Contacts of the helix formed by residues 1571 - 1581 (chain H) 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 H).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1550H VAL* 4.4 11.3 - - - +
1557H LEU* 4.5 9.1 + - - +
1565H LEU* 4.1 22.9 - - - +
1568H ARG* 3.5 24.9 - - - +
1569H LYS 3.1 11.9 - - - +
1570H ASP* 1.3 82.0 - - - +
1572H VAL* 1.3 66.0 + - - +
1573H PHE* 3.1 17.8 + - - +
1574H ALA* 3.3 10.1 + - - +
1575H SER* 4.1 2.1 + - - -
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Residues in contact with VAL1572 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1379H ARG* 6.4 0.2 - - - +
1550H VAL* 5.5 4.9 - - + +
1557H LEU* 5.8 7.6 - - + -
1570H ASP 4.9 3.8 - - - +
1571H SER* 1.3 72.4 + - - +
1573H PHE* 1.3 59.9 + - - +
1574H ALA 3.1 2.2 - - - -
1575H SER* 3.0 17.8 + - - +
1576H PHE* 2.9 53.2 + - + -
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Residues in contact with PHE1573 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1377H CYS* 3.6 20.9 - - - -
1539H VAL* 3.5 27.6 - - + -
1542H ILE* 3.4 27.8 - - + -
1543H LEU* 3.7 28.9 - - + -
1548H VAL* 4.6 16.2 - - + -
1550H VAL* 4.0 15.0 - - + +
1562H PRO* 5.3 4.3 - - + -
1565H LEU* 4.8 14.8 - - + -
1566H LEU* 5.3 8.1 - - + -
1571H SER* 3.1 14.0 + - - +
1572H VAL* 1.3 74.8 - - - +
1574H ALA* 1.3 61.5 + - - +
1576H PHE* 3.5 16.6 - + + -
1577H VAL* 2.9 35.9 + - + +
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Residues in contact with ALA1574 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1565H LEU 4.2 9.2 + - - +
1566H LEU* 4.7 6.7 - - - +
1569H LYS* 3.4 37.7 - - + +
1571H SER* 3.3 16.6 + - - +
1572H VAL 3.1 0.2 - - - -
1573H PHE* 1.3 79.9 - - - +
1575H SER* 1.3 56.8 + - - +
1577H VAL* 3.1 9.8 - - - +
1578H ARG* 2.9 38.0 + - + +
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Residues in contact with SER1575 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1569H LYS 5.5 1.0 + - - -
1571H SER 4.1 1.2 + - - -
1572H VAL* 3.0 24.0 + - - +
1574H ALA* 1.3 78.4 - - - +
1576H PHE* 1.3 59.9 + - - +
1578H ARG* 3.9 6.5 - - - +
1579H ALA* 2.9 33.8 + - - +
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Residues in contact with PHE1576 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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861H ILE* 4.4 16.1 - - + +
862H HIS* 3.3 36.6 - + - -
1377H CYS* 5.0 2.5 - - - -
1378H GLY* 4.3 22.2 - - - -
1379H ARG* 4.5 15.7 - - - -
1539H VAL* 4.3 13.0 - - + -
1550H VAL* 4.6 10.8 - - + -
1572H VAL* 2.9 37.3 + - + -
1573H PHE* 3.1 36.7 + + + +
1575H SER* 1.3 81.0 - - - +
1577H VAL* 1.3 59.4 + - - +
1579H ALA* 3.9 4.0 + - - +
1580H ASP* 3.3 26.3 + - - +
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Residues in contact with VAL1577 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1539H VAL* 4.1 15.3 - - + -
1540H HIS* 6.1 0.4 - - - -
1543H LEU* 4.0 27.4 - - + -
1566H LEU* 5.1 10.8 - - + -
1573H PHE* 2.9 26.2 + - + +
1574H ALA* 3.1 21.1 - - - +
1576H PHE* 1.3 76.3 - - - +
1578H ARG* 1.3 83.0 + - + +
1580H ASP* 3.9 1.5 - - + +
1581H LYS* 2.9 26.5 + - - -
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Residues in contact with ARG1578 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1569H LYS* 6.3 2.2 - - + -
1574H ALA* 2.9 28.9 + - + +
1575H SER* 3.9 6.5 - - - +
1577H VAL* 1.3 102.0 + - + +
1579H ALA* 1.3 64.9 + - - +
1580H ASP 3.1 2.1 + - - -
1581H LYS* 3.6 30.9 + - - +
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Residues in contact with ALA1579 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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861H ILE* 5.2 8.7 - - + -
865H ASP* 4.8 14.4 - - - +
891H GLN* 4.2 5.5 - - - +
1575H SER 2.9 17.8 + - - +
1576H PHE* 4.2 4.9 - - - +
1578H ARG* 1.3 76.4 - - - +
1580H ASP* 1.3 65.4 + - - +
1581H LYS* 5.2 0.2 - - - +
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Residues in contact with ASP1580 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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861H ILE* 3.6 29.5 - - - +
865H ASP* 5.6 1.2 - - - +
889H LYS* 6.1 0.2 - - - +
891H GLN* 3.2 39.2 + - - +
1538H ARG* 5.9 2.0 + - - -
1539H VAL* 3.4 22.5 + - + +
1540H HIS* 6.1 2.0 - - + +
1576H PHE 3.3 15.7 + - - +
1577H VAL* 3.6 8.0 + - + +
1578H ARG 3.1 0.6 - - - -
1579H ALA* 1.3 81.9 - - - +
1581H LYS* 1.3 78.0 + - - +
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Residues in contact with LYS1581 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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891H GLN* 4.5 4.5 + - - +
929H THR* 3.8 9.3 - - - +
930H LEU* 3.1 37.3 - - - +
1540H HIS* 6.3 2.0 - - - -
1577H VAL* 2.9 22.2 + - - -
1578H ARG* 3.6 30.7 + - - +
1580H ASP* 1.3 87.0 - - - +
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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