Contacts of the helix formed by residues 105 - 116 (chain C) in PDB entry 1QDV
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 PRO 105 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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99B ARG* 3.4 32.5 - - + +
100B ARG 6.1 1.1 - - - +
101B PRO* 6.3 2.2 - - + -
102B VAL* 6.1 5.2 - - + -
100C ARG* 4.1 3.4 - - - +
103C ASN 3.7 7.9 - - - +
104C VAL* 1.3 91.0 - - + +
106C LEU* 1.3 66.8 + - - +
107C ASP* 3.7 4.0 - - - +
108C ILE* 3.1 24.4 + - + -
109C PHE* 2.9 21.0 + - - +
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Residues in contact with LEU 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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100C ARG* 3.1 33.0 - - - +
104C VAL 3.7 0.8 + - - -
105C PRO* 1.3 73.3 - - - +
107C ASP* 1.3 54.4 + - - +
109C PHE* 3.5 0.7 + - - -
110C SER* 2.5 41.7 + - - +
126C PHE* 3.4 29.5 - - + -
130C GLU* 3.0 40.2 - - + +
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Residues in contact with ASP 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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97B ARG* 3.7 10.2 + - - -
99B ARG* 2.8 42.6 + - - -
105C PRO* 3.7 3.6 - - - +
106C LEU* 1.3 74.1 + - - +
108C ILE* 1.3 67.4 + - - +
110C SER* 3.6 7.7 - - - -
111C GLU* 3.1 22.9 + - - +
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Residues in contact with ILE 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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90B TYR* 3.5 39.7 - - + +
99B ARG* 3.5 30.3 - - + +
81C ASN* 3.6 29.4 - - + +
84C SER* 4.3 0.4 - - - +
104C VAL* 3.6 18.2 - - + -
105C PRO* 3.1 28.1 + - + +
107C ASP* 1.3 75.8 + - - +
109C PHE* 1.3 64.9 + - - +
111C GLU* 3.2 7.5 + - - +
112C GLU* 3.2 23.4 + - + +
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Residues in contact with PHE 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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84C SER* 3.8 35.7 - - - -
87C ALA* 3.9 3.6 - - + -
88C ILE* 4.3 11.2 - - + -
98C LEU* 3.7 28.0 - - + -
99C ARG 3.9 4.9 - - - -
100C ARG* 3.5 44.0 - - + -
101C PRO* 3.5 23.6 - - + -
104C VAL* 3.7 5.5 - - + +
105C PRO 2.9 15.4 + - - +
106C LEU 4.0 0.9 - - - +
108C ILE* 1.3 77.6 - - - +
110C SER* 1.3 61.6 + - - +
112C GLU* 3.1 3.8 + - + +
113C ILE* 2.9 58.1 + - + +
126C PHE* 3.7 8.5 - + - -
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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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106C LEU* 2.5 30.2 + - - +
107C ASP* 3.6 9.4 - - - -
109C PHE* 1.3 76.0 - - - +
111C GLU* 1.3 63.1 + - - +
113C ILE* 3.3 7.2 + - - +
114C ARG* 3.1 22.7 + - - +
126C PHE* 3.1 27.1 - - - -
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Residues in contact with GLU 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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80C ARG* 3.1 26.7 + - - +
107C ASP 3.1 14.6 + - - +
108C ILE* 3.2 9.8 + - - +
110C SER* 1.3 75.0 - - - +
112C GLU* 1.3 63.2 + - - +
114C ARG* 2.9 43.7 + - - +
115C PHE* 2.9 25.1 + - - +
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Residues in contact with GLU 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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80C ARG* 2.9 49.0 + - - +
81C ASN* 3.7 22.3 + - + +
84C SER* 3.7 29.8 - - - +
88C ILE* 4.5 5.8 - - + -
108C ILE* 3.2 13.8 + - - +
109C PHE* 3.1 8.1 + - + +
111C GLU* 1.3 79.8 - - - +
113C ILE* 1.3 64.9 + - - +
115C PHE* 3.2 2.6 + - - +
116C TYR* 2.9 50.2 + - + -
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Residues in contact with ILE 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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88C ILE* 4.4 6.5 - - + -
98C LEU* 3.9 15.5 - - + -
109C PHE* 2.9 55.4 + - + +
110C SER* 3.3 5.6 + - - +
112C GLU* 1.3 75.7 - - - +
114C ARG* 1.3 61.9 + - - +
116C TYR 3.6 0.7 + - - -
117C GLU 3.1 15.9 + - - -
118C LEU* 3.3 33.2 + - + +
123C MET* 3.7 29.0 - - + +
126C PHE* 3.7 31.4 - - + -
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Residues in contact with ARG 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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110C SER 3.1 13.5 + - - +
111C GLU* 2.9 46.4 + - - +
113C ILE* 1.3 77.3 - - - +
115C PHE* 1.3 95.0 + - - +
117C GLU* 3.0 21.4 + - - +
123C MET* 5.1 13.2 - - - -
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Residues in contact with PHE 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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58C LEU* 3.3 30.0 - - + +
68C TYR* 3.4 35.0 - + - -
78C PHE* 3.6 19.1 - + - -
80C ARG* 3.3 57.4 - - + +
111C GLU* 2.9 18.2 + - - +
112C GLU 3.2 2.9 + - - +
114C ARG* 1.3 95.7 - - - +
116C TYR* 1.3 80.2 + + - +
117C GLU* 3.2 9.0 + - - +
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Residues in contact with TYR 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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39C ILE* 3.5 23.2 - - - +
57C THR* 3.7 4.5 - - - -
58C LEU* 3.1 27.0 + - + -
59C LEU* 4.3 20.0 - - + -
78C PHE* 4.1 16.2 - + - +
80C ARG* 3.7 17.2 - - - +
81C ASN 5.3 1.0 + - - -
84C SER* 6.1 0.7 - - - -
85C PHE* 3.6 26.6 - + + +
88C ILE* 4.0 19.7 - - + -
92C TYR* 4.6 0.9 + - - +
112C GLU* 2.9 49.8 + - + +
115C PHE* 1.3 99.0 - + - +
117C GLU* 1.3 66.2 + - - +
118C LEU* 3.3 19.8 + - + +
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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