Contacts of the helix formed by residues 139 - 149 (chain J) in PDB entry 6AHU
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 139 (chain J).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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313A C 5.2 8.3 + - - -
314A C 3.4 27.6 + - - -
2E VAL* 3.1 54.7 - - + +
137J PHE 5.2 0.9 - - - +
138J LYS* 1.3 72.0 - - - +
140J PRO* 1.3 70.3 - - + +
142J ILE* 3.1 3.7 + - - +
143J ASN* 2.9 57.4 + - - +
179J ILE* 3.7 37.9 + - + +
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Residues in contact with PRO 140 (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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2E VAL* 6.3 1.1 - - + -
114J HIS* 5.3 1.7 + - - -
118J THR* 5.3 0.3 + - - -
138J LYS* 3.7 17.3 - - + -
139J ARG* 1.3 92.7 - - + +
141J PRO* 1.4 68.1 - - + +
142J ILE 3.4 0.3 + - - -
143J ASN* 4.6 5.4 - - + +
144J VAL* 3.3 27.7 + - - +
67T G 3.3 40.6 - - - +
68T G 3.7 24.0 - - - +
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Residues in contact with PRO 141 (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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113J PHE* 4.0 29.2 - - + -
114J HIS* 4.2 28.3 - - + +
117J CYS* 3.4 30.8 - - + +
118J THR* 5.0 4.5 - - - +
138J LYS* 3.3 34.3 - - + +
140J PRO* 1.4 97.0 - - + +
142J ILE* 1.3 58.9 + - - -
144J VAL* 4.4 2.0 - - + +
145J ALA* 3.7 10.0 + - - +
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Residues in contact with ILE 142 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
113J PHE* 4.0 20.4 - - + -
137J PHE* 5.6 4.0 - - + -
138J LYS 3.3 19.7 - - - +
139J ARG* 3.1 8.8 + - - +
141J PRO* 1.3 77.0 - - - +
143J ASN* 1.3 65.9 + - - +
144J VAL 3.2 1.8 - - - -
145J ALA* 3.1 19.1 + - - +
146J ILE* 3.2 16.7 + - + +
152J PHE* 3.7 27.8 - - + -
176J LEU* 4.5 15.3 - - + -
179J ILE* 4.6 12.1 - - + +
180J CYS* 3.7 41.1 - - - +
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Residues in contact with ASN 143 (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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313A C 5.7 5.1 + - - +
139J ARG* 2.9 54.1 + - - +
140J PRO* 4.4 5.8 - - + +
141J PRO 3.7 0.2 - - - -
142J ILE* 1.3 80.4 - - - +
144J VAL* 1.3 61.0 + - + +
146J ILE* 3.3 30.6 - - + +
147J ASP* 4.3 3.8 + - - +
179J ILE 5.3 4.0 - - - +
180J CYS 5.7 0.5 - - - +
183J LYS* 5.2 4.5 + - - -
67T G 5.6 2.9 + - - +
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Residues in contact with VAL 144 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117J CYS 4.4 12.3 - - - +
118J THR* 4.5 22.4 - - + +
140J PRO 3.3 19.0 + - - +
141J PRO 4.8 1.8 - - - +
142J ILE 3.2 0.4 - - - -
143J ASN* 1.3 78.3 - - + +
145J ALA* 1.3 60.8 + - - +
146J ILE 3.3 0.7 - - - -
147J ASP* 3.3 5.9 + - - +
148J ARG* 3.0 32.0 + - + +
66T C 4.1 20.4 - - - +
67T G 4.7 9.2 - - - -
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Residues in contact with ALA 145 (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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117J CYS* 4.5 6.2 + - + -
141J PRO 3.7 14.5 + - - +
142J ILE 3.1 9.4 + - - +
144J VAL* 1.3 80.1 - - - +
146J ILE* 1.3 58.2 + - - +
148J ARG* 4.2 4.0 - - - -
149J GLY 3.2 3.3 + - - -
150J LEU* 2.9 64.7 + - + +
152J PHE* 4.3 14.4 - - + -
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Residues in contact with ILE 146 (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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142J ILE* 3.2 14.5 + - + +
143J ASN* 3.3 31.4 - - + +
145J ALA* 1.3 78.2 - - + +
147J ASP* 1.3 75.9 + - + +
149J GLY* 4.1 4.3 + - - -
152J PHE* 5.6 1.6 - - + -
180J CYS* 4.5 16.4 - - - +
183J LYS* 3.4 52.0 - - + +
184J ASN* 3.4 32.0 + - - +
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Residues in contact with ASP 147 (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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216D GLY* 4.9 4.9 - - - -
143J ASN 4.5 3.6 - - - +
144J VAL* 3.3 7.2 + - - +
145J ALA 3.3 0.2 - - - -
146J ILE* 1.3 89.4 - - + +
148J ARG* 1.3 64.5 + - - +
149J GLY* 3.3 1.0 + - - -
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Residues in contact with ARG 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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214D ALA 5.9 0.8 + - - -
215D LYS* 6.0 1.6 - - - -
216D GLY* 3.3 32.0 + - - +
116J ALA 4.2 1.4 + - - -
117J CYS 3.2 25.3 + - - -
118J THR* 3.0 29.1 + - - +
119J HIS 4.1 0.6 + - - -
120J LEU 3.0 22.1 + - - -
121J ASP* 2.4 36.3 + - - +
122J VAL 4.7 4.3 + - - +
144J VAL* 3.0 21.9 + - + +
145J ALA* 4.0 5.2 - - - +
146J ILE 3.5 0.2 - - - -
147J ASP* 1.3 78.8 - - - +
149J GLY* 1.3 55.5 + - - +
150J LEU* 4.4 12.0 - - - +
231J HIS* 4.4 14.9 + - - +
47T U 3.6 9.4 + - - -
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Residues in contact with GLY 149 (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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216D GLY* 5.5 0.2 - - - -
217D THR* 4.9 8.9 - - - +
123J ASP 4.5 0.7 - - - +
145J ALA 3.2 3.8 + - - -
146J ILE 4.1 3.2 + - - -
147J ASP 3.3 3.4 - - - -
148J ARG* 1.3 78.4 - - - +
150J LEU* 1.3 63.5 + - - +
151J ALA* 3.6 3.6 + - - +
184J ASN* 4.2 9.6 + - - -
227J ALA* 4.6 6.4 - - - +
228J ALA* 5.4 1.4 - - - -
231J HIS* 3.7 25.6 - - - +
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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