Contacts of the helix formed by residues 106 - 119 (chain C) in PDB entry 3KHU
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 LEU 106 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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323A PHE* 3.7 24.4 + - + +
325A THR* 4.1 18.0 - - + -
91C THR* 4.4 3.1 - - + -
104C ALA 3.7 5.6 + - - +
105C ASP* 1.3 72.7 + - - +
107C LYS* 1.3 63.9 + - - +
108C TYR 3.2 3.1 + - - -
109C ILE* 3.2 29.6 + - + -
110C GLU* 2.9 24.5 + - + +
133C PRO* 3.9 37.7 - - + -
135C ARG 5.5 1.1 - - - +
136C ALA* 4.1 14.4 - - + +
139C SER* 4.1 23.3 - - - +
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Residues in contact with LYS 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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325A THR* 3.9 15.3 - - + +
327A THR* 4.5 28.0 - - + +
92C PRO* 4.8 7.2 - - - -
96C TYR* 5.4 2.2 + - - -
105C ASP* 3.1 33.7 + - - +
106C LEU* 1.3 76.0 - - - +
108C TYR* 1.3 100.9 + - + +
110C GLU* 3.5 4.9 + - - +
111C ALA* 2.9 28.4 + - - +
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Residues in contact with TYR 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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89C VAL* 3.7 20.9 - - + -
90C ASN* 3.4 44.0 - - - +
92C PRO* 4.1 12.6 - - + -
105C ASP 4.6 0.4 + - - -
106C LEU 3.2 0.8 - - - -
107C LYS* 1.3 113.4 + - + +
109C ILE* 1.3 67.9 + - - +
111C ALA* 3.4 8.1 + - + +
112C CYS* 3.0 27.4 + - - -
502C UPG 4.2 23.4 + - - +
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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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87C ILE* 3.7 26.1 - - + +
89C VAL* 3.9 14.4 - - + +
90C ASN 5.2 0.2 + - - -
91C THR* 3.5 30.7 - - + -
106C LEU* 3.2 23.8 + - + +
108C TYR* 1.3 76.8 - - - +
110C GLU* 1.3 59.8 + - - +
112C CYS* 3.2 7.2 + - - +
113C ALA* 2.9 26.0 + - - +
128C GLU* 5.8 2.0 - - + -
130C SER* 6.0 0.9 - - - -
132C VAL* 4.0 18.2 - - + -
136C ALA* 5.3 4.7 - - + +
139C SER* 6.1 1.6 - - - -
140C ILE* 3.8 34.1 - - + -
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Residues in contact with GLU 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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323A PHE* 3.6 17.5 - - + -
325A THR* 3.7 9.2 - - - +
329A LYS* 2.7 40.6 + - - -
409A HIS* 4.0 1.2 - - - -
106C LEU* 2.9 17.3 + - + +
107C LYS* 3.7 5.0 - - - +
109C ILE* 1.3 78.4 - - - +
111C ALA* 1.3 62.7 + - - +
113C ALA* 3.1 3.0 + - - +
114C ARG* 2.8 60.2 + - - +
143C ILE* 3.6 20.4 - - + -
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Residues in contact with ALA 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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107C LYS 2.9 17.7 + - - +
108C TYR* 3.8 10.5 - - + +
109C ILE 3.3 0.2 - - - -
110C GLU* 1.3 77.6 - - - +
112C CYS* 1.3 57.7 + - - +
114C ARG* 3.4 7.7 + - - +
115C ARG* 3.0 30.2 + - - +
502C UPG 5.7 4.7 - - - +
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Residues in contact with CYS 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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10C ILE* 3.5 38.4 - - + -
87C ILE* 4.1 25.4 - - + -
89C VAL* 3.8 17.0 - - - -
108C TYR 3.0 17.8 + - - +
109C ILE 3.5 7.6 - - - +
111C ALA* 1.3 74.2 - - - +
113C ALA* 1.3 60.5 + - - +
115C ARG* 3.4 5.2 + - - +
116C ILE* 2.8 36.0 + - - +
502C UPG 4.5 8.3 - - - -
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Residues in contact with ALA 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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87C ILE* 4.6 1.8 - - + +
109C ILE 2.9 13.5 + - - +
110C GLU* 3.1 8.0 + - - +
112C CYS* 1.3 76.0 - - - +
114C ARG* 1.3 63.8 + - - +
116C ILE* 3.3 5.5 + - - -
117C VAL* 3.1 24.8 + - - +
140C ILE* 4.3 19.1 - - + -
143C ILE* 3.9 22.4 - - + -
144C PHE* 3.4 24.8 - - + -
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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
----------------------------------------------------------
323A PHE* 4.9 2.8 - - - -
329A LYS* 5.1 0.2 - - - +
409A HIS* 3.5 26.1 + - - -
433A LEU* 4.5 13.8 - - - +
434A LYS 2.9 34.7 + - - +
435A PRO* 4.3 10.3 + - - +
110C GLU* 2.8 52.5 + - + +
111C ALA* 3.8 6.7 - - - +
113C ALA* 1.3 75.7 - - - +
115C ARG* 1.3 61.1 + - - +
117C VAL* 3.1 11.4 - - - +
118C GLN* 3.1 31.2 + - - +
143C ILE* 3.9 17.8 - - + +
147C ASN* 4.1 8.6 + - - +
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Residues in contact with ARG 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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10C ILE* 5.6 1.6 - - + -
37C VAL* 4.2 12.3 - - - +
75C ILE* 3.6 37.9 - - + +
76C ASP* 3.0 34.4 + - - -
79C ILE* 3.7 19.3 - - + -
111C ALA 3.0 18.0 + - - +
112C CYS* 3.8 6.3 - - - +
114C ARG* 1.3 74.5 - - - +
116C ILE* 1.3 64.5 + - - +
118C GLN* 3.2 11.1 + - - -
119C ASN* 3.1 33.3 + - - +
502C UPG 5.0 3.2 + - - -
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Residues in contact with ILE 116 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10C ILE* 3.9 20.0 - - + -
79C ILE* 4.1 14.4 - - + -
85C VAL* 3.7 27.6 - - + -
87C ILE* 4.0 12.3 - - + -
112C CYS 2.8 26.2 + - - +
113C ALA* 3.7 6.5 - - - +
115C ARG* 1.3 72.0 - - - +
117C VAL* 1.3 60.9 + - - +
119C ASN 3.2 2.6 + - - -
120C SER* 2.6 40.6 + - - +
124C LYS* 5.4 0.2 - - + -
126C VAL* 3.9 39.9 - - + -
144C PHE* 4.2 8.1 - - + -
154C LEU* 4.4 7.6 - - + -
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Residues in contact with VAL 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 ALA 3.1 14.9 + - - +
114C ARG* 3.1 23.6 - - - +
116C ILE* 1.3 77.4 - - - +
118C GLN* 1.3 58.3 + - - +
119C ASN 3.4 0.3 + - - -
120C SER* 3.5 4.8 + - - +
143C ILE* 4.4 8.7 - - + -
144C PHE* 4.2 15.5 - - + +
147C ASN* 3.1 46.2 - - + +
149C LYS* 2.8 28.5 + - - -
152C LEU* 4.0 12.9 - - + +
154C LEU* 4.5 8.3 - - + -
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Residues in contact with GLN 118 (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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114C ARG* 3.1 25.5 + - - +
115C ARG* 3.2 10.7 + - - +
117C VAL* 1.3 79.9 - - - +
119C ASN* 1.3 64.8 + - - +
149C LYS* 3.2 16.0 + - - +
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Residues in contact with ASN 119 (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 ASP* 3.0 52.1 + - - +
79C ILE* 3.9 14.4 - - + -
80C LYS* 3.6 31.3 - - + +
115C ARG* 3.1 36.4 + - - +
116C ILE 3.2 0.4 + - - -
118C GLN* 1.3 83.6 - - - +
120C SER* 1.3 60.0 + - - +
121C ASN* 5.4 2.0 + - - -
149C LYS* 4.6 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