1637 (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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1633r GLU 2.9 15.9 + - - -
1634r GLN* 4.2 2.5 - - - -
1636r PHE* 1.3 77.5 - - - +
1638r SER* 1.3 63.1 + - - +
1639r GLY* 3.2 1.4 + - - -
1656r VAL* 4.8 14.3 - - - +
1657r ALA 6.1 0.7 - - - -
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Residues in contact with SER1638 (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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1634r GLN 2.9 20.2 + - - -
1635r LEU* 4.2 4.5 - - - -
1637r SER* 1.3 76.4 - - - +
1639r GLY* 1.3 59.4 + - - +
1640r ALA* 3.5 4.5 - - - -
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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