Contacts of the helix formed by residues 147 - 156 (chain A) in PDB entry 1K63
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 ASP 147 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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143A PHE* 4.0 8.1 - - + -
144A PRO* 3.2 11.2 + - + +
146A GLN* 1.3 104.4 + - - +
148A ARG* 1.3 66.6 + - - +
149A ASP 3.4 2.5 - - - -
150A LEU* 3.3 20.5 + - + +
151A PHE* 3.0 47.4 + - + -
173A VAL* 5.2 5.7 - - - +
177A LEU* 4.0 20.4 - - - +
2001A BRP 5.9 0.8 - - + +
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Residues in contact with ARG 148 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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140A TRP* 3.2 47.1 + - + -
141A ALA* 3.8 14.0 + - - +
143A PHE* 2.7 38.9 + - + +
144A PRO 3.3 5.3 + - - +
145A GLU* 3.3 42.2 + - - +
146A GLN 3.6 0.4 - - - -
147A ASP* 1.3 78.4 - - - +
149A ASP* 1.3 69.1 + - - +
151A PHE* 3.3 0.7 + - - -
152A GLN* 3.0 39.4 + - - +
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Residues in contact with ASP 149 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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145A GLU 4.9 0.8 + - - -
146A GLN 5.4 0.6 + - - -
147A ASP 3.4 0.6 - - - -
148A ARG* 1.3 82.5 - - - +
150A LEU* 1.3 57.8 + - - +
152A GLN* 3.3 18.0 + - - +
153A ALA* 2.9 27.5 + - - +
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Residues in contact with LEU 150 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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147A ASP* 3.3 22.5 + - - +
148A ARG 3.3 1.0 - - - -
149A ASP* 1.3 79.6 - - - +
151A PHE* 1.3 58.4 + - + +
153A ALA* 3.1 7.2 + - + +
154A PHE* 2.9 50.5 + - + -
162A LEU* 4.4 17.0 - - + -
168A VAL* 4.2 15.7 - - + -
172A GLN* 4.8 12.6 - - + +
173A VAL* 3.7 29.8 - - + +
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Residues in contact with PHE 151 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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140A TRP* 4.0 10.8 - - + -
143A PHE* 3.4 30.5 - + + -
147A ASP* 3.0 42.3 + - + +
148A ARG 4.1 1.8 - - - +
150A LEU* 1.3 76.9 - - + +
152A GLN* 1.3 66.8 + - - +
154A PHE* 3.4 14.9 + + - +
155A ARG* 3.1 28.4 + - - +
169A PHE* 3.4 40.6 - + - -
173A VAL* 4.0 16.6 - - + -
208A PRO* 3.9 10.5 - - + -
211A ILE* 3.9 23.6 - - + -
1001A BR 4.1 2.2 - - + -
2001A BRP 4.0 18.4 - - + -
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Residues in contact with GLN 152 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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140A TRP* 3.5 48.0 - - + +
148A ARG* 3.0 28.8 + - - +
149A ASP* 3.6 22.5 - - - +
150A LEU 3.2 0.2 - - - -
151A PHE* 1.3 77.2 - - - +
153A ALA* 1.3 62.7 + - - +
155A ARG* 3.2 6.5 + - - +
156A SER* 3.1 20.8 + - - -
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Residues in contact with ALA 153 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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149A ASP 2.9 13.6 + - - +
150A LEU* 3.1 12.1 + - + +
152A GLN* 1.3 75.4 - - - +
154A PHE* 1.3 65.0 + - - +
156A SER* 2.7 26.5 + - - +
158A ALA* 3.8 5.6 - - + +
159A GLY 3.3 11.4 + - - -
162A LEU* 3.6 20.9 - - + -
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Residues in contact with PHE 154 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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150A LEU* 2.9 54.9 + - + -
151A PHE* 3.7 19.3 - + - +
153A ALA* 1.3 76.9 - - - +
155A ARG* 1.3 60.9 + - - +
156A SER 3.4 4.5 - - - +
159A GLY* 3.7 5.6 - - - -
162A LEU* 4.1 13.2 - - + -
163A VAL* 3.7 27.6 - - + -
168A VAL* 4.0 14.4 - - + -
169A PHE* 3.5 39.0 - + - -
173A VAL* 3.9 12.8 - - + -
205A LEU* 3.5 5.8 - - + +
208A PRO* 4.0 23.8 - - + -
209A ARG* 2.9 26.9 + - - -
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Residues in contact with ARG 155 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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140A TRP* 3.6 27.3 - - - +
151A PHE* 3.1 19.8 + - - +
152A GLN* 3.7 6.1 - - - +
153A ALA 3.1 0.8 - - - -
154A PHE* 1.3 78.7 - - + +
156A SER* 1.3 57.2 + - - +
157A GLN* 5.7 0.9 + - - -
208A PRO* 2.9 33.3 + - - +
209A ARG* 3.8 31.0 + - + +
211A ILE* 2.9 28.1 + - - +
213A ILE* 3.8 20.3 + - - +
216A THR* 2.8 35.4 + - - +
217A PRO* 4.2 0.6 - - - +
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Residues in contact with SER 156 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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152A GLN 3.1 10.7 + - - -
153A ALA* 2.7 19.4 + - - -
154A PHE 3.4 0.2 - - - +
155A ARG* 1.3 77.0 - - - +
157A GLN* 1.3 61.1 + - - +
158A ALA* 3.0 17.7 + - - +
159A GLY 3.0 10.2 + - - -
209A ARG* 3.0 21.7 + - - -
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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