Contacts of the helix formed by residues 1617 - 1629 (chain A) in PDB entry 5M64
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 THR1617 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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461A GLU* 3.7 12.6 + - - -
1600A ARG* 4.1 17.2 + - - +
1616A GLU* 1.3 89.9 + - + +
1618A THR* 1.3 58.9 + - - +
1619A CYS* 3.1 4.7 + - - +
1620A GLN* 3.5 15.1 + - - +
1621A PHE* 3.0 45.7 + - - -
17T G 3.3 44.4 - - - +
18T C 3.7 5.5 + - - +
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Residues in contact with THR1618 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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460A LEU* 3.7 20.2 - - + -
461A GLU* 3.2 20.5 + - - +
467A PHE* 3.3 25.3 - - + -
1613A MET* 3.2 39.0 - - - +
1616A GLU 3.2 3.3 - - - -
1617A THR* 1.3 76.8 - - - +
1619A CYS* 1.3 59.5 + - - +
1621A PHE* 4.1 7.2 - - - -
1622A LEU* 2.9 38.9 + - + +
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Residues in contact with CYS1619 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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89A LEU* 4.7 16.6 - - + +
457A LYS* 3.6 37.2 - - + -
460A LEU* 4.9 4.3 - - - -
461A GLU* 4.1 18.4 - - - -
1617A THR* 3.1 2.2 - - - -
1618A THR* 1.3 80.3 - - - +
1620A GLN* 1.3 66.1 + - - +
1622A LEU* 3.0 10.3 + - - +
1623A THR* 3.0 25.9 + - - +
17T G 5.2 5.4 - - - +
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Residues in contact with GLN1620 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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93A GLN* 6.1 0.4 - - - +
1617A THR* 3.5 13.0 + - - +
1619A CYS* 1.3 78.4 - - - +
1621A PHE* 1.3 66.2 + - + +
1623A THR* 2.2 37.6 + - + +
1624A LYS* 3.0 15.8 + - + +
16T C 4.1 10.4 + - - +
17T G 3.7 29.6 + - - +
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Residues in contact with PHE1621 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1025A LYS* 5.6 4.3 - - - -
1600A ARG* 3.6 37.9 - - + -
1604A GLU* 5.3 5.2 - - + -
1612A LYS* 3.3 48.6 - - + +
1613A MET* 3.5 22.3 - - - +
1615A TYR* 6.0 0.4 - + - -
1616A GLU 3.2 21.1 - - - -
1617A THR* 3.0 32.9 + - - +
1618A THR 4.1 1.1 - - - +
1620A GLN* 1.3 85.0 - - + +
1622A LEU* 1.3 58.0 + - - +
1624A LYS* 3.5 9.5 + - + +
1625A ALA* 3.0 27.7 + - - +
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Residues in contact with LEU1622 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16A PHE* 5.6 7.9 - - + -
460A LEU* 6.6 0.2 - - + -
467A PHE* 5.9 1.8 - - + -
1613A MET* 3.6 24.2 - - + -
1618A THR* 2.9 40.6 + - + +
1619A CYS* 3.4 6.3 - - - +
1621A PHE* 1.3 73.9 - - - +
1623A THR* 1.3 61.8 + - + +
1625A ALA* 4.3 3.1 - - + -
1626A VAL* 2.9 42.9 + - + +
1189B LEU* 5.0 13.2 - - + -
1192B MET* 3.8 31.9 - - + -
1194B ILE* 5.2 9.5 - - + +
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Residues in contact with THR1623 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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88A PRO 5.2 0.9 - - - +
89A LEU* 3.1 47.1 - - + +
90A PHE* 4.7 5.7 - - - -
93A GLN* 4.5 18.2 + - - +
1619A CYS 3.1 15.9 - - - +
1620A GLN* 2.2 38.9 + - + +
1622A LEU* 1.3 77.9 - - + +
1624A LYS* 1.3 60.9 + - - +
1627A LEU* 3.0 31.5 + - - +
1194B ILE* 6.5 0.9 - - - -
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Residues in contact with LYS1624 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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93A GLN* 4.3 22.5 + - - +
217A LYS* 4.9 23.8 - - + +
220A VAL* 5.4 7.5 - - + +
221A HIS* 4.2 22.8 + - - -
224A HIS* 5.6 4.4 + - - -
1612A LYS* 6.2 3.6 - - + -
1620A GLN* 3.0 13.9 + - + +
1621A PHE* 3.9 12.8 - - + +
1623A THR* 1.3 82.4 + - - +
1625A ALA* 1.3 63.2 + - - +
1627A LEU* 4.0 11.2 - - + +
1628A ASP* 3.8 11.1 + - - +
1630A GLU* 3.4 8.1 - - - +
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Residues in contact with ALA1625 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16A PHE* 4.3 15.3 - - + -
1609A SER* 4.7 3.8 - - - +
1613A MET* 3.8 20.0 - - + -
1621A PHE 3.0 17.4 + - - +
1622A LEU* 3.9 3.6 - - - +
1623A THR 3.3 0.4 - - - -
1624A LYS* 1.3 75.6 - - - +
1626A VAL* 1.3 61.7 + - + +
1628A ASP 3.2 1.4 + - - -
1629A ASN* 2.9 16.8 + - - -
1630A GLU* 2.9 35.1 - - - +
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Residues in contact with VAL1626 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16A PHE* 4.0 20.6 - - + -
17A GLY* 3.5 33.9 - - - +
18A ILE* 5.1 3.8 - - + -
90A PHE* 4.2 14.3 - - + -
1622A LEU* 2.9 25.9 + - + +
1625A ALA* 1.3 73.0 - - + +
1627A LEU* 1.3 65.7 + - - +
1628A ASP 3.3 0.3 + - - -
1629A ASN* 3.4 16.7 + - - +
1194B ILE* 3.6 37.5 - - + -
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Residues in contact with LEU1627 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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90A PHE* 4.3 10.1 - - + -
93A GLN* 3.3 49.4 - - + +
97A TYR* 5.8 1.3 - - + -
220A VAL* 6.1 5.4 - - + -
224A HIS* 6.0 2.2 - - + +
338A VAL 5.7 0.2 - - - +
339A PHE* 3.4 54.5 - - + +
355A PHE* 4.0 20.8 - - + -
1623A THR 3.0 20.9 + - - +
1624A LYS* 4.0 14.6 - - + +
1626A VAL* 1.3 78.0 - - - +
1628A ASP* 1.3 58.5 + - + +
1629A ASN* 5.1 0.3 - - - +
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Residues in contact with ASP1628 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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216A ARG* 2.8 45.7 + - - -
338A VAL 3.9 5.7 - - - +
339A PHE* 3.1 15.8 - - - +
340A HIS* 3.1 18.7 + - - -
341A SER* 3.2 14.4 + - - -
1624A LYS 3.8 5.3 + - - +
1625A ALA 3.2 1.6 + - - -
1627A LEU* 1.3 78.5 - - + +
1629A ASN* 1.3 68.9 + - - +
1630A GLU* 3.3 21.6 - - - +
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Residues in contact with ASN1629 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15A ASP* 3.4 15.8 + - - +
16A PHE* 3.1 34.5 + - - +
17A GLY* 4.6 8.4 - - - -
339A PHE 4.1 7.9 - - - +
340A HIS* 4.6 18.6 + - - -
341A SER 4.2 6.2 + - - -
342A ARG* 5.2 2.1 + - - +
1625A ALA 2.9 12.9 + - - -
1626A VAL* 3.4 14.6 + - - +
1627A LEU 5.1 0.2 - - - +
1628A ASP* 1.3 82.3 - - - +
1630A GLU* 1.3 61.6 + - - +
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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