Contacts of the strand formed by residues 106 - 114 (chain C) in PDB entry 1DGH
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 LYS 106 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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84C TYR* 3.9 38.7 + - + -
85C PHE 3.1 4.9 - - - +
86C GLU* 3.5 33.6 + - + -
104C GLY 3.4 9.3 + - - +
105C LYS* 1.3 81.4 - - - +
107C THR* 1.3 63.0 + - - +
108C PRO* 4.3 2.6 - - - +
380C ARG* 4.3 14.4 + - - -
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Residues in contact with THR 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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84C TYR* 3.3 3.3 - - - -
85C PHE* 2.8 40.7 + - - -
99C VAL* 3.6 29.1 + - - +
105C LYS* 4.6 9.7 + - - +
106C LYS* 1.3 75.5 + - - +
108C PRO* 1.3 70.4 - - + +
109C ILE* 3.5 2.1 - - - +
136C PHE* 4.2 5.8 - - + -
137C TYR 3.3 38.1 - - - +
138C THR* 4.0 13.7 - - + +
139C GLU* 5.0 2.4 + - - -
380C ARG* 5.1 2.7 + - - +
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Residues in contact with PRO 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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83C GLY 3.6 9.6 - - - +
84C TYR* 4.3 2.9 - - + -
106C LYS 4.3 1.6 - - - +
107C THR* 1.3 87.2 - - + +
109C ILE* 1.3 62.0 + - - +
137C TYR* 3.0 35.0 + - + +
379C TYR* 3.4 26.7 - - + +
380C ARG* 3.6 39.5 - - - +
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Residues in contact with ILE 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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82C PHE* 3.5 7.6 - - - +
83C GLY 3.0 34.0 + - - +
84C TYR 3.4 30.7 - - - +
85C PHE* 3.8 15.7 - - + -
107C THR 3.5 10.5 - - - +
108C PRO* 1.3 80.9 - - - +
110C ALA* 1.3 60.9 + - - +
111C VAL* 4.2 8.3 - - + -
134C VAL* 4.1 8.7 - - + -
135C LYS 3.0 11.7 - - - +
136C PHE* 3.9 14.6 - - + -
137C TYR* 4.1 4.7 - - - -
316C LEU* 3.9 19.7 - - + -
317C VAL 4.0 3.1 - - - +
318C LEU* 3.8 22.9 - - + -
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Residues in contact with ALA 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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81C ALA 3.9 0.4 - - - -
82C PHE* 3.6 18.2 - - + -
109C ILE* 1.3 74.7 - - - +
111C VAL* 1.3 66.7 + - - +
133C ALA 3.8 0.3 - - - +
134C VAL* 3.5 0.3 - - - -
135C LYS* 2.7 38.6 + - + +
137C TYR* 3.5 24.7 - - - +
332C ILE* 3.6 22.4 - - + -
334C PHE* 3.8 2.7 - - - -
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Residues in contact with VAL 111 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80C GLY* 3.1 4.2 - - - -
81C ALA 2.9 36.2 + - - +
82C PHE* 5.1 1.2 - - - -
109C ILE* 4.2 6.3 - - + -
110C ALA* 1.3 82.1 - - - +
112C ARG* 1.3 66.5 + - - +
113C PHE* 3.7 36.1 - - + -
132C PHE* 3.9 13.0 - - + -
133C ALA 3.3 13.5 - - - +
134C VAL* 4.1 20.6 - - + -
316C LEU* 6.2 0.7 - - + -
318C LEU* 3.8 25.8 - - + -
332C ILE* 5.4 2.6 - - - +
334C PHE* 4.3 2.9 - - - -
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Residues in contact with ARG 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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72C ARG* 3.3 40.9 - - - +
75C HIS 3.0 21.2 + - - -
76C ALA 3.0 28.1 + - - -
78C GLY* 3.4 18.4 - - - +
79C ALA 3.1 13.9 - - - +
80C GLY* 4.7 0.9 - - - -
111C VAL* 1.3 76.8 - - - +
113C PHE* 1.3 63.4 + - - +
114C SER* 3.7 10.1 - - - -
131C GLY 3.8 2.9 - - - +
132C PHE* 3.8 0.3 - - - -
133C ALA* 3.1 30.6 + - - +
325C TYR* 4.7 1.6 + - - -
329C VAL* 3.8 25.9 + - + +
330C GLU* 4.7 3.0 + - - -
332C ILE* 3.8 6.7 - - + -
334C PHE* 3.8 13.1 - - + -
2002C HEM 2.7 39.3 + - - +
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Residues in contact with PHE 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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78C GLY* 3.0 3.5 - - - -
79C ALA 2.7 32.9 + - - +
80C GLY* 5.4 0.2 - - - -
81C ALA* 5.3 0.4 - - + -
111C VAL* 3.7 20.4 - - + -
112C ARG* 1.3 75.1 - - - +
114C SER* 1.3 63.4 + - - +
131C GLY 3.1 11.0 - - - +
132C PHE* 3.5 36.8 - + - -
209C HIS* 3.4 43.3 - + + +
212C MET* 3.5 22.9 - - + -
265C LEU* 3.7 31.9 - - + -
277C TRP* 3.8 13.9 - + - -
318C LEU* 3.8 19.5 - - + -
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Residues in contact with SER 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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75C HIS* 3.0 29.0 + - - +
77C LYS 3.2 15.9 - - - -
78C GLY* 4.0 0.7 - - - -
112C ARG* 3.7 19.6 + - - -
113C PHE* 1.3 79.1 - - - +
115C THR* 1.3 66.0 + - - +
130C ARG* 3.0 13.4 - - - +
131C GLY* 2.6 36.3 + - - -
209C HIS* 4.3 5.6 - - - -
2002C HEM 4.2 3.6 + - - +
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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