Contacts of the helix formed by residues 135 - 147 (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 ARG 135 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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244E THR* 5.4 5.8 - - + -
106F LEU* 5.7 1.3 - - - -
134F VAL* 1.3 87.6 - - + +
136F ALA* 1.3 64.2 + - - +
137F ALA 3.3 2.5 - - - -
138F GLU* 3.2 34.8 + - - +
139F SER* 3.2 16.3 + - - +
214F TRP* 4.7 14.1 - - + +
217F GLU* 3.0 11.6 + - - -
287F LEU* 5.3 6.5 - - + -
291F LEU* 6.5 1.6 - - + -
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Residues in contact with ALA 136 (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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106F LEU* 4.3 21.5 - - + -
109F ILE* 5.2 2.4 - - + +
128F GLU* 3.0 19.3 - - - +
132F VAL* 3.5 18.8 - - + -
133F PRO* 3.1 20.6 + - - +
134F VAL 3.4 0.8 + - - -
135F ARG* 1.3 76.9 - - - +
137F ALA* 1.3 60.7 + - - +
139F SER* 2.9 20.1 + - - -
140F ILE* 3.1 16.1 + - + +
217F GLU* 3.5 3.1 + - - +
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Residues in contact with ALA 137 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
128F GLU* 2.9 13.3 + - - +
135F ARG 3.3 0.4 - - - -
136F ALA* 1.3 72.4 - - - +
138F GLU* 1.3 58.0 + - - +
140F ILE* 3.4 4.5 + - - +
141F ARG* 2.9 29.5 + - - +
156F VAL* 3.9 21.3 - - + +
157F LEU 5.5 0.2 - - - +
213F THR* 3.4 33.0 - - + -
217F GLU* 2.9 18.5 + - - +
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Residues in contact with GLU 138 (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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135F ARG* 3.2 34.2 + - - +
137F ALA* 1.3 80.3 - - - +
139F SER* 1.3 56.9 + - - +
141F ARG* 3.5 7.2 + - + +
142F ARG* 3.0 59.3 + - + +
214F TRP* 4.5 24.5 + - + +
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Residues in contact with SER 139 (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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323B PHE* 3.4 40.7 - - - +
106F LEU* 4.2 14.7 - - - +
109F ILE* 6.1 2.0 - - - -
135F ARG* 3.2 10.3 + - - +
136F ALA* 2.9 12.0 + - - -
138F GLU* 1.3 76.5 + - - +
140F ILE* 1.3 68.1 + - - +
142F ARG* 3.0 13.6 + - - +
143F ILE* 3.1 21.4 + - - +
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Residues in contact with ILE 140 (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* 4.2 12.6 - - + -
109F ILE* 3.8 28.3 - - + -
113F ALA* 4.2 15.9 - - + -
126F VAL* 4.6 6.3 - - + -
128F GLU* 3.6 37.7 - - + +
136F ALA 3.1 7.2 + - - +
137F ALA* 3.7 7.4 - - - +
139F SER* 1.3 75.1 - - - +
141F ARG* 1.3 63.8 + - - +
143F ILE* 3.1 5.9 + - + +
144F PHE* 3.0 56.0 + - + -
156F VAL* 4.0 11.9 - - + -
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Residues in contact with ARG 141 (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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137F ALA 2.9 18.3 + - - +
138F GLU* 3.7 8.3 - - - +
140F ILE* 1.3 78.4 - - - +
142F ARG* 1.3 58.0 + - + +
144F PHE* 3.4 25.3 + - - +
145F ASP* 2.9 68.7 + - - +
154F LEU* 2.8 35.9 + - - +
155F GLN* 4.2 5.7 + - - +
156F VAL* 3.9 25.7 - - + +
183F ASP* 5.3 8.5 + - - -
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Residues in contact with ARG 142 (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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321B SER* 5.7 2.6 + - - +
323B PHE* 4.5 24.5 - - + -
435B PRO* 4.6 7.1 - - + +
437B PHE* 6.4 1.8 - - - -
458B GLN* 5.6 12.1 + - - +
138F GLU* 3.0 43.4 + - + +
139F SER* 3.0 9.5 + - - +
141F ARG* 1.3 75.6 - - + +
143F ILE* 1.3 66.2 + - - +
145F ASP* 4.0 5.9 - - + +
146F ALA* 3.0 26.3 + - - +
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Residues in contact with ILE 143 (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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323B PHE* 3.7 31.4 - - + -
435B PRO* 4.6 5.4 - - + -
110F GLU* 3.7 26.7 - - + +
113F ALA* 3.8 30.1 - - + +
114F ARG* 3.9 33.2 - - + +
117F VAL* 4.4 3.1 - - + -
139F SER* 3.1 15.2 + - - +
140F ILE* 3.1 6.3 + - + +
142F ARG* 1.3 77.0 - - - +
144F PHE* 1.3 61.3 + - + +
146F ALA 3.3 0.7 + - - -
147F ASN* 2.8 44.1 + - - +
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Residues in contact with PHE 144 (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* 3.3 36.8 - - + -
116F ILE* 4.2 7.2 - - + -
117F VAL* 4.1 9.7 - - + +
126F VAL* 3.9 22.7 - - + -
140F ILE* 3.0 37.4 + - + +
141F ARG* 3.6 19.3 - - - +
143F ILE* 1.3 77.1 - - + +
145F ASP* 1.3 63.3 + - - +
147F ASN* 3.2 22.0 + - - -
148F THR* 3.5 6.6 + - - -
152F LEU* 5.7 2.1 - - + +
154F LEU* 3.7 45.3 - - + -
156F VAL* 3.7 23.3 - - + -
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Residues in contact with ASP 145 (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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141F ARG* 2.9 56.8 + - - +
142F ARG* 4.0 7.2 - - - +
144F PHE* 1.3 76.9 - - - +
146F ALA* 1.3 60.6 + - - +
148F THR* 4.1 15.0 - - - +
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Residues in contact with ALA 146 (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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434B LYS* 3.5 15.6 - - + +
435B PRO* 3.7 39.3 - - + -
142F ARG 3.0 18.4 + - - +
143F ILE 3.8 3.6 - - - +
144F PHE 3.2 0.2 - - - -
145F ASP* 1.3 76.3 - - - +
147F ASN* 1.3 60.1 + - - +
148F THR* 3.6 1.7 + - - -
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Residues in contact with ASN 147 (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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434B LYS* 2.9 48.8 + - - +
114F ARG* 4.1 4.5 + - - +
117F VAL* 3.1 38.4 - - + +
143F ILE* 2.8 35.3 + - - +
144F PHE 3.2 4.7 + - - -
146F ALA* 1.3 79.1 - - - +
148F THR* 1.3 63.4 + - - +
149F LYS* 3.9 4.0 + - - +
152F LEU* 4.4 0.5 - - - +
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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