Contacts of the helix formed by residues 1570 - 1581 (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 ASN1570 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1388A GLU* 3.5 35.9 + - + +
1569B GLY* 1.3 78.7 - - - +
1571B ILE* 1.3 64.5 + - + +
1572B LEU* 3.7 23.7 - - - +
1573B ASP* 2.6 46.6 + - - +
1574B ARG* 3.1 20.0 + - - +
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Residues in contact with ILE1571 (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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1416B ILE* 3.8 19.7 - - + +
1417B CYS* 3.4 44.2 - - - +
1418B LYS* 3.7 13.0 - - + +
1552B VAL* 3.8 15.7 - - + -
1570B ASN* 1.3 79.9 - - + +
1572B LEU* 1.3 73.4 + - + +
1574B ARG* 3.5 9.8 + - - +
1575B HIS* 3.0 33.6 + - + +
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Residues in contact with LEU1572 (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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695B PRO 4.3 5.8 - - - +
696B ASN* 3.8 38.1 - - - +
697B LEU 4.7 2.0 - - - +
698B ALA* 4.2 16.6 - - + -
1418B LYS* 3.9 20.0 - - + -
1530B THR 4.4 0.2 - - - +
1531B ASN* 3.7 26.0 - - - +
1570B ASN* 3.3 14.3 + - - +
1571B ILE* 1.3 92.0 - - + +
1573B ASP* 1.3 69.5 + - - +
1575B HIS* 3.3 8.9 + - + +
1576B ARG* 3.1 30.7 + - - +
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Residues in contact with ASP1573 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1388A GLU* 5.6 0.5 - - - +
1173B TRP* 3.6 30.1 - - + -
1175B PRO* 3.5 19.3 - - + +
1568B PHE 3.8 10.8 - - - +
1569B GLY* 4.1 2.8 - - - -
1570B ASN* 2.6 44.6 + - - +
1572B LEU* 1.3 78.8 - - - +
1574B ARG* 1.3 63.5 + - - +
1576B ARG 3.3 0.3 + - - -
1577B GLN* 3.1 30.7 + - - +
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Residues in contact with ARG1574 (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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1568A PHE* 6.3 0.6 - - - -
1387B SER* 5.4 4.3 + - - -
1414B ASP* 2.7 47.7 + - - -
1416B ILE* 4.6 9.2 - - - +
1552B VAL* 3.9 14.6 - - + -
1567B PHE* 2.9 40.2 + - + -
1568B PHE* 4.0 8.3 - - - +
1569B GLY 2.7 27.5 + - - +
1570B ASN 3.1 16.4 + - - +
1571B ILE* 3.7 8.1 - - - +
1573B ASP* 1.3 73.4 - - - +
1575B HIS* 1.3 66.4 + - - +
1577B GLN* 3.4 10.5 + - - +
1578B VAL* 3.0 28.3 + - - +
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Residues in contact with HIS1575 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1416B ILE 4.7 0.8 + - - -
1417B CYS* 5.1 0.6 - - - -
1418B LYS* 4.5 10.2 - - + +
1529B VAL 4.2 3.1 + - - +
1530B THR* 3.2 19.6 - - - +
1531B ASN* 4.8 0.7 - - - -
1532B PRO* 3.6 36.1 - - + +
1550B VAL 4.0 6.7 + - - -
1551B SER 4.0 1.8 - - - -
1552B VAL* 3.4 41.8 + - + +
1555B CYS* 3.9 19.2 - - - +
1571B ILE* 3.0 38.7 + - + +
1572B LEU* 3.3 8.9 + - + +
1574B ARG* 1.3 76.3 - - - +
1576B ARG* 1.3 57.8 + - - +
1578B VAL* 3.3 5.4 + - - +
1579B GLY* 2.8 27.9 + - - -
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Residues in contact with ARG1576 (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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698B ALA* 4.0 21.6 - - - +
699B VAL* 2.9 39.9 + - - +
700B LYS* 4.4 6.5 - - - +
702B ALA* 5.7 6.9 - - - +
1173B TRP* 3.6 32.0 - - + -
1530B THR* 3.1 40.3 + - - +
1531B ASN* 4.4 9.9 - - - +
1572B LEU* 3.1 20.6 + - - +
1573B ASP 3.7 4.0 - - - +
1574B ARG 3.2 0.2 - - - -
1575B HIS* 1.3 75.1 - - - +
1577B GLN* 1.3 59.7 + - - +
1580B ASN* 2.8 54.4 + - - +
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Residues in contact with GLN1577 (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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1151B CYS* 3.6 23.9 + - + +
1173B TRP* 3.8 13.7 - - + -
1175B PRO* 3.5 26.2 + - - +
1176B ALA* 4.3 8.7 - - + -
1179B ALA* 3.7 11.6 - - - +
1567B PHE* 3.3 17.4 - - + +
1568B PHE 2.6 44.0 + - - -
1573B ASP 3.1 18.2 + - - +
1574B ARG* 3.4 3.3 + - - +
1576B ARG* 1.3 76.7 - - - +
1578B VAL* 1.3 63.8 + - - +
1580B ASN* 3.6 4.7 + - - +
1581B ALA* 3.3 21.8 + - - +
1603B SAH 4.9 0.5 - - - +
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Residues in contact with VAL1578 (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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1528B THR* 4.5 0.7 - - + -
1552B VAL* 4.4 11.7 - - + +
1555B CYS* 3.5 42.0 - - + +
1556B ALA* 3.7 7.6 - - + +
1559B GLN* 2.9 29.1 + - + +
1561B PHE* 4.4 10.7 - - + -
1567B PHE* 3.8 32.1 - - + -
1574B ARG 3.0 17.9 + - - +
1575B HIS* 3.4 7.2 - - - +
1577B GLN* 1.3 75.8 - - - +
1579B GLY* 1.3 63.1 + - - +
1581B ALA* 3.1 11.1 + - - +
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Residues in contact with GLY1579 (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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1313B ARG* 2.7 29.1 + - - -
1528B THR* 3.9 18.8 - - - +
1529B VAL 4.0 15.3 - - - -
1530B THR* 4.1 11.4 - - - +
1559B GLN* 4.0 0.2 - - - -
1575B HIS 2.8 19.5 + - - -
1576B ARG 3.8 1.1 - - - -
1578B VAL* 1.3 75.1 - - - +
1580B ASN* 1.3 56.2 + - - +
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Residues in contact with ASN1580 (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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702B ALA* 4.5 12.1 - - - +
1173B TRP* 5.3 1.8 - - - -
1269B GLU* 5.4 1.4 - - - +
1313B ARG* 3.9 5.8 + - - +
1315B ARG* 5.4 4.5 + - - -
1530B THR* 3.7 14.7 - - - +
1576B ARG* 2.8 50.8 + - - +
1577B GLN* 4.2 4.7 - - - +
1579B GLY* 1.3 72.7 - - - +
1581B ALA* 1.3 64.3 + - - +
1582B VAL* 5.4 0.7 - - - +
1603B SAH 4.1 48.5 + - + +
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Residues in contact with ALA1581 (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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1151B CYS* 4.3 1.8 - - - -
1153B GLY* 4.1 3.1 - - - +
1313B ARG* 3.3 12.4 + - - -
1315B ARG* 6.1 0.4 - - - -
1559B GLN* 3.3 16.7 + - - +
1561B PHE* 3.7 28.5 - - + -
1577B GLN 3.3 17.0 + - - +
1578B VAL 3.1 9.5 + - - +
1580B ASN* 1.3 79.1 - - - +
1582B VAL* 1.3 62.9 + - - +
1583B PRO* 3.6 1.7 - - - +
1603B SAH 3.3 21.1 - - - +
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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