Contacts of the helix formed by residues 1507 - 1513 (chain B) in PDB entry 3PT6
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 ASN1507 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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978B ARG* 3.5 8.7 - - - +
1464B ASP* 3.1 19.0 + - - -
1466B LYS* 4.5 9.3 - - + +
1467B ASN* 2.8 41.1 + - - +
1482B ALA* 5.7 1.4 - - - +
1503B PRO 5.3 2.0 + - - -
1504B HIS 5.5 0.6 - - - +
1505B THR* 3.3 1.3 - - - -
1506B GLY* 1.3 77.2 - - - +
1508B ARG* 1.3 62.4 + - + +
1509B HIS 3.5 0.3 + - - -
1510B ASN* 4.1 5.2 + - - -
1511B HIS* 3.1 20.4 - - - -
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Residues in contact with ARG1508 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1481B CYS* 5.4 15.2 + - - +
1505B THR* 3.3 8.3 + - - +
1506B GLY 3.2 0.8 - - - -
1507B ASN* 1.3 80.3 - - - +
1509B HIS* 1.3 80.1 + - + +
1510B ASN 3.7 0.9 - - - -
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Residues in contact with HIS1509 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1505B THR* 3.0 29.4 - - - +
1506B GLY 3.0 3.2 + - - -
1508B ARG* 1.3 95.7 + - + +
1510B ASN* 1.3 70.5 + - - +
1511B HIS 3.1 3.1 + - - -
1512B TRP* 3.2 61.2 + + + +
1537B LYS* 5.4 5.5 + - - -
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Residues in contact with ASN1510 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1440B ARG* 5.3 0.2 + - - -
1506B GLY 3.3 1.8 + - - -
1507B ASN 4.1 4.8 + - - -
1508B ARG 3.7 2.0 + - - -
1509B HIS* 1.3 78.7 - - - +
1511B HIS* 1.3 75.8 + - - +
1512B TRP 3.3 0.8 + - - -
1513B ALA* 3.9 17.7 + - + +
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Residues in contact with HIS1511 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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978B ARG* 3.2 53.5 + - + +
980B TYR* 2.9 50.5 + + - -
1439B TRP* 3.2 15.5 + - - -
1440B ARG* 3.3 7.7 + - - +
1467B ASN* 4.7 0.9 - - - -
1506B GLY* 2.7 20.9 + - - -
1507B ASN* 3.1 36.1 - - - -
1510B ASN* 1.3 80.1 - - - +
1512B TRP* 1.3 59.5 + - - +
1513B ALA 2.7 16.1 + - - -
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Residues in contact with TRP1512 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1439B TRP* 3.4 15.5 + + + +
1501B CYS 4.5 0.8 + - - -
1502B LEU* 3.5 24.5 + - + +
1505B THR* 3.2 25.7 + - - -
1506B GLY* 3.5 29.6 - - - +
1509B HIS* 3.2 54.7 + + + -
1510B ASN 3.3 2.0 - - - -
1511B HIS* 1.3 75.8 - - - +
1513B ALA* 1.3 66.2 + - - +
1514B GLY 3.1 0.3 + - - -
1515B LEU* 2.9 54.3 + - + +
1536B GLY 5.8 0.9 - - - -
1537B LYS* 4.8 25.4 - - + -
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Residues in contact with ALA1513 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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985B LYS* 4.1 17.1 + - + +
1440B ARG* 3.1 31.0 - - - +
1509B HIS 5.0 0.2 + - - -
1510B ASN* 3.9 18.9 + - + +
1511B HIS 2.7 7.7 + - - -
1512B TRP* 1.3 72.4 - - - +
1514B GLY* 1.3 58.7 + - - +
1515B LEU* 3.7 3.3 + - - +
1537B LYS 5.7 0.5 - - - +
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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
------------------------------------------------------------
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