Contacts of the helix formed by residues 104 - 114 (chain C) in PDB entry 3WHD
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 THR 104 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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103C LYS* 1.3 73.9 - - - +
105C TRP* 1.3 56.2 + - - +
106C ALA* 3.7 5.9 + - - +
107C GLU* 3.2 29.6 + - + +
108C SER* 2.7 34.5 + - - -
142C PHE* 3.7 1.6 - - - -
199C CYS 3.9 8.5 - - - -
200C ASN* 3.8 22.9 - - + +
201C PHE 3.3 8.7 - - - -
202C GLU* 4.1 14.6 + - + +
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Residues in contact with TRP 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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104C THR* 1.3 75.1 - - - +
106C ALA* 1.3 73.0 + - + +
108C SER* 3.2 3.9 + - - -
109C GLU* 2.9 33.0 + - + +
119C LEU* 3.3 17.9 - - + +
142C PHE* 3.4 35.7 - + + -
143C LEU 2.9 22.3 + - - -
144C GLY 3.9 20.4 - - - -
145C LEU 4.4 1.8 + - - -
146C ARG* 3.6 45.8 - - + -
157C VAL* 3.9 27.8 - - + -
182C CYS* 3.1 31.1 - - + +
199C CYS* 3.1 19.9 + - + +
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Residues in contact with ALA 106 (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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104C THR* 3.3 6.1 + - - +
105C TRP* 1.3 95.1 - - + +
107C GLU* 1.3 60.0 + - + +
109C GLU* 3.4 3.8 + - - +
110C ARG* 3.0 28.4 + - - +
146C ARG* 6.1 1.6 - - - +
199C CYS* 4.5 1.8 + - - +
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Residues in contact with GLU 107 (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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103C LYS* 3.7 28.5 + - + +
104C THR* 3.2 25.1 + - + +
106C ALA* 1.3 80.1 - - + +
108C SER* 1.3 56.8 + - - +
110C ARG* 3.0 48.5 + - - +
111C ASN* 3.0 28.2 + - - +
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Residues in contact with SER 108 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103C LYS* 3.4 19.3 + - - +
104C THR 2.7 24.4 + - - -
105C TRP* 3.2 8.5 + - - -
107C GLU* 1.3 74.5 - - - +
109C GLU* 1.3 59.7 + - - +
111C ASN* 3.1 4.3 + - - +
112C CYS* 3.0 31.5 + - - -
119C LEU* 4.0 14.8 - - - -
142C PHE* 3.8 8.9 - - - -
203C ALA 4.5 1.9 + - - -
205C ARG* 3.6 27.4 - - - +
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Residues in contact with GLU 109 (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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105C TRP* 2.9 27.6 + - + +
106C ALA* 3.9 3.8 - - - +
108C SER* 1.3 75.6 - - - +
110C ARG* 1.3 57.4 + - - +
112C CYS* 3.3 1.5 + - - +
113C SER* 2.7 38.0 + - - -
118C HIS* 2.7 32.3 + - - -
119C LEU* 2.9 41.6 + - + +
157C VAL* 3.4 30.4 - - + +
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Residues in contact with ARG 110 (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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103C LYS* 5.8 1.8 - - - +
106C ALA 3.0 18.2 + - - +
107C GLU* 3.0 44.5 + - - +
109C GLU* 1.3 78.1 - - - +
111C ASN* 1.3 57.3 + - - +
113C SER* 3.3 7.4 + - - -
114C GLY* 3.0 26.0 + - - -
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Residues in contact with ASN 111 (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 LEU* 3.6 11.8 - - - +
103C LYS* 4.0 14.9 - - - +
107C GLU 3.0 14.7 + - - +
108C SER 3.1 8.3 + - - +
110C ARG* 1.3 80.4 - - - +
112C CYS* 1.3 62.2 + - - +
114C GLY* 3.4 7.6 + - - -
115C MET* 3.6 20.9 + - - +
205C ARG* 2.9 39.2 + - - +
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Residues in contact with CYS 112 (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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108C SER 3.0 10.2 + - - -
109C GLU* 3.6 6.7 - - - +
111C ASN* 1.3 75.8 - - - +
113C SER* 1.3 53.6 + - - +
115C MET* 2.9 13.8 + - - -
117C ALA* 2.8 32.2 + - - +
118C HIS* 3.7 20.6 - - - -
119C LEU* 3.5 33.7 - - - +
205C ARG* 4.5 2.5 - - - -
206C ILE 4.4 0.2 - - - -
207C CYS* 2.1 52.7 - - - -
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Residues in contact with SER 113 (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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60C MET* 5.4 0.9 - - - +
109C GLU* 2.7 30.3 + - - -
110C ARG* 3.4 11.2 - - - -
112C CYS* 1.3 72.4 - - - +
114C GLY* 1.3 55.2 + - - +
116C GLY* 2.8 24.6 + - - -
117C ALA 3.3 12.1 + - - -
118C HIS* 5.2 4.9 - - - -
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Residues in contact with GLY 114 (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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60C MET* 4.0 16.0 - - - +
110C ARG 3.0 15.6 + - - -
111C ASN* 3.4 3.8 + - - -
112C CYS 3.3 0.6 - - - -
113C SER* 1.3 74.8 - - - +
115C MET* 1.3 60.4 + - - +
116C GLY 3.3 1.5 + - - -
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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