Contacts of the helix formed by residues 105 - 117 (chain C) in PDB entry 6Q3W
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 ARG 105 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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83C ASP* 2.7 28.8 + - - +
102C GLY 4.3 6.7 - - - +
103C THR* 5.8 0.4 - - - -
104C PRO* 1.3 70.8 - - - +
106C TRP* 1.3 65.3 + - - +
108C ASN* 3.0 32.8 + - - +
109C TYR* 3.9 11.2 - - + -
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Residues in contact with TRP 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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75C LEU* 3.9 34.3 - - + -
77C THR* 3.5 27.0 - - + +
82C ALA* 3.9 20.0 - - + -
83C ASP* 3.1 35.5 + - - +
85C PRO 3.1 20.1 + - - -
86C GLN 3.3 30.5 - - - -
87C ARG* 4.0 4.9 - - - -
88C LEU 4.5 3.1 - - - -
104C PRO* 3.2 15.9 - - + +
105C ARG* 1.3 79.0 - - - +
107C ALA* 1.3 74.4 + - + +
109C TYR* 3.4 25.6 + - + +
110C VAL* 4.3 5.0 + - + +
129C VAL* 4.8 12.1 - - + -
135C LEU* 6.4 0.7 - - + -
145C LEU* 3.5 20.4 - - + +
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Residues in contact with ALA 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 LEU* 4.8 5.2 - - + -
88C LEU* 3.5 31.9 - - + -
104C PRO* 3.3 13.2 + - + +
105C ARG 3.1 0.6 - - - -
106C TRP* 1.3 102.6 - - + +
108C ASN* 1.3 60.3 + - - +
109C TYR 3.2 1.3 - - - -
110C VAL* 3.1 7.7 + - - +
111C LYS* 2.9 32.9 + - + +
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Residues in contact with ASN 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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101C PRO* 3.3 8.7 - - - +
102C GLY* 2.9 47.5 + - - +
104C PRO 3.9 2.5 - - - +
105C ARG* 3.0 24.0 + - - +
107C ALA* 1.3 77.6 - - - +
109C TYR* 1.3 59.4 + - + +
111C LYS* 3.6 13.5 + - - +
112C GLY 2.9 23.4 + - - -
177C PHE* 3.3 40.6 + - + +
178C ALA* 5.2 3.1 - - + +
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Residues in contact with TYR 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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105C ARG* 3.9 15.0 - - + -
106C TRP* 3.4 22.9 - - - -
107C ALA 3.2 0.6 - - - -
108C ASN* 1.3 78.1 - - - +
110C VAL* 1.3 61.9 + - - +
112C GLY* 3.5 1.1 + - - -
113C VAL* 3.3 28.6 + - - +
142C SER* 3.3 31.4 - - - -
145C LEU* 3.7 26.2 - - + -
146C GLU* 3.4 26.9 - - + -
149C THR* 5.2 0.7 - - - -
173C ALA* 4.2 4.1 - - - +
174C GLU* 3.4 17.5 + - - -
177C PHE* 5.4 0.2 - - - -
178C ALA* 3.4 24.4 - - + +
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Residues in contact with VAL 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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63C LEU* 5.6 2.2 - - + -
75C LEU* 3.9 33.7 - - + -
90C PHE* 4.8 0.2 - - + -
106C TRP* 4.4 6.5 - - + +
107C ALA* 3.1 8.6 + - - +
109C TYR* 1.3 73.8 - - - +
111C LYS* 1.3 66.1 + - - +
112C GLY 3.3 0.2 + - - -
113C VAL* 3.4 3.3 + - - +
114C ILE* 3.0 43.1 + - + +
125C PHE* 4.6 4.3 - - + -
129C VAL* 4.9 8.5 - - + -
145C LEU* 3.9 23.6 - - + -
149C THR* 3.6 35.0 - - + +
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Residues in contact with LYS 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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88C LEU* 3.6 28.5 - - - +
90C PHE* 4.0 27.1 - - + -
99C LEU* 3.5 22.0 - - + +
100C GLU 2.9 30.1 + - - +
102C GLY* 4.3 6.5 - - - +
103C THR 4.8 6.5 + - - +
104C PRO 5.8 0.2 + - - -
107C ALA* 2.9 19.6 + - - +
108C ASN* 3.6 20.7 + - - +
110C VAL* 1.3 77.7 - - - +
112C GLY* 1.3 57.9 + - - +
114C ILE* 3.4 3.8 + - - -
115C GLN* 2.8 30.5 + - - +
177C PHE* 3.9 11.7 - - + -
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Residues in contact with GLY 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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108C ASN 2.9 13.8 + - - -
109C TYR 3.5 0.4 + - - -
110C VAL 3.2 0.2 - - - -
111C LYS* 1.3 72.2 - - - +
113C VAL* 1.3 65.5 + - - +
115C GLN* 3.2 1.0 + - - +
116C TYR* 3.0 30.8 + - - -
173C ALA* 3.5 15.7 - - - -
177C PHE* 3.6 30.7 - - - -
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Residues in contact with VAL 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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109C TYR 3.3 18.1 + - - +
110C VAL 3.8 3.6 - - - +
112C GLY* 1.3 73.9 - - - +
114C ILE* 1.3 56.9 + - - +
116C TYR 3.3 1.6 + - - -
117C TYR* 2.9 29.5 + - - +
146C GLU* 3.5 29.6 - - + +
149C THR* 3.8 10.5 - - + -
150C TYR* 3.8 46.2 - - + +
153C LEU* 4.0 5.2 - - + -
169C VAL* 4.1 6.9 - - + +
170C CYS* 4.4 7.0 - - - -
173C ALA* 3.5 14.1 - - + +
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Residues in contact with ILE 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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73C VAL* 4.1 2.2 - - + -
90C PHE* 3.7 29.4 - - + -
92C LEU* 4.5 5.4 - - + -
93C PRO* 3.7 30.2 - - + +
99C LEU* 4.0 4.0 - - + -
110C VAL* 3.0 33.3 + - + +
111C LYS 3.5 6.5 - - - +
113C VAL* 1.3 76.6 - - - +
115C GLN* 1.3 62.9 + - - +
117C TYR* 3.3 15.4 + - - +
122C LEU* 4.2 17.3 - - + +
125C PHE* 3.9 19.7 - - + -
149C THR* 4.6 0.7 - - + -
153C LEU* 3.9 25.8 - - + -
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Residues in contact with GLN 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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93C PRO* 3.2 24.3 - - - +
94C THR 5.5 1.4 + - - -
98C SER* 3.3 26.3 - - - +
99C LEU* 2.9 28.0 + - + +
111C LYS 2.8 20.4 + - - +
112C GLY 3.2 5.6 + - - +
114C ILE* 1.3 74.3 - - - +
116C TYR* 1.3 75.7 + - + +
117C TYR 3.8 1.9 + - - +
177C PHE* 4.0 24.0 - - + -
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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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112C GLY 3.0 23.8 + - - +
113C VAL 3.6 2.2 - - - -
115C GLN* 1.3 89.7 - - + +
117C TYR* 1.3 65.3 + - - +
118C PRO* 3.3 8.8 - - - +
169C VAL* 3.6 27.8 - - + +
172C GLN* 3.7 41.9 + - + -
173C ALA 4.1 6.5 - - - -
176C SER* 3.3 19.6 + - - -
177C PHE* 3.8 30.5 - + - -
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Residues in contact with TYR 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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113C VAL 2.9 13.0 + - - +
114C ILE* 3.3 12.6 + - - +
115C GLN 4.8 1.9 - - - +
116C TYR* 1.3 77.6 - - - +
118C PRO* 1.3 72.8 - - + +
119C ALA* 3.5 34.7 + - + +
122C LEU* 4.1 26.2 - - + -
150C TYR* 3.5 37.5 - + - -
153C LEU* 3.6 34.3 - - + -
154C GLN* 3.1 17.6 - - - +
157C CYS* 2.6 30.5 + - + -
159C ASP* 3.5 15.0 - - + +
169C VAL* 4.6 1.3 - - - -
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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