Contacts of the helix formed by residues 107 - 117 (chain B) 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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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102B ASP 5.3 0.2 - - - -
103B GLN* 3.9 15.0 - - - -
106B TYR* 1.3 73.8 - - - +
108B PHE* 1.3 60.6 + - - +
109B ASP* 3.7 9.8 + - - +
110B SER* 2.6 35.9 + - - -
111B THR* 2.9 31.3 + - - -
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Residues in contact with PHE 108 (chain B).
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* 4.2 7.2 - + - -
64B HIS* 3.4 48.7 - + + +
65B THR* 5.0 2.2 - - - -
71B SER* 3.5 16.8 - - - -
73B PHE* 3.4 33.7 - + - -
102B ASP 5.9 0.2 - - - -
103B GLN* 3.4 32.4 + - + +
107B SER* 1.3 73.5 - - - +
109B ASP* 1.3 66.1 + - - +
111B THR* 3.4 5.7 + - - -
112B THR* 2.5 53.6 + - + -
183B THR* 3.7 12.3 - - + -
117C LEU* 3.8 24.2 - - + -
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Residues in contact with ASP 109 (chain B).
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* 2.9 32.1 + - - -
65B THR* 4.9 11.7 + - - +
107B SER* 3.2 9.2 + - - +
108B PHE* 1.3 81.7 - - - +
110B SER* 1.3 58.1 + - - +
112B THR* 3.4 2.2 + - - -
113B ALA* 2.9 30.3 + - - +
109C ASP* 3.9 6.4 - - + +
110C SER* 3.5 39.4 + - - +
113C ALA* 3.5 14.3 - - + +
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Residues in contact with SER 110 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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106B TYR* 4.7 14.6 - - - -
107B SER* 2.6 32.5 + - - -
109B ASP* 1.3 74.3 - - - +
111B THR* 1.3 60.9 + - - +
113B ALA* 3.4 2.1 + - - +
114B ALA* 2.9 29.8 + - - +
61C HIS* 4.9 2.3 - - - -
109C ASP* 3.5 29.7 + - - +
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Residues in contact with THR 111 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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73B PHE* 3.9 28.3 - - + -
101B ALA* 4.7 5.4 - - + +
102B ASP 5.1 0.7 + - - -
106B TYR* 4.0 8.9 + - - +
107B SER 2.9 18.3 + - - -
108B PHE* 3.7 7.5 - - - -
110B SER* 1.3 74.5 - - - +
112B THR* 1.3 60.1 + - - +
114B ALA* 3.1 5.7 + - - +
115B ILE* 2.9 39.6 + - + +
145B HIS* 3.3 38.1 + - + +
147B LEU* 4.3 1.8 - - + -
150B LEU* 4.0 6.5 - - + -
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Residues in contact with THR 112 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73B PHE* 4.5 3.2 - - - -
108B PHE* 2.5 46.4 + - + -
109B ASP* 3.7 6.3 - - - -
111B THR* 1.3 76.5 - - - +
113B ALA* 1.3 58.6 + - - +
115B ILE* 3.2 7.7 + - - -
116B MET* 2.9 47.7 + - + +
181B LEU* 4.7 7.9 - - + -
113C ALA* 4.6 9.6 - - + -
116C MET* 5.8 1.1 - - + -
117C LEU* 4.0 33.7 - - + -
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Residues in contact with ALA 113 (chain B).
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 2.9 17.9 + - - +
110B SER 3.7 4.9 - - - +
112B THR* 1.3 76.1 - - - +
114B ALA* 1.3 58.4 + - - +
116B MET* 4.9 2.5 - - - -
117B LEU* 2.9 41.4 + - + +
61C HIS* 4.1 7.2 - - + +
109C ASP* 3.7 33.4 - - - +
112C THR* 4.6 13.7 - - - -
113C ALA* 5.3 1.7 - - - +
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Residues in contact with ALA 114 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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110B SER 2.9 18.1 + - - +
111B THR* 3.1 6.7 + - - +
113B ALA* 1.3 77.8 - - - +
115B ILE* 1.3 61.4 + - - +
117B LEU 4.1 1.4 + - - -
118B ALA* 4.0 4.7 + - - +
120B TYR* 3.8 0.3 + - - -
137B ARG* 3.0 26.1 + - - +
142B ILE* 3.8 29.6 - - + -
145B HIS* 5.5 1.6 - - + +
150B LEU* 4.1 11.2 - - + -
61C HIS* 4.1 15.4 - - + +
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Residues in contact with ILE 115 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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53B PRO* 3.4 5.1 - - + +
73B PHE* 3.8 35.2 - - + -
75B LEU* 4.7 7.4 - - + -
98B LEU* 4.3 16.8 - - + -
111B THR* 2.9 29.6 + - + +
112B THR* 3.2 4.2 + - - +
114B ALA* 1.3 79.3 - - - +
116B MET* 1.3 61.9 + - - +
117B LEU 3.6 0.2 + - - -
118B ALA 3.9 1.2 + - - -
120B TYR* 2.5 43.0 + - + +
147B LEU* 4.3 7.9 - - + -
150B LEU* 3.8 17.9 - - + -
181B LEU* 3.9 27.1 - - + -
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Residues in contact with MET 116 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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52B ARG* 4.3 0.5 - - - -
53B PRO* 3.2 54.1 - - - +
54B ILE* 3.8 0.4 - - - -
55B ALA* 3.4 30.7 - - + +
112B THR* 2.9 34.2 + - + +
113B ALA* 4.4 2.7 - - - +
115B ILE* 1.3 76.6 - - - +
117B LEU* 1.3 60.6 + - + +
118B ALA 3.3 5.8 + - - +
181B LEU* 3.6 27.8 - - + -
55C ALA* 3.2 19.5 - - + +
112C THR* 6.0 0.7 - - + -
116C MET* 4.0 36.6 - - + -
117C LEU* 5.8 0.2 - - + -
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Residues in contact with LEU 117 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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52B ARG* 3.0 16.8 + - - +
113B ALA* 2.9 22.6 + - + +
114B ALA 4.4 2.2 - - - +
115B ILE 3.4 0.4 - - - -
116B MET* 1.3 78.0 - - + +
118B ALA* 1.3 58.3 + - - +
137B ARG* 4.9 2.1 + - - -
55C ALA* 3.7 22.0 - - + -
59C ILE* 4.1 29.0 - - + +
61C HIS* 3.8 49.5 + - + +
108C PHE* 4.0 19.1 - - + -
112C THR* 4.0 24.9 - - + -
116C MET* 5.8 0.9 - - + -
181C LEU* 5.8 2.9 - - + -
183C THR* 6.1 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