Contacts of the helix formed by residues 96 - 103 (chain A) in PDB entry 3S3O
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 CYS 96 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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59A LEU* 6.5 1.1 - - + -
62A HIS* 3.5 10.8 - - + +
63A ASN* 4.9 0.7 - - - -
66A HIS* 3.4 14.6 - - - -
92A GLN* 3.0 13.5 + - - +
93A LEU* 3.3 8.3 + - - +
94A GLY 3.6 0.4 - - - -
95A ARG* 1.3 76.2 - - - +
97A GLN* 1.3 66.6 + - - +
98A GLN* 3.2 9.4 + - - -
99A CYS* 3.2 9.8 + - + +
100A LEU* 3.1 24.7 + - - +
393A ZN 2.3 37.5 - - - -
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Residues in contact with GLN 97 (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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95A ARG 3.2 9.8 + - - +
96A CYS* 1.3 70.9 - - - +
98A GLN* 1.3 71.9 + - + +
100A LEU* 3.2 17.7 + - - +
101A ILE* 3.1 42.5 + - + +
339A LYS* 3.5 38.1 - - + +
340A PRO* 4.2 15.0 - - - +
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Residues in contact with GLN 98 (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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66A HIS* 4.2 26.6 + - + +
96A CYS* 3.2 10.2 - - - -
97A GLN* 1.3 87.7 + - + +
99A CYS* 1.3 60.9 + - - +
101A ILE* 3.7 9.1 + - + +
102A THR* 2.8 32.4 + - - +
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Residues in contact with CYS 99 (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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62A HIS* 3.2 17.3 - - + -
66A HIS* 3.4 20.6 - - - -
67A THR 5.5 0.2 - - - -
93A LEU* 4.8 8.1 - - + +
96A CYS* 3.2 12.4 + - + +
98A GLN* 1.3 77.9 - - - +
100A LEU* 1.3 60.8 + - + +
102A THR* 4.9 0.9 - - - -
103A ASN* 3.0 55.3 + - - +
393A ZN 2.3 34.5 - - - -
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Residues in contact with LEU 100 (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 LEU 3.7 16.2 - - - +
94A GLY* 3.6 21.5 - - - +
95A ARG 5.0 0.7 - - - -
96A CYS 3.1 21.8 + - - +
97A GLN* 3.2 21.3 + - - +
99A CYS* 1.3 79.1 - - + +
101A ILE* 1.3 59.0 + - + +
103A ASN* 5.6 0.4 - - - -
324A GLN* 3.0 20.2 + - - +
340A PRO* 4.5 8.3 - - + -
370A LYS* 2.9 27.0 + - - +
372A THR* 4.1 20.2 - - + -
373A SER* 3.9 27.8 - - - +
374A HIS* 4.4 6.7 - - + -
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Residues in contact with ILE 101 (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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97A GLN* 3.1 30.3 + - + +
98A GLN* 3.7 10.8 - - + +
100A LEU* 1.3 81.1 - - + +
102A THR* 1.3 61.0 + - - +
324A GLN* 3.9 6.5 - - - +
335A PRO* 3.5 27.2 - - + +
336A ARG 3.5 4.5 + - - -
337A TRP* 3.0 44.7 + - - +
338A HIS 3.9 20.0 - - - +
339A LYS* 4.2 17.9 - - + +
340A PRO* 4.9 1.1 - - + -
394A SO4 5.4 5.8 - - - +
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Residues in contact with THR 102 (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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98A GLN* 2.8 23.6 + - - +
99A CYS* 4.3 1.1 - - - -
101A ILE* 1.3 83.5 - - - +
103A ASN* 1.3 73.4 - - - +
334A ARG 6.2 0.4 - - - -
335A PRO* 4.2 14.4 - - + +
336A ARG* 4.7 11.8 - - - +
337A TRP* 4.3 3.3 - - - -
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Residues in contact with ASN 103 (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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66A HIS 5.0 5.4 + - - +
67A THR 6.3 0.8 - - - -
99A CYS* 3.0 44.3 + - - +
100A LEU* 5.6 0.2 - - - -
101A ILE 3.9 0.2 - - - -
102A THR* 1.3 85.8 - - - +
104A ALA* 1.3 66.8 + - - +
337A TRP* 3.1 9.8 + - - -
370A LYS* 3.0 22.0 + - - +
374A HIS* 6.2 0.2 + - - -
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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