Contacts of the strand formed by residues 1559 - 1563 (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 VAL1559 (chain r).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1550r ILE* 5.5 11.0 - - + -
1554r SER* 5.4 3.8 - - - +
1557r LYS 4.2 4.7 - - - +
1558r PRO* 1.3 75.0 - - - +
1560r ILE* 1.3 61.7 + - - +
1642r GLN 2.9 13.8 + - - +
1643r VAL* 3.3 10.2 - - + +
1644r VAL* 2.9 26.9 + - - +
1658r ALA* 4.3 3.1 - - - +
1660r LEU* 3.3 17.0 - - + +
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Residues in contact with ILE1560 (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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1559r VAL* 1.3 75.4 - - - +
1561r VAL* 1.3 62.2 + - - +
1562r PHE 4.2 1.0 + - - -
1644r VAL* 3.5 9.0 - - + +
1646r ALA* 6.1 3.4 - - + -
1657r ALA 6.1 0.2 - - - -
1658r ALA* 4.0 15.1 - - + +
1660r LEU 3.0 8.4 + - - +
1661r VAL* 3.4 11.5 - - + +
1662r ILE* 3.0 24.3 + - - +
1690r HIS* 5.8 6.5 - - + +
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Residues in contact with VAL1561 (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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1559r VAL 4.3 0.2 + - - -
1560r ILE* 1.3 74.3 - - - +
1562r PHE* 1.3 59.3 + - - +
1563r VAL* 5.0 1.1 - - - +
1572r THR* 6.3 2.0 - - - -
1644r VAL 3.0 9.4 + - - +
1645r VAL* 3.5 15.9 - - + +
1646r ALA* 2.7 33.8 + - - +
1662r ILE* 3.4 15.9 - - + +
1664r MET* 6.2 2.2 - - + -
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Residues in contact with PHE1562 (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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1560r ILE 4.2 1.2 - - - -
1561r VAL* 1.3 73.1 - - - +
1563r VAL* 1.3 59.4 + - - +
1646r ALA* 3.3 8.5 - - + +
1647r SER 5.1 1.1 - - - +
1648r ARG* 4.9 12.1 - - + -
1651r CYS* 6.0 3.4 - - + -
1662r ILE 3.2 9.0 + - - +
1663r ILE* 4.7 10.5 - - + -
1664r MET* 3.1 32.4 + - - +
1687r MET* 5.1 14.1 - - + -
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Residues in contact with VAL1563 (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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1561r VAL 5.0 2.0 - - - +
1562r PHE* 1.3 76.4 - - - +
1564r PRO* 1.3 62.7 - - - +
1565r SER 3.3 5.6 + - - +
1568r GLN* 4.2 27.8 - - + +
1569r THR* 4.7 5.4 - - - +
1572r THR* 5.6 5.8 - - - -
1645r VAL* 6.2 1.6 - - + -
1646r ALA 3.1 13.1 + - - +
1647r SER* 3.9 0.7 - - - -
1648r ARG* 3.1 28.5 + - - +
1664r MET* 4.4 9.4 - - + -
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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