Contacts of the helix formed by residues 107 - 117 (chain C) in PDB entry 4LDD
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 SER 107 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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102C ASP 5.2 0.2 - - - -
103C GLN* 3.9 15.7 - - - -
106C TYR* 1.3 74.1 - - - +
108C PHE* 1.3 59.8 - - - +
109C ASP* 3.7 9.3 + - - +
110C SER* 2.6 35.5 + - - -
111C THR* 2.9 30.9 + - - -
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Residues in contact with PHE 108 (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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117B LEU* 4.0 22.7 - - + -
59C ILE* 5.5 0.2 - - + -
61C HIS* 4.2 8.1 - + - -
64C HIS* 3.4 48.7 - + + +
65C THR* 5.0 2.9 - - - +
71C SER* 3.5 17.0 - - - -
73C PHE* 3.4 33.7 - + - -
102C ASP 5.9 0.2 - - - -
103C GLN* 3.4 32.4 + - + +
107C SER* 1.3 72.4 - - - +
109C ASP* 1.3 63.8 + - - +
111C THR* 3.4 5.7 + - - -
112C THR* 2.5 54.0 + - + -
183C THR* 3.7 13.0 - - + -
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Residues in contact with ASP 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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109B ASP* 3.9 6.3 - - + +
110B SER* 3.5 40.8 + - - +
113B ALA* 3.7 9.2 - - + +
61C HIS* 2.9 33.7 + - - -
65C THR* 4.9 12.4 + - - +
107C SER* 3.2 8.9 - - - +
108C PHE* 1.3 82.6 - - - +
110C SER* 1.3 57.6 + - - +
112C THR* 3.4 2.8 + - - -
113C ALA* 2.9 30.1 + - - +
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Residues in contact with SER 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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61B HIS* 4.8 2.6 - - - -
109B ASP* 3.5 27.6 + - - +
106C TYR* 4.7 15.0 - - - -
107C SER* 2.6 32.6 + - - -
109C ASP* 1.3 74.3 - - - +
111C THR* 1.3 60.4 + - - +
113C ALA* 3.4 1.9 + - - +
114C ALA* 2.9 29.5 + - - +
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Residues in contact with THR 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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73C PHE* 3.9 28.9 - - + -
101C ALA* 4.7 5.0 - - + +
102C ASP 5.1 0.7 + - - -
106C TYR* 4.0 8.7 + - - +
107C SER 2.9 18.4 + - - -
108C PHE* 3.7 7.5 - - - -
110C SER* 1.3 73.9 - - - +
112C THR* 1.3 59.1 + - - +
114C ALA* 3.1 4.9 + - - +
115C ILE* 2.9 40.4 + - + +
145C HIS* 3.3 38.8 + - + +
147C LEU* 4.3 1.1 - - + -
150C LEU* 4.0 6.5 - - + -
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Residues in contact with THR 112 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
113B ALA* 4.6 9.2 - - + -
116B MET* 6.0 0.9 - - + -
117B LEU* 4.0 31.4 - - + -
73C PHE* 4.5 3.6 - - + -
108C PHE* 2.5 46.4 + - + -
109C ASP* 3.7 6.1 - - - -
111C THR* 1.3 75.9 - - - +
113C ALA* 1.3 58.9 + - - +
115C ILE* 3.2 8.4 + - - +
116C MET* 2.9 49.1 + - + +
181C LEU* 4.7 8.1 - - + -
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Residues in contact with ALA 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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61B HIS* 4.0 6.3 - - + +
109B ASP* 3.5 37.9 - - + +
112B THR* 4.6 12.3 - - - -
113B ALA* 5.3 2.0 - - - +
109C ASP 2.9 18.5 + - - +
110C SER 3.7 3.4 - - - +
112C THR* 1.3 77.3 - - - +
114C ALA* 1.3 58.5 + - - +
116C MET* 4.9 2.0 - - - -
117C LEU* 2.9 42.1 + - + +
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Residues in contact with ALA 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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61B HIS* 4.0 17.0 - - + +
110C SER 2.9 17.7 + - - +
111C THR* 3.1 7.2 + - - +
113C ALA* 1.3 76.3 - - - +
115C ILE* 1.3 61.5 + - - +
117C LEU 4.1 1.7 + - - -
118C ALA* 4.0 4.2 - - - +
120C TYR* 3.8 0.2 + - - -
137C ARG* 3.0 26.7 + - - +
142C ILE* 3.8 29.6 - - + -
145C HIS* 5.5 1.6 - - + +
150C LEU* 4.1 11.2 - - + -
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Residues in contact with ILE 115 (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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53C PRO* 3.4 5.0 - - + +
73C PHE* 3.8 33.9 - - + -
75C LEU* 4.7 7.4 - - + -
98C LEU* 4.3 17.0 - - + -
111C THR* 2.9 29.6 + - + +
112C THR* 3.7 4.3 - - - +
114C ALA* 1.3 77.4 - - - +
116C MET* 1.3 61.5 + - - +
117C LEU 3.6 0.3 + - - -
118C ALA 3.9 1.0 + - - -
120C TYR* 2.5 42.3 + - + +
147C LEU* 4.3 8.7 - - + -
150C LEU* 3.8 19.1 - - + -
181C LEU* 3.9 28.0 - - + -
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Residues in contact with MET 116 (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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55B ALA* 3.2 19.6 - - - +
112B THR* 5.8 0.9 - - + -
116B MET* 4.0 34.8 - - + -
117B LEU* 5.8 0.2 - - + -
52C ARG* 4.3 0.5 - - - -
53C PRO* 3.2 50.8 - - - +
54C ILE* 3.8 0.2 - - - -
55C ALA* 3.4 31.9 - - + +
112C THR* 2.9 33.9 + - + +
113C ALA* 4.4 3.4 - - - +
115C ILE* 1.3 76.9 - - - +
117C LEU* 1.3 61.6 + - + +
118C ALA 3.3 5.9 + - - +
181C LEU* 3.6 27.4 - - + -
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Residues in contact with LEU 117 (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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55B ALA* 3.9 20.6 - - + -
59B ILE* 4.1 26.9 - - + +
61B HIS* 3.8 41.2 + - + +
108B PHE* 3.8 31.2 - - + -
112B THR* 4.0 25.6 - - + -
116B MET* 5.8 0.9 - - + -
181B LEU* 5.8 2.5 - - + -
183B THR* 6.0 0.2 - - + -
52C ARG* 3.1 14.4 + - - +
113C ALA* 2.9 21.4 + - + +
114C ALA 4.4 2.0 - - - +
115C ILE 3.4 0.4 - - - -
116C MET* 1.3 77.0 - - + +
118C ALA* 1.3 60.4 + - - +
137C ARG* 4.9 2.1 + - - -
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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