Contacts of the helix formed by residues 100 - 105 (chain C) in PDB entry 1D1T
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 100 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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97C CYS* 3.1 5.4 - - - -
99C GLU* 1.3 82.0 - - - +
101C ASN* 1.3 58.0 + - - +
102C ALA* 4.1 5.8 - - - +
103C CYS* 2.8 13.9 + - - -
104C ARG* 2.8 34.3 + - - +
111C CYS* 3.9 2.0 - - - -
112C ILE* 3.3 44.9 - - + -
375C ZN 2.2 35.7 - - - -
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Residues in contact with ASN 101 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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99C GLU 4.1 0.4 + - - -
100C CYS* 1.3 71.4 - - + +
102C ALA* 1.3 64.5 + - - +
104C ARG* 3.0 8.8 + - - +
105C ASN* 3.0 24.1 + - - +
259D GLY 2.8 19.2 + - - -
260D ASN* 2.6 33.2 + - - +
261D ASN* 4.1 6.7 - - - +
283D HIS* 4.5 2.9 - - - +
286D TYR* 3.4 20.9 + - + +
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Residues in contact with ALA 102 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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100C CYS* 3.4 6.3 - - - -
101C ASN* 1.3 78.5 - - - +
103C CYS* 1.3 59.9 + - - +
105C ASN 3.3 5.1 - - - +
108C GLY 2.8 28.7 - - - +
109C ASN* 4.6 0.9 - - - -
110C LEU 3.3 37.7 - - - +
283D HIS* 4.1 10.9 + - + +
285D ASN* 4.4 2.7 - - - +
286D TYR* 3.5 23.9 - - + -
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Residues in contact with CYS 103 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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95C PRO 4.8 0.2 - - - -
96C GLN* 3.8 21.7 + - + -
97C CYS 3.5 6.7 - - - -
98C ARG* 3.4 32.8 - - - +
99C GLU 4.0 0.4 - - - +
100C CYS* 2.8 11.7 + - - +
102C ALA* 1.3 74.6 - - - +
104C ARG* 1.3 60.9 + - - +
105C ASN 3.1 4.9 - - - -
109C ASN* 5.5 3.6 - - - +
111C CYS* 3.8 7.9 - - - -
323C LYS* 2.9 23.0 + - - +
375C ZN 2.5 32.3 - - - -
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Residues in contact with ARG 104 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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98C ARG 3.1 22.4 + - - -
99C GLU* 3.3 51.2 + - - -
100C CYS 2.8 13.6 + - - +
101C ASN* 3.0 6.9 + - - +
103C CYS* 1.3 73.1 - - - +
105C ASN* 1.3 56.5 + - - +
106C PRO* 3.5 9.9 - - - +
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Residues in contact with ASN 105 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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101C ASN 3.0 14.1 + - - +
102C ALA 4.0 3.8 - - - +
103C CYS 3.1 0.4 - - - -
104C ARG* 1.3 78.1 - - - +
106C PRO* 1.3 62.7 - - - +
107C ASP* 2.8 37.6 + - - +
108C GLY 2.7 37.5 + - - +
323C LYS* 3.1 4.9 + - - -
261D ASN* 5.5 0.4 + - - -
286D TYR* 3.5 40.4 + - + +
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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