Contacts of the helix formed by residues 1397 - 1405 (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 SER1397 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1038B TYR 4.2 11.2 - - - -
1039B HIS* 4.7 0.4 - - - +
1366B ARG* 5.7 0.2 - - - -
1372B ASP* 3.5 33.4 - - - -
1375B SER* 5.3 0.4 - - - -
1395B PRO 3.5 1.6 + - - -
1396B LEU* 1.3 81.8 - - - +
1398B TRP* 1.3 61.1 + - - +
1399B PHE 3.9 2.7 - - - -
1400B GLN* 3.1 17.7 + - - -
1401B ARG* 2.8 41.5 + - - +
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Residues in contact with TRP1398 (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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1038B TYR 4.9 0.4 + - - -
1040B THR 3.7 19.3 + - - +
1041B ASP* 3.6 26.7 - - + -
1042B ILE* 3.5 57.5 - - + +
1043B ASN* 4.5 6.5 + - - -
1079B SER* 6.0 3.2 - - - -
1308B GLY* 6.0 0.7 - - - -
1335B HIS* 4.7 7.0 - + - -
1366B ARG* 5.8 3.5 - - - +
1368B ILE* 4.6 8.3 - - + -
1397B SER* 1.3 73.3 - - - +
1399B PHE* 1.3 98.7 + + + +
1401B ARG* 3.3 17.5 + - - +
1402B GLN* 3.0 62.3 + - + +
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Residues in contact with PHE1399 (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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1308B GLY 3.3 26.9 - - - -
1309B VAL* 4.8 4.9 - - + -
1368B ILE* 4.1 14.1 - - + -
1372B ASP* 3.7 19.7 - - + +
1373B THR* 3.5 44.4 - - + -
1397B SER* 3.1 1.2 - - - -
1398B TRP* 1.3 103.5 - + + +
1400B GLN* 1.3 62.3 + - - +
1402B GLN* 3.1 15.4 + - + +
1403B LEU* 3.2 47.2 + - + +
1557B ARG* 3.5 19.5 - - - -
1559B GLN 4.4 3.6 - - - -
1560B GLY* 5.0 2.5 - - - -
1585B PRO* 5.5 2.2 - - + -
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Residues in contact with GLN1400 (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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1372B ASP 3.3 19.5 + - - +
1373B THR 4.0 0.7 - - - +
1374B MET 3.7 2.6 - - - +
1375B SER* 3.0 39.0 + - - +
1376B ASP* 3.1 23.7 + - - +
1395B PRO* 4.2 11.0 - - + -
1396B LEU* 3.1 20.1 + - - +
1397B SER* 3.1 23.4 + - - +
1399B PHE* 1.3 80.7 - - + +
1401B ARG* 1.3 61.5 + - - +
1403B LEU* 3.4 2.6 + - - +
1404B ARG* 3.1 29.9 + - - +
1557B ARG* 3.4 24.7 - - - +
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Residues in contact with ARG1401 (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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1039B HIS 2.5 31.5 + - - -
1040B THR 3.8 2.2 + - - -
1041B ASP* 2.5 32.1 + - - -
1395B PRO* 3.2 35.4 + - + -
1396B LEU 5.3 0.2 - - - -
1397B SER 2.8 20.7 + - - +
1398B TRP* 3.3 29.2 + - - +
1400B GLN* 1.3 72.5 - - - +
1402B GLN* 1.3 64.8 + - - +
1404B ARG* 4.0 2.0 - - - +
1405B GLY* 3.2 25.6 + - - +
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Residues in contact with GLN1402 (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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1080B GLN* 4.7 20.0 + - - +
1398B TRP* 3.0 65.0 + - + +
1399B PHE* 3.5 7.6 - - + +
1400B GLN 3.1 1.0 - - - -
1401B ARG* 1.3 85.1 + - - +
1403B LEU* 1.3 68.2 + - + +
1404B ARG 3.1 5.5 + - - -
1405B GLY* 3.5 9.4 + - - -
1562B PRO* 5.5 1.7 - - - +
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Residues in contact with LEU1403 (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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1399B PHE* 3.2 52.0 + - + +
1400B GLN 3.4 2.4 + - - +
1402B GLN* 1.3 80.4 - - + +
1404B ARG* 1.3 59.2 + - - +
1557B ARG* 3.5 29.4 - - - +
1559B GLN 4.7 1.3 - - - +
1560B GLY* 3.4 26.7 - - - +
1561B PHE 3.8 15.7 - - - +
1562B PRO* 3.7 10.5 - - + +
1563B ASP* 2.8 41.6 + - - +
1564B SER* 4.6 1.7 + - - -
1585B PRO* 6.1 0.7 - - + -
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Residues in contact with ARG1404 (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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1376B ASP* 2.7 40.4 + - - +
1391B TYR* 3.3 52.2 - - + +
1393B GLY 3.4 19.0 + - - -
1394B GLU* 3.9 4.0 + - - +
1395B PRO* 3.6 36.5 - - + +
1400B GLN 3.1 19.1 + - - +
1401B ARG 4.7 0.4 - - - +
1402B GLN 3.1 0.4 - - - -
1403B LEU* 1.3 80.0 - - - +
1405B GLY* 1.3 68.4 + - - +
1407B HIS* 4.1 8.8 - - - +
1409B GLN* 4.8 8.6 + - - +
1557B ARG* 3.9 7.9 - - - +
1563B ASP* 3.5 21.5 - - - +
1564B SER* 5.6 2.6 + - - -
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Residues in contact with GLY1405 (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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1395B PRO* 5.6 2.9 - - - +
1401B ARG* 3.2 20.7 + - - +
1402B GLN 3.5 8.4 + - - -
1404B ARG* 1.3 86.6 - - - +
1406B SER* 1.3 63.4 + - - -
1407B HIS* 3.3 6.2 + - - +
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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