Contacts of the strand formed by residues 105 - 112 (chain C) in PDB entry 1LQB
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 105 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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76C PHE 4.2 0.2 - - - +
78C ASN* 2.9 27.7 + - - +
101C LEU* 3.9 9.1 - - - +
102C PRO* 2.7 49.2 + - + +
103C PRO 3.5 14.1 - - - +
104C GLY* 1.3 79.1 - - - +
106C GLY* 1.3 61.7 + - - +
571D ASP* 4.5 7.3 + - + -
572D PHE 3.3 9.4 - - - -
573D GLN* 3.7 26.2 - - - +
574D LEU* 3.6 4.6 - - - +
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Residues in contact with GLY 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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76C PHE 3.1 11.7 - - - -
101C LEU* 4.2 2.0 - - - -
105C THR* 1.3 75.3 - - - +
107C ARG* 1.3 63.1 + - - +
571D ASP* 3.5 8.0 - - - +
572D PHE* 2.6 56.5 + - - -
574D LEU* 4.0 5.7 - - - +
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Residues in contact with ARG 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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75C ILE* 3.3 5.0 - - - -
76C PHE* 2.9 36.8 + - + -
86C PRO* 5.6 0.2 - - - +
99C PRO* 3.6 16.7 + - - +
100C THR 2.7 31.1 + - - -
101C LEU* 3.4 25.3 - - + +
102C PRO* 4.8 1.0 - - - +
106C GLY* 1.3 75.2 - - - +
108C ARG* 1.3 72.8 + - - +
109C ILE* 3.7 12.4 - - + +
566D ILE* 3.5 41.4 - - - +
569D ASP 5.3 3.8 - - - +
571D ASP* 2.7 37.8 + - - +
572D PHE* 3.7 7.5 - - - -
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Residues in contact with ARG 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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73C GLN* 3.1 41.7 - - + +
74C VAL 3.6 5.4 - - - +
75C ILE* 4.4 6.3 - - + +
107C ARG* 1.3 77.0 - - - +
109C ILE* 1.3 73.2 + - - +
110C HIS* 4.6 5.8 - - - -
146C PRO* 6.4 0.4 - - + -
566D ILE* 3.9 1.9 - - - +
567D PRO* 3.4 38.5 - - + +
569D ASP* 2.6 36.5 + - + +
572D PHE* 4.5 9.8 - - + -
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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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73C GLN* 3.5 5.8 - - - +
74C VAL* 2.5 49.1 + - + +
76C PHE* 3.6 46.7 - - + -
98C TYR* 6.2 1.8 - - + -
107C ARG* 3.7 23.6 - - + +
108C ARG* 1.3 85.8 - - - +
110C HIS* 1.3 76.6 + - - +
111C SER* 3.6 5.1 + - - +
117C TRP* 4.4 15.7 - - + -
564D HYP 5.0 1.8 - - + -
565D TYR 4.3 4.9 - - - +
566D ILE* 3.7 24.9 - - + -
567D PRO* 4.1 2.5 - - - -
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Residues in contact with HIS 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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71C PRO* 6.6 0.2 - - + -
72C SER 4.1 2.2 - - - -
73C GLN* 3.3 36.3 + - + -
108C ARG* 4.5 5.5 + - - -
109C ILE* 1.3 75.8 - - - +
111C SER* 1.3 61.7 - - - +
112C TYR* 4.4 1.1 - - + -
564D HYP 3.4 3.5 - - - +
565D TYR* 3.0 82.2 + + + +
567D PRO* 3.3 25.6 - - + +
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Residues in contact with SER 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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71C PRO* 3.6 3.3 - - - +
72C SER 2.9 32.6 + - - -
74C VAL* 4.4 8.1 - - - -
109C ILE* 3.6 4.4 + - - -
110C HIS* 1.3 77.5 - - - +
112C TYR* 1.3 76.5 + - - +
115C HIS* 3.8 2.8 + - - +
117C TRP* 3.0 29.8 + - - -
138C PRO* 3.6 15.4 - - - +
564D HYP 2.7 23.7 + - - -
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Residues in contact with TYR 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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68C SER* 3.7 6.7 - - - +
69C ARG* 3.7 11.0 - - - +
70C GLU 3.3 8.5 - - - +
71C PRO* 3.5 36.8 - - + -
72C SER* 3.9 6.1 - - - +
110C HIS* 4.4 4.3 - - + -
111C SER* 1.3 84.7 + - - +
113C ARG* 1.3 66.6 + - - +
114C GLY 3.3 0.2 + - - -
115C HIS* 3.2 51.1 + + - +
138C PRO* 3.4 8.3 - - - +
562D LEU* 3.5 41.0 - - + +
563D ALA 3.4 22.6 + - - -
564D HYP 3.7 5.7 + - - -
565D TYR* 3.6 22.8 - + - -
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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