Contacts of the helix formed by residues 106 - 119 (chain F) 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 F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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323B PHE* 3.8 36.5 + - + +
325B THR* 4.0 11.1 - - + -
91F THR* 4.4 3.4 - - + -
104F ALA 3.7 5.2 + - - +
105F ASP* 1.3 72.3 + - - +
107F LYS* 1.3 64.8 + - - +
108F TYR 3.2 3.0 + - - -
109F ILE* 3.2 30.6 + - + +
110F GLU* 2.9 23.4 + - + +
133F PRO* 3.9 37.0 - - + -
135F ARG 5.7 0.7 - - - -
136F ALA* 4.3 14.6 - - + +
139F SER* 4.2 17.3 - - - +
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Residues in contact with LYS 107 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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325B THR* 3.8 16.0 - - + +
327B THR* 4.4 30.3 + - + +
329B LYS* 6.4 0.2 - - - +
92F PRO* 4.8 7.0 - - - -
96F TYR* 5.4 1.2 + - - -
105F ASP* 3.1 34.1 + - - +
106F LEU* 1.3 75.3 - - - +
108F TYR* 1.3 102.1 + - + +
110F GLU* 3.4 4.8 + - - +
111F ALA* 3.0 27.7 + - - +
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Residues in contact with TYR 108 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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89F VAL* 3.6 21.8 - - + -
90F ASN* 3.4 43.5 - - - +
92F PRO* 4.0 13.0 - - + -
105F ASP 4.6 1.0 + - - -
106F LEU 3.2 0.6 - - - -
107F LYS* 1.3 113.5 + - + +
109F ILE* 1.3 67.8 + - - +
111F ALA* 3.3 8.5 + - + +
112F CYS* 3.0 27.5 + - - -
502F UPG 4.1 21.4 + - - +
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Residues in contact with ILE 109 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87F ILE* 3.5 27.2 - - + +
89F VAL* 3.8 14.6 - - + +
90F ASN 5.1 0.2 + - - -
91F THR* 3.5 30.5 - - + -
106F LEU* 3.2 24.5 + - + +
108F TYR* 1.3 75.9 - - - +
110F GLU* 1.3 58.5 + - - +
112F CYS* 3.2 6.2 + - - +
113F ALA* 2.9 26.2 + - - +
128F GLU* 5.8 2.0 - - + -
130F SER* 6.0 1.1 - - - -
132F VAL* 4.1 16.8 - - + -
136F ALA* 5.2 4.0 - - + +
139F SER* 6.1 1.8 - - - -
140F ILE* 3.8 33.4 - - + -
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Residues in contact with GLU 110 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
323B PHE* 3.4 20.8 - - + -
325B THR* 3.7 8.7 - - - +
329B LYS* 2.8 41.0 + - - -
409B HIS* 3.9 1.1 - - - -
106F LEU* 2.9 17.0 + - + +
107F LYS* 3.7 5.3 - - - +
109F ILE* 1.3 77.0 - - - +
111F ALA* 1.3 66.0 + - - +
113F ALA* 3.2 2.1 + - - +
114F ARG* 2.8 64.1 + - - +
143F ILE* 3.7 17.9 - - + -
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Residues in contact with ALA 111 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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107F LYS 3.0 17.6 + - - +
108F TYR* 3.3 10.5 + - + +
110F GLU* 1.3 77.5 - - - +
112F CYS* 1.3 63.5 + - - +
114F ARG* 3.3 8.6 + - - +
115F ARG* 3.0 25.9 + - - +
502F UPG 5.6 6.7 - - - +
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Residues in contact with CYS 112 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10F ILE* 3.6 36.1 - - + -
87F ILE* 4.1 26.7 - - + -
89F VAL* 3.8 18.8 - - - -
108F TYR 3.0 17.4 + - - -
109F ILE 3.2 8.0 + - - +
111F ALA* 1.3 76.6 - - - +
113F ALA* 1.3 57.2 + - - +
115F ARG* 3.3 5.7 + - - +
116F ILE* 2.8 36.7 + - - +
502F UPG 4.5 8.5 - - - -
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Residues in contact with ALA 113 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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87F ILE* 4.7 2.6 - - + +
109F ILE 2.9 13.1 + - - +
110F GLU* 3.6 7.2 - - - +
112F CYS* 1.3 76.1 - - - +
114F ARG* 1.3 62.5 + - - +
116F ILE* 4.5 4.5 - - - +
117F VAL* 3.1 24.5 + - - +
140F ILE* 4.2 18.6 - - + -
143F ILE* 3.8 23.8 - - + -
144F PHE* 3.3 25.8 - - + -
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Residues in contact with ARG 114 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
323B PHE* 4.8 2.6 - - - -
409B HIS* 3.6 27.1 + - - -
433B LEU* 4.4 14.6 - - - +
434B LYS 2.6 37.3 + - - +
435B PRO* 4.0 12.1 + - - +
110F GLU* 2.8 53.3 + - - +
111F ALA* 3.8 6.5 - - - +
113F ALA* 1.3 74.2 - - - +
115F ARG* 1.3 65.7 + - - +
117F VAL* 3.1 12.3 - - + +
118F GLN* 3.0 29.7 + - - +
143F ILE* 3.9 17.2 - - + +
147F ASN* 4.1 6.4 + - - +
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Residues in contact with ARG 115 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10F ILE* 5.8 1.1 - - + -
37F VAL* 4.2 11.9 - - - +
75F ILE* 3.5 38.0 - - + +
76F ASP* 3.1 34.4 + - - -
79F ILE* 3.8 19.5 - - + -
111F ALA 3.0 16.9 + - - +
112F CYS* 3.7 6.3 - - - +
114F ARG* 1.3 75.8 - - - +
116F ILE* 1.3 63.2 + - - +
118F GLN* 3.2 11.1 + - - -
119F ASN* 3.0 33.2 + - - +
502F UPG 4.7 5.3 + - - -
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Residues in contact with ILE 116 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10F ILE* 3.9 21.3 - - + -
79F ILE* 4.1 15.7 - - + +
85F VAL* 3.7 26.7 - - + -
87F ILE* 4.0 13.0 - - + -
112F CYS 2.8 25.4 + - - +
113F ALA* 3.7 6.5 - - - +
115F ARG* 1.3 75.0 - - - +
117F VAL* 1.3 59.1 + - - +
119F ASN 3.4 0.9 + - - -
120F SER* 2.5 43.8 + - - +
124F LYS* 5.4 0.4 - - + -
126F VAL* 4.0 38.1 - - + -
144F PHE* 4.2 8.3 - - + -
154F LEU* 4.3 6.7 - - + -
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Residues in contact with VAL 117 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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113F ALA 3.1 13.2 + - - +
114F ARG* 3.1 23.6 - - - +
116F ILE* 1.3 81.6 - - - +
118F GLN* 1.3 50.8 + - - +
119F ASN 3.5 0.3 + - - -
120F SER* 3.6 4.9 + - - +
143F ILE* 4.4 8.3 - - + -
144F PHE* 4.1 15.9 - - + +
147F ASN* 3.1 46.2 - - + +
149F LYS* 2.8 33.4 + - - +
152F LEU* 3.9 13.4 - - + +
154F LEU* 4.5 6.5 - - + -
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Residues in contact with GLN 118 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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114F ARG* 3.0 24.3 + - - +
115F ARG* 3.2 11.1 + - - +
117F VAL* 1.3 79.2 - - - +
119F ASN* 1.3 65.3 + - - +
120F SER 3.4 0.2 - - - -
149F LYS* 3.1 16.2 + - - +
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Residues in contact with ASN 119 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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76F ASP* 3.0 51.5 + - - +
79F ILE* 4.0 14.3 - - + +
80F LYS* 3.5 32.8 + - + +
115F ARG* 3.0 36.7 + - - +
116F ILE 3.4 0.2 + - - -
117F VAL 3.3 0.2 - - - -
118F GLN* 1.3 82.8 - - - +
120F SER* 1.3 60.5 + - - +
121F ASN* 5.3 2.6 + - - -
149F 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