Contacts of the helix formed by residues 147 - 159 (chain J) in PDB entry 3V6K
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 ASN 147 (chain J).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1J MET* 6.1 4.5 - - - -
145J SER 3.8 7.3 - - - +
146J LYS* 1.3 82.8 - - - +
148J LYS* 1.3 63.7 + - - +
149J VAL* 3.1 23.0 + - - +
150J PHE* 3.4 27.3 - - - +
151J ALA* 3.6 11.3 + - - +
171J VAL* 5.2 4.6 - - - +
228J LEU* 3.8 11.7 - - - +
231J ASP* 4.9 10.4 + - - +
233J TYR* 3.1 46.6 - - + +
234J ASN* 5.3 1.1 - - - -
235J GLU 5.9 0.4 - - - +
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Residues in contact with LYS 148 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1J MET* 6.1 1.2 - - - +
108J TYR* 5.1 21.9 + - + -
147J ASN* 1.3 70.7 + - - +
149J VAL* 1.3 67.8 + - + +
151J ALA* 3.1 18.5 + - - +
152J LYS* 3.4 8.3 + - - +
233J TYR* 4.5 16.3 - - + +
235J GLU* 5.0 7.3 + - + +
237J ILE* 4.2 24.7 - - + -
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Residues in contact with VAL 149 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
108J TYR* 6.0 1.1 - - - -
147J ASN* 3.1 11.8 + - - +
148J LYS* 1.3 72.1 - - + +
150J PHE* 1.3 64.5 + - - +
152J LYS* 3.1 23.7 + - - +
153J ILE* 3.4 9.7 - - + +
183J VAL* 4.6 1.8 - - + -
184J PRO* 3.8 23.3 - - + -
224J TYR* 2.9 42.2 - - + +
228J LEU* 3.9 20.0 - - + -
233J TYR* 3.9 19.1 - - + +
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Residues in contact with PHE 150 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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145J SER* 3.6 20.8 + - - +
147J ASN* 3.4 23.9 + - - +
148J LYS 3.2 0.6 - - - -
149J VAL* 1.3 81.6 - - - +
151J ALA* 1.3 63.6 + - - +
153J ILE* 2.8 26.3 + - - +
154J ALA* 3.1 8.8 + - - +
166J ILE* 4.7 6.7 - - + +
171J VAL* 5.2 9.4 - - + -
174J LEU* 5.3 9.2 - - + -
228J LEU* 5.4 0.2 - - - +
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Residues in contact with ALA 151 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5J PHE* 3.8 23.3 - - + +
109J LEU* 5.0 3.8 - - + -
143J GLY* 3.3 13.0 - - - -
144J ILE* 3.9 2.0 - - - -
145J SER* 3.4 36.6 - - - +
147J ASN 3.6 5.1 + - - +
148J LYS* 3.1 13.5 + - - +
150J PHE* 1.3 78.1 - - - +
152J LYS* 1.3 63.3 + - - +
154J ALA* 3.1 14.5 - - - +
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Residues in contact with LYS 152 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5J PHE* 3.6 28.1 - - + -
108J TYR* 4.8 8.7 - - - +
148J LYS 3.4 5.0 + - - +
149J VAL* 3.1 14.5 + - - +
150J PHE 2.9 0.8 + - - -
151J ALA* 1.3 73.8 - - - +
153J ILE* 1.3 57.0 + - - +
154J ALA 2.9 0.9 - - - -
155J ALA* 2.5 32.1 + - - +
156J ASP* 2.7 20.6 + - - +
184J PRO* 4.5 11.9 - - + -
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Residues in contact with ILE 153 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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149J VAL* 3.4 14.1 - - + +
150J PHE* 2.8 18.9 + - - +
152J LYS* 1.3 70.9 - - - +
154J ALA* 1.3 63.0 + - - +
156J ASP* 3.1 16.6 - - + +
157J MET* 2.9 52.4 + - + +
166J ILE* 6.3 0.9 - - + -
178J LEU* 4.5 24.0 - - + -
182J ASP* 4.4 7.6 - - + +
183J VAL* 4.9 2.9 - - + -
184J PRO* 3.3 35.9 - - + -
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Residues in contact with ALA 154 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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144J ILE 3.6 16.2 - - - +
150J PHE 3.1 7.2 + - - +
151J ALA* 3.1 16.8 - - - +
152J LYS 2.6 3.6 + - - -
153J ILE* 1.3 74.5 - - - +
155J ALA* 1.3 63.7 + - - +
157J MET* 3.4 7.0 + - - +
158J ALA 3.3 9.2 + - - -
164J LYS* 3.2 51.6 - - + +
166J ILE* 4.4 9.3 - - + +
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Residues in contact with ALA 155 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5J PHE* 3.3 31.2 - - + -
7J ASP* 5.0 3.4 - - + -
141J THR* 3.3 37.0 - - + +
142J VAL 4.1 3.6 - - - -
143J GLY* 3.7 8.0 - - - -
151J ALA 3.5 0.6 + - - -
152J LYS 2.5 7.5 + - - -
154J ALA* 1.3 74.3 - - - +
156J ASP* 1.3 64.3 + - - +
158J ALA* 2.9 12.5 + - - -
159J LYS* 3.2 13.9 + - - +
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Residues in contact with ASP 156 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5J PHE* 5.1 2.4 - - - -
152J LYS* 2.7 20.1 + - - +
153J ILE* 3.1 40.8 + - + +
155J ALA* 1.3 72.0 - - - +
157J MET* 1.3 62.6 + - + +
159J LYS* 4.3 9.2 + - - +
182J ASP 5.1 4.5 - - - +
184J PRO* 4.8 4.0 - - - +
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Residues in contact with MET 157 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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153J ILE* 2.9 43.8 + - + +
154J ALA* 4.1 9.0 - - - +
156J ASP* 1.3 80.8 - - + +
158J ALA* 1.3 62.0 + - + +
159J LYS 3.4 4.8 + - - +
164J LYS* 4.9 13.5 - - + -
166J ILE* 5.5 11.4 - - + -
178J LEU* 5.1 9.9 - - + -
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Residues in contact with ALA 158 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
141J THR* 3.8 7.0 - - + -
154J ALA 3.3 3.4 + - - +
155J ALA 2.9 5.6 + - - +
157J MET* 1.3 76.1 - - - +
159J LYS* 1.3 63.3 + - - +
160J PRO 3.8 2.4 - - - +
162J GLY* 3.5 20.2 - - - -
163J ILE 4.6 0.4 - - - +
164J LYS* 3.5 44.2 - - + +
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Residues in contact with LYS 159 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7J ASP* 5.9 2.9 - - - +
9J ASP* 5.5 2.2 - - + -
141J THR* 3.7 13.2 - - + +
155J ALA 3.2 10.5 + - - +
156J ASP* 4.5 7.9 - - - +
157J MET 3.4 6.0 - - - +
158J ALA* 1.3 80.3 - - - +
160J PRO* 1.3 70.2 - - + +
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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