Contacts of the helix formed by residues 1571 - 1581 (chain F) in PDB entry 6C3P
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 SER1571 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1550F VAL* 4.4 11.8 - - - +
1557F LEU* 4.5 9.0 + - - +
1558F GLU* 5.6 0.2 - - - -
1565F LEU* 4.1 23.0 - - - +
1568F ARG* 3.5 25.2 - - - +
1569F LYS 3.1 11.9 - - - +
1570F ASP* 1.3 83.7 - - - +
1572F VAL* 1.3 64.9 + - - +
1573F PHE* 3.2 18.3 + - - +
1574F ALA* 3.3 10.4 + - - +
1575F SER* 4.1 1.6 + - - -
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Residues in contact with VAL1572 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1379F ARG* 6.4 0.2 - - - +
1550F VAL* 5.5 5.4 - - + +
1557F LEU* 5.8 7.6 - - + -
1570F ASP 4.9 3.1 - - - +
1571F SER* 1.3 73.9 + - - +
1573F PHE* 1.3 59.7 + - - +
1574F ALA 3.1 2.2 - - - -
1575F SER* 3.0 16.3 + - - +
1576F PHE* 2.9 53.6 + - + -
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Residues in contact with PHE1573 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1377F CYS* 3.6 20.4 - - - -
1539F VAL* 3.5 27.1 - - + -
1542F ILE* 3.4 27.4 - - + -
1543F LEU* 3.7 27.8 - - + -
1548F VAL* 4.6 15.7 - - + -
1550F VAL* 4.0 15.7 - - + +
1562F PRO* 5.3 4.7 - - + -
1565F LEU* 4.8 15.7 - - + -
1566F LEU* 5.3 8.1 - - + -
1571F SER* 3.1 14.5 + - - +
1572F VAL* 1.3 76.5 - - - +
1574F ALA* 1.3 61.4 + - - +
1576F PHE* 3.3 16.6 - + + +
1577F VAL* 2.9 37.0 + - + +
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Residues in contact with ALA1574 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1565F LEU 4.2 8.8 + - - +
1566F LEU* 4.7 6.5 - - - +
1569F LYS* 3.4 37.7 - - + +
1571F SER* 3.3 16.4 + - - +
1572F VAL 3.1 0.2 - - - -
1573F PHE* 1.3 80.2 - - - +
1575F SER* 1.3 58.4 + - - +
1577F VAL* 3.1 11.0 - - - +
1578F ARG* 2.9 37.6 + - + +
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Residues in contact with SER1575 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1569F LYS 5.5 0.9 + - - -
1571F SER 4.1 1.4 + - - -
1572F VAL* 3.0 23.2 + - - +
1574F ALA* 1.3 78.4 - - - +
1576F PHE* 1.3 61.3 + - - +
1578F ARG* 4.3 6.1 - - - -
1579F ALA* 2.9 33.6 + - - +
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Residues in contact with PHE1576 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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861F ILE* 4.4 17.4 - - + +
862F HIS* 3.3 37.0 - + - -
1377F CYS* 5.0 2.9 - - - -
1378F GLY* 4.3 21.1 - - - -
1379F ARG* 4.5 15.3 - - - -
1539F VAL* 4.1 12.9 - - + +
1550F VAL* 4.6 11.2 - - + -
1551F LEU 6.0 0.2 - - - -
1572F VAL* 2.9 38.9 + - + -
1573F PHE* 3.1 36.7 + + + +
1575F SER* 1.3 82.5 - - - +
1577F VAL* 1.3 60.6 + - - +
1579F ALA* 4.2 3.9 - - - +
1580F ASP* 3.3 25.8 + - - +
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Residues in contact with VAL1577 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1539F VAL* 4.1 14.8 - - + +
1540F HIS* 6.1 0.2 - - - -
1543F LEU* 4.0 27.6 - - + -
1566F LEU* 5.1 11.2 - - + -
1573F PHE* 2.9 27.7 + - + +
1574F ALA* 3.1 21.1 - - - +
1576F PHE* 1.3 75.5 - - - +
1578F ARG* 1.3 81.2 + - - +
1580F ASP* 3.6 1.8 + - + +
1581F LYS* 2.9 26.4 + - - +
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Residues in contact with ARG1578 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1569F LYS* 6.3 2.0 - - + -
1574F ALA* 2.9 29.1 + - + +
1575F SER* 3.3 5.8 + - - +
1577F VAL* 1.3 102.1 + - + +
1579F ALA* 1.3 65.0 + - - +
1580F ASP 3.1 1.9 + - - -
1581F LYS* 3.6 30.9 + - - +
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Residues in contact with ALA1579 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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861F ILE* 5.2 9.4 - - + -
865F ASP* 4.8 14.3 - - - +
891F GLN* 4.2 5.4 - - - +
1575F SER 2.9 17.0 + - - +
1576F PHE* 4.2 5.8 - - - +
1578F ARG* 1.3 76.0 - - - +
1580F ASP* 1.3 64.7 + - - +
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Residues in contact with ASP1580 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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861F ILE* 3.6 31.0 - - - +
865F ASP* 5.6 0.9 - - - +
891F GLN* 3.2 40.2 + - - +
1538F ARG* 5.9 1.4 + - - -
1539F VAL* 3.4 23.1 + - + +
1540F HIS* 6.4 1.3 - - + -
1576F PHE 3.3 14.9 + - - +
1577F VAL* 3.6 8.6 + - + +
1578F ARG 3.1 0.4 - - - -
1579F ALA* 1.3 82.4 - - - +
1581F LYS* 1.3 76.6 + - - +
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Residues in contact with LYS1581 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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891F GLN* 4.5 5.0 + - - +
929F THR* 3.8 9.2 - - - +
930F LEU* 3.1 36.5 - - - +
1540F HIS* 6.3 2.0 - - - -
1577F VAL* 2.9 22.6 + - - -
1578F ARG* 3.6 30.0 + - - +
1580F ASP* 1.3 87.1 - - - +
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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
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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